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Chia-BERT.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Some weights of the model checkpoint at bert-base-uncased were not used when initializing BertNerModel: ['cls.predictions.bias', 'cls.predictions.transform.dense.weight', 'cls.predictions.transform.dense.bias', 'cls.predictions.decoder.weight', 'cls.seq_relationship.weight', 'cls.seq_relationship.bias', 'cls.predictions.transform.LayerNorm.weight', 'cls.predictions.transform.LayerNorm.bias']\n",
"- This IS expected if you are initializing BertNerModel from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).\n",
"- This IS NOT expected if you are initializing BertNerModel from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).\n",
"Some weights of BertNerModel were not initialized from the model checkpoint at bert-base-uncased and are newly initialized: ['classifier.weight', 'classifier.bias']\n",
"You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.\n",
"2021-01-12 21:54:18 - BioEval - WARNING - Using beta=1 for calculating F-score\n",
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},
{
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"output_type": "stream",
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{
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{
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{
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{
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"output_type": "stream",
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{
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{
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{
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{
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"output_type": "stream",
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{
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{
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]
}
],
"source": [
"! python ./ClinicalTransformerNER/src/run_transformer_ner.py \\\n",
" --model_type bert \\\n",
" --pretrained_model bert-base-uncased \\\n",
" --data_dir ./chia/ \\\n",
" --new_model_dir ./chia_bert_model \\\n",
" --overwrite_model_dir \\\n",
" --max_seq_length 128 \\\n",
" --data_has_offset_information \\\n",
" --save_model_core \\\n",
" --do_train \\\n",
" --model_selection_scoring strict-f_score-1 \\\n",
" --do_lower_case \\\n",
" --train_batch_size 8 \\\n",
" --train_steps 1000 \\\n",
" --learning_rate 1e-5 \\\n",
" --num_train_epochs 20 \\\n",
" --gradient_accumulation_steps 1 \\\n",
" --do_warmup \\\n",
" --seed 13 \\\n",
" --warmup_ratio 0.1 \\\n",
" --max_num_checkpoints 1 \\\n",
" --log_file ./chia_bert_log.txt \\\n",
" --progress_bar \\\n",
" --early_stop 3"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2021-01-12 21:53:59 - Transformer_NER - INFO - Task will use cuda device: GPU_0.\r\n",
"2021-01-12 21:53:59 - Transformer_NER - WARNING - set tokenizer as bert-base-uncased\r\n",
"2021-01-12 21:53:59 - Transformer_NER - WARNING - set config as bert-base-uncased\r\n",
"2021-01-12 21:53:59 - Transformer_NER - INFO - Training/evaluation parameters: {'model_type': 'bert', 'pretrained_model': 'bert-base-uncased', 'config_name': 'bert-base-uncased', 'tokenizer_name': 'bert-base-uncased', 'data_dir': './chia/', 'data_has_offset_information': True, 'new_model_dir': './chia_bert_model', 'save_model_core': True, 'predict_output_file': None, 'overwrite_model_dir': True, 'seed': 13, 'max_seq_length': 128, 'do_train': True, 'model_selection_scoring': 'strict-f_score-1', 'do_predict': False, 'use_crf': False, 'do_lower_case': True, 'train_batch_size': 8, 'eval_batch_size': 8, 'train_steps': 1000, 'learning_rate': 1e-05, 'num_train_epochs': 20.0, 'gradient_accumulation_steps': 1, 'do_warmup': True, 'warmup_ratio': 0.1, 'weight_decay': 0.0, 'adam_epsilon': 1e-08, 'max_grad_norm': 1.0, 'max_num_checkpoints': 1, 'log_file': './chia_bert_log.txt', 'log_lvl': 'i', 'progress_bar': True, 'early_stop': 3, 'fp16': False, 'logger': <Logger Transformer_NER (INFO)>, 'device': device(type='cuda'), 'num_labels': 26, 'label2idx': {'O': 3, 'X': 2, 'PAD': 0, 'CLS': 1, 'B-Condition': 4, 'I-Condition': 5, 'B-Device': 6, 'I-Device': 7, 'I-Drug': 8, 'B-Drug': 9, 'B-Measurement': 10, 'I-Measurement': 11, 'I-Mood': 12, 'B-Mood': 13, 'I-Observation': 14, 'B-Observation': 15, 'I-Person': 16, 'B-Person': 17, 'I-Pregnancy_considerations': 18, 'B-Pregnancy_considerations': 19, 'I-Procedure': 20, 'B-Procedure': 21, 'B-Temporal': 22, 'I-Temporal': 23, 'I-Value': 24, 'B-Value': 25}, 'idx2label': {3: 'O', 2: 'X', 0: 'PAD', 1: 'CLS', 4: 'B-Condition', 5: 'I-Condition', 6: 'B-Device', 7: 'I-Device', 8: 'I-Drug', 9: 'B-Drug', 10: 'B-Measurement', 11: 'I-Measurement', 12: 'I-Mood', 13: 'B-Mood', 14: 'I-Observation', 15: 'B-Observation', 16: 'I-Person', 17: 'B-Person', 18: 'I-Pregnancy_considerations', 19: 'B-Pregnancy_considerations', 20: 'I-Procedure', 21: 'B-Procedure', 22: 'B-Temporal', 23: 'I-Temporal', 24: 'I-Value', 25: 'B-Value'}}\r\n",
"2021-01-12 21:54:01 - Transformer_NER - INFO - New Model Config:\r\n",
"BertConfig {\r\n",
" \"architectures\": [\r\n",
" \"BertForMaskedLM\"\r\n",
" ],\r\n",
" \"attention_probs_dropout_prob\": 0.1,\r\n",
" \"gradient_checkpointing\": false,\r\n",
" \"hidden_act\": \"gelu\",\r\n",
" \"hidden_dropout_prob\": 0.1,\r\n",
" \"hidden_size\": 768,\r\n",
" \"id2label\": {\r\n",
" \"0\": \"LABEL_0\",\r\n",
" \"1\": \"LABEL_1\",\r\n",
" \"2\": \"LABEL_2\",\r\n",
" \"3\": \"LABEL_3\",\r\n",
" \"4\": \"LABEL_4\",\r\n",
" \"5\": \"LABEL_5\",\r\n",
" \"6\": \"LABEL_6\",\r\n",
" \"7\": \"LABEL_7\",\r\n",
" \"8\": \"LABEL_8\",\r\n",
" \"9\": \"LABEL_9\",\r\n",
" \"10\": \"LABEL_10\",\r\n",
" \"11\": \"LABEL_11\",\r\n",
" \"12\": \"LABEL_12\",\r\n",
" \"13\": \"LABEL_13\",\r\n",
" \"14\": \"LABEL_14\",\r\n",
" \"15\": \"LABEL_15\",\r\n",
" \"16\": \"LABEL_16\",\r\n",
" \"17\": \"LABEL_17\",\r\n",
" \"18\": \"LABEL_18\",\r\n",
" \"19\": \"LABEL_19\",\r\n",
" \"20\": \"LABEL_20\",\r\n",
" \"21\": \"LABEL_21\",\r\n",
" \"22\": \"LABEL_22\",\r\n",
" \"23\": \"LABEL_23\",\r\n",
" \"24\": \"LABEL_24\",\r\n",
" \"25\": \"LABEL_25\"\r\n",
" },\r\n",
" \"initializer_range\": 0.02,\r\n",
" \"intermediate_size\": 3072,\r\n",
" \"label2id\": {\r\n",
" \"LABEL_0\": 0,\r\n",
" \"LABEL_1\": 1,\r\n",
" \"LABEL_10\": 10,\r\n",
" \"LABEL_11\": 11,\r\n",
" \"LABEL_12\": 12,\r\n",
" \"LABEL_13\": 13,\r\n",
" \"LABEL_14\": 14,\r\n",
" \"LABEL_15\": 15,\r\n",
" \"LABEL_16\": 16,\r\n",
" \"LABEL_17\": 17,\r\n",
" \"LABEL_18\": 18,\r\n",
" \"LABEL_19\": 19,\r\n",
" \"LABEL_2\": 2,\r\n",
" \"LABEL_20\": 20,\r\n",
" \"LABEL_21\": 21,\r\n",
" \"LABEL_22\": 22,\r\n",
" \"LABEL_23\": 23,\r\n",
" \"LABEL_24\": 24,\r\n",
" \"LABEL_25\": 25,\r\n",
" \"LABEL_3\": 3,\r\n",
" \"LABEL_4\": 4,\r\n",
" \"LABEL_5\": 5,\r\n",
" \"LABEL_6\": 6,\r\n",
" \"LABEL_7\": 7,\r\n",
" \"LABEL_8\": 8,\r\n",
" \"LABEL_9\": 9\r\n",
" },\r\n",
" \"label2idx\": {\r\n",
" \"B-Condition\": 4,\r\n",
" \"B-Device\": 6,\r\n",
" \"B-Drug\": 9,\r\n",
" \"B-Measurement\": 10,\r\n",
" \"B-Mood\": 13,\r\n",
" \"B-Observation\": 15,\r\n",
" \"B-Person\": 17,\r\n",
" \"B-Pregnancy_considerations\": 19,\r\n",
" \"B-Procedure\": 21,\r\n",
" \"B-Temporal\": 22,\r\n",
" \"B-Value\": 25,\r\n",
" \"CLS\": 1,\r\n",
" \"I-Condition\": 5,\r\n",
" \"I-Device\": 7,\r\n",
" \"I-Drug\": 8,\r\n",
" \"I-Measurement\": 11,\r\n",
" \"I-Mood\": 12,\r\n",
" \"I-Observation\": 14,\r\n",
" \"I-Person\": 16,\r\n",
" \"I-Pregnancy_considerations\": 18,\r\n",
" \"I-Procedure\": 20,\r\n",
" \"I-Temporal\": 23,\r\n",
" \"I-Value\": 24,\r\n",
" \"O\": 3,\r\n",
" \"PAD\": 0,\r\n",
" \"X\": 2\r\n",
" },\r\n",
" \"layer_norm_eps\": 1e-12,\r\n",
" \"max_position_embeddings\": 512,\r\n",
" \"model_type\": \"bert\",\r\n",
" \"num_attention_heads\": 12,\r\n",
" \"num_hidden_layers\": 12,\r\n",
" \"pad_token_id\": 0,\r\n",
" \"position_embedding_type\": \"absolute\",\r\n",
" \"type_vocab_size\": 2,\r\n",
" \"use_crf\": false,\r\n",
" \"vocab_size\": 30522\r\n",
"}\r\n",
"\r\n",
"2021-01-12 21:54:08 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'na', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 6583, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:08 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'who', 'meet', '1987', 'ac', '##r', 'criteria', 'for', 'sl', '##e', 'with', '1996', 'modifications', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 5022, 2040, 3113, 3055, 9353, 2099, 9181, 2005, 22889, 2063, 2007, 2727, 12719, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 10, 11, 2, 11, 11, 11, 2, 11, 11, 11, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 2, 3, 4, 5, 5, 6, 7, 8, 8, 9, 10, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:08 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'sl', '##eda', '##i', '>', '/', '=', '6', 'at', 'screening', 'visit', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 22889, 11960, 2072, 1028, 1013, 1027, 1020, 2012, 11326, 3942, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 10, 2, 2, 25, 24, 2, 24, 22, 23, 23, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 1, 1, 2, 3, 3, 4, 5, 6, 7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:08 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 172).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Patients may have any of the following indications for cardiac catheterization : Thoracic pain under study . Stable chronic coronary disease . Acute myocardial infarction with ST segment elevation , not perfused ( without timely reperfusion therapy ) with less than 4 weeks of evolution . Acute myocardial infarction with ST - segment elevation , successful thrombolytic therapy , which will undergo drug - invasive therapy . Acute myocardial infarction without ST segment elevation . Unstable angina . Any acute coronary syndrome , to intervene non - infarct - related artery . Disease of any heart valve . Myocarditis or pericarditis . Dilated cardiomyopathy . Patients in renal or cardiac transplantation protocol for any etiology . Congenital heart disease that requires knowing the coronary anatomy prior to surgical correction .\r\n",
"\r\n",
"2021-01-12 21:54:08 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 130).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Subjects with abnormal EKG at screening ( if applicable ) . To mitigate the risk of enrolling at risk subjects and potentially jeopardizing subject safety an EKG will be performed prior to vaccination with ACAM2000 smallpox vaccine in all potential subjects = 50 years old and for all potential subjects < 50 with two cardiac risk factors as listed immediately below including ; severely or morbidly obese or higher obesity classification ( BMI = 36 ) ; high blood pressure ; high blood cholesterol ; diabetes or high blood sugar ; a first degree relative who had a heart condition before the age of 50 ; and current tobacco smokers .\r\n",
"\r\n",
"2021-01-12 21:54:08 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 159).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"In sustained clinical remission for the last 6 months while receiving treatment with either etanercept , infliximab , or adalimumab , and greater than or equal to 1 DMARD ( methotrexate , hydroxychloroquine , sulfasalazine , leflunomide , minocycline , cyclosporine , azathioprine , gold , penicillamine ) . DAS28 should be less than 2.6 on each visit over the preceding 6 months , with at least one visit 2 - 4 months before enrollment . If there is no visit 6 months before enrollment , the nearest visit in the 6 - 12 month period before enrollment should be considered and have a DAS28 less than 2.6 .\r\n",
"\r\n",
"2021-01-12 21:54:09 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 171).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Acute or serious medical illness or unstable chronic medical illness ( e.g. , unstable angina , myocardial infarction within 6 months , congestive heart failure , clinically significant or concerning cardiac arrhythmias ; preexisting hypotension [ systolic blood pressure<110 ] or orthostatic hypotension [ systolic drop > 20 mm Hg after 2 min standing accompanied by lightheadedness ] , chronic renal or hepatic failure , acute pancreatitis , Meniere 's disease , or diagnosed but untreated sleep apnea ) . The eligibility of potential participants having acute serious and/or chronic medical illnesses other than those listed will be evaluated on a case - by - case basis by a study physician , PA - C , or ARNP .\r\n",
"\r\n",
"2021-01-12 21:54:09 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 147).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"The use of HA rescue or symptom - relieving medications will be allowed during the study . This includes triptans , ergotamines , opioids , simple analgesics ( e.g. acetaminophen , aspirin , or non - steroidal anti - inflammatories [ NSAIDS ] , and combination analgesics . Their use will be recorded on the concurrent medication CRF during the Preliminary Screening Period ( P1 ) and throughout the remainder of the study . Randomization of participants will be stratified based on whether their use of HA medications meets ICHD-3 beta criteria for overuse of these medications , as described in section 5.5 below .\r\n",
"\r\n",
"2021-01-12 21:54:10 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 173).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Potentially fertile women should use high reliability contraceptive methods ( Pearl - Index < 1 ) in order to avoid pregnancy during the entire duration of the study and up to 6 weeks after the end of their treatment with Mycophenolate Mofetil ( MMF ) . Potentially Fertile Women include any woman who has experienced menarche and who has not undergone successful surgical sterilization ( hysterectomy , bilateral tubal ligation or bilateral oophorectomy ) or who is not post - menopausal ( defined as amenorrhea = 12 consecutive months , or women who are receiving hormone replacement therapy with a documented level of follicle stimulating hormone ( FSH ) > 35 mlU / ml ) . Potentially fertile women must have a pregnancy test with a negative result in the 72 hours prior to the start of the trial .\r\n",
"\r\n",
"2021-01-12 21:54:10 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 128).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"traumatic brain injury ( as defined by The American Congress of Rehabilitation as a person who has had a traumatically induced physiological disruption of brain function ( i.e. , the head being struck , the head striking an object , and/or the brain undergoing an acceleration / deceleration movement ( i.e. , whiplash ) without direct external trauma to the head ) , as manifested by at least one of the following : any loss of consciousness ; any loss of memory for events immediately before or after the injury ; any alteration in mental status at the time of the incident ; or focal neurological deficits that may or may not be transient )\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 128).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Available Organ function : white blood cell=3.5×109 / L , Neutrophils = 1.5×109 / L , Hemoglobin = 80g / L , Blood platelet>100×109 / L ; Alanine aminotransferase ( ALT ) and Aspartate aminotransferase ( AST)= 2.5 upper limit of normal(ULN ) ; Total bilirubin ( TBIL ) < 1.5 ULN;serum creatinine=1.5 ULN ; creatinine clearance of = 50ml / min\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 182).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"IFG impaired fast glucose , FPG fasting plasma glucose , IGT impaired glucose tolerance , OGTT oral glucose tolerance test , PG plasma glucose , HbA1C hemoglobin A1C , LDL - C low - density lipoprotein cholesterol , TG triglycerides , SBP systolic blood pressure , DBP diastolic blood pressure , ALT alanine aminotransferase , AST aspartate aminotransferase , GFR glomerular filtration rate , ASCVD arteriosclerotic cardiovascular disease , ACS acute coronary syndrome , SCAD stable coronary artery disease , ICM ischemic cardiomyopathy , TIA transient ischemic attack , PASD peripheral atherosclerotic disease , SAS sleep apnea syndrome , PA primary aldosteronism , RAS renal arterial stenosis\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 135).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Active syphilis or treatment for syphilis within 90 days prior to study entry . NOTE : Active syphilis is defined as four - fold increase in serum rapid plasma reagin ( RPR ) or venereal disease research laboratory ( VDRL ) tests in an individual with past syphilis , or newly reactive serum RPR or VDRL with a reactive confirmatory test ( enzyme immunoassays [ EIA ] or chemiluminescent assay [ CIA ] , T. pallidum particle agglutination [ TP - PA ] , or fluorescent treponemal antibody absorbed [ FTA - ABS ] ) .\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 256).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"a licensed rapid HIV test or HIV enzyme or chemiluminescence immunoassay ( E / CIA ) test kit at any time prior to study entry and confirmed by a licensed Western blot or a second antibody test by a method other than the initial rapid HIV and/or E / CIA , or by HIV-1 antigen or plasma HIV-1 RNA viral load . NOTE : The term \" licensed \" refers to a United States Food and Drug Administration ( FDA)-approved kit , which is required for all IND studies , or for sites located in countries other than the United States , a kit that has been certified or licensed by an oversight body within that country and validated internally . Non - US sites are encouraged to use US FDA - approved methods for IND studies . WHO ( World Health Organization ) and CDC ( Centers for Disease Control and Prevention ) guidelines mandate that confirmation of the initial test result must use a test that is different from the one used for the initial assessment . A reactive initial rapid test should be confirmed by either another type of rapid assay or an E / CIA that is based on a different antigen preparation and/or different test principle ( eg , indirect versus competitive ) , or a Western blot or a plasma HIV-1 RNA . OR\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 149).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Females of reproductive potential ( women who have not been post - menopausal for at least 24 consecutive months , ie , who have had menses within the preceding 24 months , or women who have not undergone surgical sterilization , hysterectomy or bilateral salpingectomy or bilateral oophorectomy or tubal ligation ) must have a negative serum or urine pregnancy test by any US clinic or laboratory that has a CLIA certification or its equivalent , or is using a point of care ( POC ) / CLIA - waived test , or at any network - approved non - US laboratory or clinic that operates in accordance with GCLP and participates in appropriate external quality assurance programs within 48 hours prior to study entry\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 133).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Any subject who has been taking benzodiazepines before entering the study who : 1 ) can not tolerate being free of benzodiazepines for 4 weeks , or 2 ) has signs or symptoms of benzodiazepine withdrawal or rebound at the end of those 4 weeks . Should a patient entering the study , who is currently on benzodiazepines develop discontinuation symptoms with discontinuation of their benzodiazepine , we will treat these symptoms with a more gradual benzodiazepine taper . Study will be delayed until the patient is able to tolerate the discontinuation for 4 weeks .\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 144).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Requirement for vasoactive drugs via a central venous catheter for the treatment of shock . Shock will be defined as mean arterial pressure less than 70 mmHg or systolic blood pressure less than 100 mmHg despite administration of at least 1000 mL of crystalloid or 500 mL of colloid , unless there is an elevation in the central venous pressure to > 12 mmHg or in the pulmonary artery occlusion pressure to > 14 mmHg coupled with signs of tissue hypoperfusion ( e.g. altered mental state , mottled skin , urine output < 0.5 mL / kg body weight for one hour , or a serum lactate level of > 2 mmol per liter ) .\r\n",
"\r\n",
"2021-01-12 21:54:11 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 150).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Any surgical or medical condition which might significantly alter the absorption , distribution , metabolism , or excretion of study drugs , including , but not limited to , any of the following : History of active inflammatory bowel disease during the 12 months . Active duodenal or gastric ulcers during the 3 months . Evidence of hepatic disease as determined by any one of the following : aspartate aminotransferase or alanine aminotransferase values exceeding 2x upper limit of normal , history of hepatic encephalopathy , history of oesophageal varices , or history of porto - caval shunt . Current treatment with cholestyramine or colestipol resins .\r\n",
"\r\n",
"2021-01-12 21:54:12 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 133).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Bloodstream infection with Enterobacter spp . , Serratia marcescens , Providencia spp . , Morganella morganii or Citrobacter freundii ( i.e. likely AmpC - producer ) , and susceptibility to 3rd generation cephalosporins ( i.e. ceftriaxone , cefotaxime or ceftazidime ) , meropenem and piperacillin - tazobactam from at least one blood culture draw . This will be determined in accordance with laboratory methods and susceptibility breakpoints defined by protocols used in the recruiting site laboratories ..\r\n",
"\r\n",
"2021-01-12 21:54:12 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 163).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"The heart team must agree that medical factors preclude operation , based on a conclusion that the probability of death or serious , irreversible morbidity exceeds the probability of meaningful improvement . Also , other factors which may increase the patients perceived surgical risk for inclusion in the trial will be clearly delineated if they are present . These include , but are not limited to the following as defined by VARC 2 : Frailty , Hostile chest , porcelain aorta , IMA or other critical conduit crossing the midline or adherent to the posterior table of sternum , severe right ventricular ( RV ) dysfunction . The surgeons ' consultation notes shall specify the medical or anatomic factors leading to that conclusion . At least one of the cardiac surgeon assessors must have interviewed and examined the patient .\r\n",
"\r\n",
"2021-01-12 21:54:12 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 131).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Females of childbearing potential must agree to be abstinent or else use any two of the following medically acceptable forms of contraception from the Screening Period through the Final Study Visit : hormonal , condom with spermicidal jelly , diaphragm or cervical cap with spermicidal jelly , or IUD . Hormonal contraception must have started at least 3 months prior to screening . A female whose male partner has had a vasectomy must agree to use one additional form of medically acceptable contraception . Subjects must agree to practice the above birth control methods for 30 days from the final visit as a safety precaution .\r\n",
"\r\n",
"2021-01-12 21:54:12 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 180).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Written informed consent from at least one parent / care giver ( legal guardian ) and accompanying informed assent from the subject ( where the subject is able to provide assent ) prior to admission to the study : ( 1 ) If applicable , subject must be able and willing to give assent to take part in the study according to the local requirement . The study investigator is accountable for determining a child 's capacity to assent to participation in a research study , taking into consideration any standards set by the responsible independent ethics committee ( IEC ) . ( 2 ) Subject and their legal guardian(s ) understand that the study requires them to be treated on an outpatient basis . ( 3 ) Subject and their legal guardian(s ) understand that they must comply with study medication and study assessments including recording of peak expiratory flow and rescue SABA use , attending scheduled study visits , and being accessible by a telephone call .\r\n",
"\r\n",
"2021-01-12 21:54:13 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 372).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"( 5)Known serious medical conditions , including : Cardiovascular : patients with clinically diagnosed cardiac dysfunction ( NYHA class III and above ) , hypertrophic obstructive cardiomyopathy , clinically significant valvular heart disease , acute coronary syndrome within the last 3 months , or percutaneous coronary intervention ( PCI ) , or coronary artery bypass graft ( CABG ) ; or abnormal pre - enrollment ECG test results with clinically significant arrhythmias ( atrial flutter , atrial fibrillation , grade II - III atrioventricular block , etc . ) ; Digestive : a previous diagnosis of various types of viral hepatitis that are still in the active phase ; abnormal pre - enrollment liver function test results ( ALT , AST , GGT , TBIL , or DBIL 3 times higher than normal , ALB = 30g / L ) ; gastrectomy and/or gastrojejunostomy ; gastrointestinal dysfunction ; Urinary : pre - enrollment serum creatinine greater than 200umol / L ; clinical diagnosis of renal artery stenosis , isolated kidney , kidney transplantation and/or other diseases ; Endocrine : type 1 diabetes or uncontrolled type 2 diabetes ( fasting blood glucose above 11.1 mmol / L at pre - enrollment ) ; previous diagnosis of hyperthyroidism and failure to correct ; Respiratory : pulmonary heart disease ; chronic obstructive pulmonary disease ; Neuropsychiatric : recent transient ischemic attack or stroke ( within the last 3 months ) ; peripheral or severe autonomic dysfunction ; mental or nervous system dysfunction , inability to express desire ; known drug or alcohol dependence ; Malignancy , malnutrition , hematopoietic disorders and other serious diseases .\r\n",
"\r\n",
"2021-01-12 21:54:13 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 131).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"7 . Active , suspected or prior documented autoimmune disease ( including inflammatory bowel disease , celiac disease , Wegner 's granulomatosis , active Hashimoto 's thyroiditis , rheumatoid arthritis , lupus , scleroderma and its variants , multiple sclerosis , myasthenia gravis ) . Vitiligo , type I diabetes mellitus , residual hypothyroidism due to autoimmune condition only requiring hormone replacement , psoriasis not requiring systemic treatment , or conditions not expected to recur in the absence of an external trigger are permitted .\r\n",
"\r\n",
"2021-01-12 21:54:13 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 139).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"1 . Subjects must have recurrent or persistent platinum - resistant epithelial ovarian , fallopian tube , or primary peritoneal carcinoma with measureable disease ( as defined by RECIST 1.1 . ) after first or second line platinum - based chemotherapy , for which treatment with PLD is indicated . Platinum - based therapy is defined as treatment with carboplatin , cisplatin or another organoplatinum compound . Platinum - resistant is defined as having a platinum - free interval ( PFI ) of < 12 months after first- or second - line platinum - based chemotherapy , or having disease progression while receiving second - line platinum - based chemotherapy .\r\n",
"\r\n",
"2021-01-12 21:54:13 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 129).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"6 . Total occluded vessels . One total occluded major epicardial vessel or side branch can be included and targeted as long as one other major vessel has a significant stenosis amenable for SA , provided the age of occlusion is less than one month e.g. recent instability , infarction with ECG changes in the area subtended by the occluded vessel . Patients with total occluded vessels of unknown duration or existing longer than one month and a reference over 1.50 mm should not be included , not even as a third or fourth vessel to be dilated ;\r\n",
"\r\n",
"2021-01-12 21:54:14 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 242).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Medical condition with safety deemed to be category 3 or 4 when using a combined hormonal contraceptive , as determined by the Center for Disease Control Medical Eligibility Criteria : current or past history of breast cancer , severe decompensated cirrhosis , history of deep vein thrombosis or pulmonary embolus , diabetes with nephropathy / retinopathy / neuropathy or other vascular disease diagnosed more than 20 years ago , current symptomatic gallbladder disease , hypertension , ischemic heart disease , known thrombogenic mutations , hepatocellular adenoma , malignant hepatoma , multiple risk factors for atherosclerotic cardiovascular disease , multiple sclerosis with prolonged immobility , history of peripartum cardiomyopathy , cigarette smoking and = 35yo , history of complicated solid organ transplant , history of stroke , history of superficial venous thrombosis not associated with catheter , systemic lupus erythematosus with positive antiphospholipid antibodies , valvular heart disease complicated by pulmonary hypertension or atrial fibrillation or bacterial endocarditis , and acute viral hepatitis\r\n",
"\r\n",
"2021-01-12 21:54:14 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 160).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Pregnant or lactating women and female volunteers of childbearing potential ( except for women who are surgically sterile ) who are not willing to use an adequate method of contraception ( oral contraceptives , intrauterine device , condom , etc . ) during the study . Women of childbearing potential who are not surgically sterile will be allowed to participate in the study only if they have negative pregnancy test at Visit 1 ( screening ) and should continue to use medically acceptable method of contraception ( basic body temperature method and rhythm method will not be allowed ) . Women with no menses for = 12 months will be considered as postmenopausal state and method of contraception using hormonal contraception such as oral contraceptive should be initiated from or prior to the screening .\r\n",
"\r\n",
"2021-01-12 21:54:14 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 172).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"concomitant oral or i.v . therapy with strong CYP3A Inhibitors ( e.g. ketoconazole , itraconazole , voriconazole , telithromycin , clarithromycin , nefazodone , ritonavir , saquinavir , nelfinavir , indinavir , atazanavir , grapefruit juice > 1 L / d ) , CYP3A substrates with narrow therapeutic indices ( e.g. cyclosporine , quinidine ) , or strong CYP3A inducers ( e.g. rifampin / rifampicin , phenytoin , carbamazepine , dexamethason , phenobarbital ) that can not be safely discontinued\r\n",
"\r\n",
"2021-01-12 21:54:14 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 133).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"community - acquired pneumonia : the presence of radiologically confirmed infiltration of the lung tissue ; the presence of at least two of the following clinical signs : acute fever early in the disease ( temperature > 38.0 ° C ) , cough with sputum , the physical signs of pneumonia ( focus of crepitate and/or fine bubble rales , bronchial breathing hard , shortening of percussion sounds ) , leukocytosis > 10 * 10 9 /l and/or stab shift > 10 % ; the occurrence of the disease outside the hospital and the organized groups ( such as nursing homes , sanatoriums , etc . ) .\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 429).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"A female subject is eligible to participate if she is of : Non - childbearing potential defined as pre - menopausal females with a documented tubal ligation or hysterectomy for this definition , \" documented \" refers to the outcome of the investigator's / designee 's review of the subject 's medical history for study eligibility , as obtained via a verbal interview with the subject or from the subject 's medical records ; or postmenopausal defined as 12 months of spontaneous amenorrhea [ in questionable cases a blood sample with simultaneous follicle stimulating hormone ( FSH ) > 40 milli - international units per milliliter ( MlU / mL ) and estradiol < 40 picograms per mililiter ( pg / mL ) [ < 147 picomole per liter ] is confirmatory ] . Females on hormone replacement therapy ( HRT ) and whose menopausal status is in doubt will be required to use one of the contraception methods if they wish to continue their HRT during the study . Otherwise , they must discontinue HRT to allow confirmation of post - menopausal status prior to study enrollment . For most forms of HRT , at least 2 - 4 weeks will elapse between the cessation of therapy and the blood draw ; this interval depends on the type and dosage of HRT . Following confirmation of their post - menopausal status , they can resume use of HRT during the study without use of a contraceptive method ; Child - bearing potential with negative pregnancy test as determined by serum human chorionic gonadotrophin ( hCG ) test at screening or prior to dosing AND ; Agrees to use one of the contraception methods listed in protocol for an appropriate period of time ( as determined by the product label or investigator ) prior to the start of dosing to sufficiently minimize the risk of pregnancy at that point . Female subjects must agree to use contraception until the follow - up contact visit ; OR has only same - sex partners , when this is her preferred and usual lifestyle .\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 157).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Sexually active males unless they use a condom during intercourse while taking drug and for 1 months after pasireotide s.c . last dose and 3 months after pasireotide LAR last dose and should not father a child in this period . A condom is required to be used also by vasectomized men in order to prevent delivery of the drug via seminal fluid If a study patient or partner becomes pregnant or suspects being pregnant during the study or within 1 month after the final dose of pasireotide s.c . or 3 months after the final dose of pasireotide LAR , the Study Doctor needs to be informed immediately and ongoing study treatment with pasireotide has to be stopped immediately For patients taking pasireotide LAR , the future dose injections will be cancelled .\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 161).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Patients at potential increased risk of iatrogenic probiotic infection ( see Section 2.6 for detailed explanation ) including specific immunocompromised populations ( HIV < 200 CD4 cells/µL , those receiving chronic immunosuppressive medications ( e.g. , azathioprine , cyclosporine , cyclophosphamide , tacrolimus , methotrexate , mycofenolate , Anti - IL2 ) , previous transplantation ( including stem cell ) at any time , malignancy requiring chemotherapy in the last 3 months , neutropenia [ absolute neutrophil count < 500 ] ) . However , patients receiving corticosteroids previously or presently or projected to receive corticosteroids are not excluded ;\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 250).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Patients at risk for endovascular infection ( previously documented rheumatic heart disease , congenital valve disease , surgically repaired congenital heart disease , unrepaired cyanotic congenital heart disease , any intracardiac repair with prosthetic material [ mechanical or bio - prosthetic cardiac valves ] , previous or current endocarditis , permanent endovascular devices ( e.g. , endovascular grafts [ e.g. , aortic aneurysm repair , stents involving large arteries such as aorta , femorals and carotids ] , inferior vena cava filters , dialysis vascular grafts ) , tunnelled ( not short - term ) hemodialysis catheters , pacemakers or defibrillators . Patients with temporary central venous catheters , central venous dialysis catheters or peripherally inserted central catheters ( PICCs ) are not excluded and patients with coronary artery stents , coronary artery bypass grafts ( CABG ) or neurovascular coils are not excluded ; patients with mitral valve prolapse or bicuspid aortic valve are not excluded providing they have no other exclusion criteria ;\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 229).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"1 . High risk profiles for ischemic adverse events such as A. ST - segment elevation myocardial infarction ( STEMI ) B. Patients with cardiogenic shock or concomitant severe decompensated heart failure C. Myocardial infarction or stent thrombosis in spite of the maintenance of antiplatelet therapy D. Restenosis in stented segments or previous sites of balloon angioplasty 2 . Patients who can not follow allocated DAPT schedule due to the planned surgery or elective procedure within 3 months after the stenting 3 . Recent history of major surgery or evident events of gastrointestinal bleeding within 1 month from the procedure 4 . Patients on anticoagulation therapy with warfarin or other anticoagulants 5 . Life expectancy less than 1 year ( such as malignancies or other chronic systemic diseases ) 6 . Pregnant women 7 . Past history of allergy or other contraindications for the following medications / materials : aspirin , clopidogrel , heparin , cobalt chromium , sirolimus\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 133).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Anxiety Cohort : Meet DSM-5 criteria for any of the following anxiety disorders : Social Anxiety Disorders , Generalized Anxiety Disorder , Separation Anxiety Disorder and/or Panic Disorder by structured interview ( MINI - KID ) ; ADIS Clinical Severity Rating ≥4 ( moderately severe ) for any of the 4 included anxiety disorders ; Failure to achieve remission with at least 1 adequate prior anxiolytic medication trial ( e.g. SSRI , SNRI , or TCA ) , meaning at least 8 weeks at therapeutic dosing , including at least 4 weeks of stable dosing ; Failure to achieve remission with previous CBT or subject declines current CBT therapy\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 133).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Men who are sexually active with a woman of childbearing potential and have not had a vasectomy must agree to use a barrier method of birth control for example , either condom with spermicidal foam / gel / film / cream / suppository or partner with occlusive cap ( diaphragm or cervical / vault caps ) with spermicidal foam / gel / film / cream / suppository , and all men must also not donate sperm during the study and for 3 months after receiving the last dose of study drug . In addition , their female partners should also use an appropriate method of birth control for at least the same duration\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 149).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Systolic pulmonary artery pressure ( SPAP ) > 40 mmHg ( and/or tricuspid regurgitation [ TR ] jet velocity > 2.9 m / s ) In cases where an actual SPAP value is not measurable due to lack of adequate TR jet , the pulmonary flow acceleration time measured at the right ventricular outflow tract ( RVOTAT ) will be used to assess eligibility . Participants with a RVOTAT = 100 milliseconds ( msec ) will be excluded , suggesting an elevated mean SPAP ; eligibility for the those participants with RVOTAT between 100 and 120 msec will be determined based on combined assessment of the TR jet , septal motion , and right ventricular size .\r\n",
"\r\n",
"2021-01-12 21:54:15 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 262).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Medication No use within the following time intervals prior to Screening or thereafter at any time during the study ( unless otherwise specified ) Inhaled Long acting beta - agonists ( LABA ) 48 hours ICS / LABA combination products 48 hours Inhaled corticosteroids 48 hours Tiotropium 1 week Systemic , Oral , parenteral , intra - articular corticosteroids 30 days ( oral and systemic corticosteroids may be used to treat COPD exacerbations during the study ) Cytochrome P450 3A4 strong inhibitors including but not limited to antiretrovirals ( protease inhibitors ) ( e.g . Indinavir , Nelfinavir , Ritonavir , Saquinavir ) ; Imidazole and Triazole anti - fungals ( e.g. Ketaconazole , Itraconazole ) ; Clarithromycin , Telithromycin , Amiodarone , and Nefazodone 6 weeks Grapefruit is allowed up to Visit 1 , then limited to no more than one glass of grapefruit juice ( 250 mL/ 8 ounces ) or one grapefruit per day Any other investigational drug 30 days or 5 half lives whichever is longer .\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 137).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Female subjects must be of non - childbearing potential ( as defined as surgically sterile [ i.e. history of hysterectomy or tubal ligation ] or postmenopausal for more than 1 year [ no bleeding for 12 consecutive months ] , or if of childbearing potential must be non - pregnant at the time of enrollment and on the morning of the first day of each study session , and must agree to use hormonal or barrier birth control such as implants , injectables , combined oral contraceptives , some intrauterine devices ( IUDs ) , sexual abstinence or a vasectomized parter\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 151).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Pleural or pericardial effusion greater than 100 ml in volume as documented by appropriate imaging ( positron emission tomography [ PET ] , computed tomography [ CT ] scan or ultrasound ) . If an effusion greater than 100 ml is documented by cytology to be free from malignancy and the investigator feels the patient is capable of receiving chemo / radiotherapy for their primary disease/ NSCLC , the investigator should discuss the patient with the study physician at Amgen . Effusions smaller than 100 ml would be acceptable , unless the investigator suspects that the effusion is malignant , in which case the effusions should be evaluated by cytology . Sponsor approval must be obtained before patient is randomized .\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 187).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Treprostinil contraindications : Known hypersensitivity to treprostinil or any of the excipients , Pulmonary arterial hypertension related to veno - occlusive disease , Congestive heart failure due to severe left ventricular dysfunction , Severe hepatic insufficiency ( Child - Pugh stage C ) , Evolving gastrointestinal ulcer , intracranial hemorrhage , recent trauma or other clinical condition that may lead to bleeding , Congenital or acquired valvular abnormalities with cardiac repercussions , Severe ischemic heart disease or unstable angina ; Myocardial infarction in the last six months ; Decompensated cardiac insufficiency not medically controlled ; Severe arrhythmias ; Cerebrovascular lesions ( such as transient ischemic attack , stroke ) that occurred within the last three months .\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 187).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Treprostinil contraindications : Known hypersensitivity to treprostinil or any of the excipients , Pulmonary arterial hypertension related to veno - occlusive disease , Congestive heart failure due to severe left ventricular dysfunction , Severe hepatic insufficiency ( Child - Pugh stage C ) , Evolving gastrointestinal ulcer , intracranial hemorrhage , recent trauma or other clinical condition that may lead to bleeding , Congenital or acquired valvular abnormalities with cardiac repercussions , Severe ischemic heart disease or unstable angina ; Myocardial infarction in the last six months ; Decompensated cardiac insufficiency not medically controlled ; Severe arrhythmias ; Cerebrovascular lesions ( such as transient ischemic attack , stroke ) that occurred within the last three months .\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 179).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"adequately controlled with appropriate therapy or would compromise the patient 's ability to tolerate this therapy ; 2 . Treatment with any systemic anticancer therapy ≤ 3 weeks prior to cycle 1 day 1 3 . Uncontrolled active infection ( Hepatitis B and C infection are NOT exclusion criteria ) and/or known HIV infection ; 4 . Renal failure requiring haemodialysis or peritoneal dialysis ; 5 . Patients who are pregnant or breast - feeding ; 6 . Patients with significantly diseased or obstructed gastrointestinal tract , malabsorption , uncontrolled vomiting or diarrhea resulting in inability to swallow oral medications ; 7 . Presence of symptomatic CNS metastasis 8 . Unresolved toxicity from previous anti - cancer therapy or incomplete recovery from surgery , in particular oxaliplatin - induced peripheral neuropathy > grade 1 .\r\n",
"\r\n",
"2021-01-12 21:54:16 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 135).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"8 . Women of childbearing potential must have a negative serum pregnancy test performed within 7 days prior to start of treatment . Women of childbearing potential or men with partners of childbearing potential must use effective birth control measures during treatment and at least 6 months after the last dose of the study treatment . If a woman becomes pregnant or suspects she is pregnant while participating in this study , she must agree to inform her treating physician immediately . Sexually active men must agree to use a medically acceptable form of birth control during treatment and at least 6 months after the last dose . If a female partner becomes pregnant during the course of the study the treating physician should be informed immediately .\r\n",
"\r\n",
"2021-01-12 21:54:17 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 175).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"1 ) pregnancy , breast - feeding women , or female patients of childbearing potential but did not take contraceptive measures;2 ) existing severe acute infection and is not controlled ; or purulent and chronic infection , delayed healing wounds ; 3 ) the original severe heart disease , including congestive heart failure , uncontrolled high - risk arrhythmias , unstable angina , myocardial infarction , severe heart valve disease and resistant hypertension ; 4 ) suffering from neurological and psychiatric diseases or mental disorders is not easy to control , poor compliance , and can not be described with treatment responders ; primary brain or central nervous metastasis disease has not been controlled , with significant cranial hypertension or neuropsychiatric symptoms ; 5 ) have bleeding tendencies ; 6 ) other researchers believe that patients should not participate in the present trial .\r\n",
"\r\n",
"2021-01-12 21:54:17 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 505).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"1 ) histologically confirmed ( patients not receiving a single sputum cytology diagnosis ) non - small cell lung cancer patients , with wild - type EGFR and ALK - negative ; 2 ) According to IASLC2009 new TNM staging of lung cancer stage < U+2162 > B or < U+2163 > , previously untreated or relapsed after 1 year of lung cancer resection ; 3 ) have at least one evaluable lesions , according to version 1.1 of the standard in accordance with a judgment RECIST(longest diameter on a spiral CT at least 10mm , on a regular CT longest diameter at least 20 mm ) ; 4 ) Male or female , aged 18 to 75 years ; 5 ) ECOG PS 0 or 1 ; 6 ) expected survival at least 3 months ; 7 ) adequate hematological function : absolute neutrophil count ( ANC ) at least 2×10 ^ 9 / L and platelet count at least 100×10 ^ 9 / L and hemoglobin at least 9 g / dL ; 8) adequate liver function : total bilirubin less than upper limit of normal ( ULN ) ; AST and ALT less than 2.5 times upper limit of normal ( ULN ) ; alkaline phosphatase less than 5 times the upper limit of normal ( ULN ) ; 9 ) adequate renal function : serum creatinine less than upper limit of normal ( ULN ) or calculated creatinine clearance at least 60 mL / min ; 10 ) ECG is normal , there is no non - healing wounds on the body ; 11 ) had not received previous treatment anticancer drugs , or had only received for previous non - metastatic tumors adjuvant or neoadjuvant chemotherapy , but when you start to study treatment has ended more than 6 months ; 12 ) have conducted previous surgery patients required to study treatment was started more than four weeks , and the patient had recovered ; 13 ) have an intact uterus in women prior to enrollment in the study must have a negative pregnancy test result ( unless it is already 24 months of amenorrhea ) within 28 days . If the pregnancy test from the first administration more than seven days , urine pregnancy test is required for authentication ( less than 7 days before the first dose ) ; 14 ) previous to biological agents , particularly E.coli genetically engineered products without serious allergic reactions ; 15 ) signed informed consent .\r\n",
"\r\n",
"2021-01-12 21:54:17 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 10032, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 4, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:17 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'all', '##er', '##gies', 'for', 'tran', '##ex', '##ami', '##c', 'acid', 'or', 'any', 'other', 'substance', 'in', 'ex', '##acy', '##l', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2124, 2035, 2121, 17252, 2005, 25283, 10288, 10631, 2278, 5648, 2030, 2151, 2060, 9415, 1999, 4654, 15719, 2140, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 4, 2, 2, 3, 9, 2, 2, 2, 8, 3, 3, 3, 3, 3, 9, 2, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 2, 2, 2, 3, 4, 4, 4, 4, 5, 6, 7, 8, 9, 10, 11, 11, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:17 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'deep', 'vein', 'th', '##rom', '##bos', '##is', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2784, 12818, 16215, 21716, 15853, 2483, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 4, 5, 5, 2, 2, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 2, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 21:54:17 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 170).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Histological confirmation of relapsed / refractory diffuse large B - cell lymphoma after prior rituximab and anthracycline - containing systemic treatment regimen such as R - CHOP ( rituximab , cyclophosphamide , doxorubicin , vincristine , and prednisone ) , R - EPOCH ( rituximab , etoposide phosphate , prednisone , vincristine sulfate , cyclophosphamide , doxorubicin hydrochloride ) , R - HyperCVAD ( rituximab , cyclophosphamide , vincristine sulfate , doxorubicin hydrochloride , dexamethasone ) etc .\r\n",
"\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - ***** Running training *****\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Num data points = 1258\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Num Epochs = 20.0\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Gradient Accumulation steps = 1\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Total optimization steps = 25160.0\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - Training steps (number of steps between two evaluation on dev) = 1000\r\n",
"2021-01-12 21:54:18 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:04:12 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:04:12 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:04:12 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:04:22 - Transformer_NER - INFO - \r\n",
" Global step: 1258; \r\n",
" Epoch: 1; \r\n",
" previous best score: 0.0000; \r\n",
" new best score: 0.4506; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.749, 'strict': {'precision': 0.4188917599770313, 'recall': 0.4874707651186101, 'f_score': 0.4505867819641754}, 'relax': {'precision': 0.7014068331897789, 'recall': 0.8162378884062813, 'f_score': 0.7544780728844966}}, 'category': {'strict': {'condition': {'precision': 0.4494175352544451, 'recall': 0.6934720908230843, 'f_score': 0.5453869047619048}, 'drug': {'precision': 0.5055928411633109, 'recall': 0.6550724637681159, 'f_score': 0.5707070707070706}, 'procedure': {'precision': 0.20123839009287925, 'recall': 0.23049645390070922, 'f_score': 0.21487603305785122}, 'measurement': {'precision': 0.2898089171974522, 'recall': 0.2879746835443038, 'f_score': 0.28888888888888886}, 'value': {'precision': 0.4869109947643979, 'recall': 0.49865951742627346, 'f_score': 0.49271523178807947}, 'temporal': {'precision': 0.34296028880866425, 'recall': 0.38461538461538464, 'f_score': 0.3625954198473283}, 'person': {'precision': 0.84, 'recall': 0.4144736842105263, 'f_score': 0.5550660792951542}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}}, 'relax': {'condition': {'precision': 0.6701410177805027, 'recall': 1.0340586565752128, 'f_score': 0.8132440476190476}, 'drug': {'precision': 0.7762863534675615, 'recall': 1.0057971014492753, 'f_score': 0.8762626262626262}, 'procedure': {'precision': 0.5727554179566563, 'recall': 0.6560283687943262, 'f_score': 0.6115702479338843}, 'measurement': {'precision': 0.8089171974522293, 'recall': 0.8037974683544303, 'f_score': 0.8063492063492064}, 'value': {'precision': 0.8324607329842932, 'recall': 0.8525469168900804, 'f_score': 0.8423841059602649}, 'temporal': {'precision': 0.6101083032490975, 'recall': 0.6842105263157895, 'f_score': 0.6450381679389313}, 'person': {'precision': 0.8666666666666667, 'recall': 0.4276315789473684, 'f_score': 0.5726872246696035}, 'pregnancy_considerations': {'precision': 0.35294117647058826, 'recall': 1.0, 'f_score': 0.5217391304347826}}}}\r\n",
" \r\n",
"2021-01-12 22:04:22 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_1258.bin\r\n",
"2021-01-12 22:04:24 - Transformer_NER - INFO - \r\n",
" Global step: 1258; \r\n",
" Epoch: 1; \r\n",
" average_train_loss: 1.6446; \r\n",
" eval_loss: 0.6507; \r\n",
" current best score: 0.4506\r\n",
"2021-01-12 22:10:21 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:10:21 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:10:21 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:10:32 - Transformer_NER - INFO - \r\n",
" Global step: 1999; \r\n",
" Epoch: 2; \r\n",
" previous best score: 0.4506; \r\n",
" new best score: 0.5822; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.7954, 'strict': {'precision': 0.5650943396226416, 'recall': 0.6004009355162044, 'f_score': 0.5822128624655759}, 'relax': {'precision': 0.7779874213836478, 'recall': 0.8265953892415636, 'f_score': 0.8015551595658513}}, 'category': {'strict': {'condition': {'precision': 0.6087689713322091, 'recall': 0.6830652790917692, 'f_score': 0.6437806509139545}, 'drug': {'precision': 0.6682577565632458, 'recall': 0.8115942028985508, 'f_score': 0.7329842931937173}, 'procedure': {'precision': 0.4033333333333333, 'recall': 0.42907801418439717, 'f_score': 0.41580756013745707}, 'measurement': {'precision': 0.49271137026239065, 'recall': 0.5348101265822784, 'f_score': 0.5128983308042488}, 'value': {'precision': 0.675, 'recall': 0.7238605898123325, 'f_score': 0.6985769728331177}, 'temporal': {'precision': 0.39792387543252594, 'recall': 0.46558704453441296, 'f_score': 0.4291044776119403}, 'person': {'precision': 0.7581699346405228, 'recall': 0.7631578947368421, 'f_score': 0.7606557377049181}, 'observation': {'precision': 0.4444444444444444, 'recall': 0.031496062992125984, 'f_score': 0.058823529411764705}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}}, 'relax': {'condition': {'precision': 0.8347386172006745, 'recall': 0.9366130558183539, 'f_score': 0.8827463218903254}, 'drug': {'precision': 0.8066825775656324, 'recall': 0.9797101449275363, 'f_score': 0.8848167539267016}, 'procedure': {'precision': 0.6266666666666667, 'recall': 0.6666666666666666, 'f_score': 0.6460481099656358}, 'measurement': {'precision': 0.8075801749271136, 'recall': 0.8765822784810127, 'f_score': 0.8406676783004552}, 'value': {'precision': 0.855, 'recall': 0.9168900804289544, 'f_score': 0.8848641655886157}, 'temporal': {'precision': 0.6539792387543253, 'recall': 0.7651821862348178, 'f_score': 0.7052238805970149}, 'person': {'precision': 0.7777777777777778, 'recall': 0.7828947368421053, 'f_score': 0.7803278688524592}, 'observation': {'precision': 0.7777777777777778, 'recall': 0.05511811023622047, 'f_score': 0.10294117647058823}, 'pregnancy_considerations': {'precision': 0.2962962962962963, 'recall': 2.0, 'f_score': 0.5161290322580645}}}}\r\n",
" \r\n",
"2021-01-12 22:10:32 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_1999.bin\r\n",
"2021-01-12 22:10:35 - Transformer_NER - INFO - \r\n",
" Global step: 1999; \r\n",
" Epoch: 2; \r\n",
" average_train_loss: 1.2691; \r\n",
" eval_loss: 0.5030; \r\n",
" current best score: 0.5822\r\n",
"2021-01-12 22:18:34 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:18:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:18:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:18:44 - Transformer_NER - INFO - \r\n",
" Global step: 2999; \r\n",
" Epoch: 3; \r\n",
" previous best score: 0.5822; \r\n",
" new best score: 0.6337; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.8014, 'strict': {'precision': 0.6148287778825008, 'recall': 0.6538590043434681, 'f_score': 0.6337435233160622}, 'relax': {'precision': 0.7898209236569275, 'recall': 0.8399599064483796, 'f_score': 0.8141191709844561}}, 'category': {'strict': {'condition': {'precision': 0.6748898678414097, 'recall': 0.7246925260170294, 'f_score': 0.6989051094890512}, 'drug': {'precision': 0.7104622871046229, 'recall': 0.8463768115942029, 'f_score': 0.7724867724867726}, 'procedure': {'precision': 0.45454545454545453, 'recall': 0.6028368794326241, 'f_score': 0.5182926829268293}, 'measurement': {'precision': 0.57, 'recall': 0.5411392405063291, 'f_score': 0.555194805194805}, 'value': {'precision': 0.7217847769028871, 'recall': 0.7372654155495979, 'f_score': 0.7294429708222812}, 'temporal': {'precision': 0.49795918367346936, 'recall': 0.4939271255060729, 'f_score': 0.4959349593495935}, 'person': {'precision': 0.8142857142857143, 'recall': 0.75, 'f_score': 0.7808219178082193}, 'observation': {'precision': 0.4, 'recall': 0.2677165354330709, 'f_score': 0.32075471698113206}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}, 'mood': {'precision': 0.07142857142857142, 'recall': 0.02127659574468085, 'f_score': 0.032786885245901634}, 'device': {'precision': 0.4, 'recall': 0.34285714285714286, 'f_score': 0.36923076923076925}}, 'relax': {'condition': {'precision': 0.8475770925110132, 'recall': 0.9101229895931883, 'f_score': 0.8777372262773723}, 'drug': {'precision': 0.8175182481751825, 'recall': 0.9739130434782609, 'f_score': 0.8888888888888888}, 'procedure': {'precision': 0.6417112299465241, 'recall': 0.851063829787234, 'f_score': 0.7317073170731708}, 'measurement': {'precision': 0.86, 'recall': 0.8164556962025317, 'f_score': 0.8376623376623378}, 'value': {'precision': 0.8661417322834646, 'recall': 0.8847184986595175, 'f_score': 0.8753315649867375}, 'temporal': {'precision': 0.6979591836734694, 'recall': 0.6923076923076923, 'f_score': 0.6951219512195121}, 'person': {'precision': 0.8428571428571429, 'recall': 0.7763157894736842, 'f_score': 0.8082191780821917}, 'observation': {'precision': 0.5529411764705883, 'recall': 0.3700787401574803, 'f_score': 0.44339622641509435}, 'pregnancy_considerations': {'precision': 0.29411764705882354, 'recall': 1.6666666666666667, 'f_score': 0.5}, 'mood': {'precision': 0.5714285714285714, 'recall': 0.1702127659574468, 'f_score': 0.2622950819672131}, 'device': {'precision': 0.8, 'recall': 0.6857142857142857, 'f_score': 0.7384615384615385}}}}\r\n",
" \r\n",
"2021-01-12 22:18:44 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_2999.bin\r\n",
"2021-01-12 22:18:46 - Transformer_NER - INFO - \r\n",
" Global step: 2999; \r\n",
" Epoch: 3; \r\n",
" average_train_loss: 1.0164; \r\n",
" eval_loss: 0.4663; \r\n",
" current best score: 0.6337\r\n",
"2021-01-12 22:26:49 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:26:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:26:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:26:58 - Transformer_NER - INFO - \r\n",
" Global step: 3999; \r\n",
" Epoch: 4; \r\n",
" previous best score: 0.6337; \r\n",
" new best score: 0.6381; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.8, 'strict': {'precision': 0.5901220550667046, 'recall': 0.6946207818242566, 'f_score': 0.6381215469613261}, 'relax': {'precision': 0.7516321317059325, 'recall': 0.8847310390912129, 'f_score': 0.8127685696746471}}, 'category': {'strict': {'condition': {'precision': 0.6669498725573492, 'recall': 0.7426679280983917, 'f_score': 0.702775290957923}, 'drug': {'precision': 0.7167487684729064, 'recall': 0.8434782608695652, 'f_score': 0.7749667110519308}, 'procedure': {'precision': 0.46511627906976744, 'recall': 0.6382978723404256, 'f_score': 0.5381165919282512}, 'measurement': {'precision': 0.5179063360881543, 'recall': 0.5949367088607594, 'f_score': 0.5537555228276877}, 'value': {'precision': 0.6947115384615384, 'recall': 0.774798927613941, 'f_score': 0.7325728770595691}, 'temporal': {'precision': 0.4469914040114613, 'recall': 0.631578947368421, 'f_score': 0.523489932885906}, 'person': {'precision': 0.7834394904458599, 'recall': 0.8092105263157895, 'f_score': 0.796116504854369}, 'observation': {'precision': 0.30578512396694213, 'recall': 0.29133858267716534, 'f_score': 0.2983870967741935}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}, 'device': {'precision': 0.6052631578947368, 'recall': 0.6571428571428571, 'f_score': 0.6301369863013698}, 'mood': {'precision': 0.2413793103448276, 'recall': 0.14893617021276595, 'f_score': 0.18421052631578946}}, 'relax': {'condition': {'precision': 0.8377230246389125, 'recall': 0.9328287606433302, 'f_score': 0.8827215756490601}, 'drug': {'precision': 0.8275862068965517, 'recall': 0.9739130434782609, 'f_score': 0.8948069241011983}, 'procedure': {'precision': 0.6072351421188631, 'recall': 0.8333333333333334, 'f_score': 0.7025411061285501}, 'measurement': {'precision': 0.7796143250688705, 'recall': 0.8955696202531646, 'f_score': 0.833578792341679}, 'value': {'precision': 0.8365384615384616, 'recall': 0.9329758713136729, 'f_score': 0.8821292775665399}, 'temporal': {'precision': 0.5988538681948424, 'recall': 0.8461538461538461, 'f_score': 0.7013422818791946}, 'person': {'precision': 0.8152866242038217, 'recall': 0.8421052631578947, 'f_score': 0.8284789644012945}, 'observation': {'precision': 0.47107438016528924, 'recall': 0.44881889763779526, 'f_score': 0.45967741935483875}, 'pregnancy_considerations': {'precision': 0.2875, 'recall': 1.9166666666666667, 'f_score': 0.5}, 'device': {'precision': 0.7631578947368421, 'recall': 0.8285714285714286, 'f_score': 0.7945205479452055}, 'mood': {'precision': 0.4827586206896552, 'recall': 0.2978723404255319, 'f_score': 0.3684210526315789}}}}\r\n",
" \r\n",
"2021-01-12 22:26:58 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_3999.bin\r\n",
"2021-01-12 22:27:01 - Transformer_NER - INFO - \r\n",
" Global step: 3999; \r\n",
" Epoch: 4; \r\n",
" average_train_loss: 0.8686; \r\n",
" eval_loss: 0.4562; \r\n",
" current best score: 0.6381\r\n",
"2021-01-12 22:34:41 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:34:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:34:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:34:51 - Transformer_NER - INFO - \r\n",
" Global step: 4999; \r\n",
" Epoch: 4; \r\n",
" previous best score: 0.6381; \r\n",
" new best score: 0.6420; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.8031, 'strict': {'precision': 0.6189147286821706, 'recall': 0.6668894086201136, 'f_score': 0.6420070762302992}, 'relax': {'precision': 0.7944186046511628, 'recall': 0.8559973270965586, 'f_score': 0.8240591830170473}}, 'category': {'strict': {'condition': {'precision': 0.682800345721694, 'recall': 0.7473982970671712, 'f_score': 0.7136404697380307}, 'drug': {'precision': 0.7610389610389611, 'recall': 0.8492753623188406, 'f_score': 0.8027397260273974}, 'procedure': {'precision': 0.5203761755485894, 'recall': 0.5886524822695035, 'f_score': 0.5524126455906823}, 'measurement': {'precision': 0.5454545454545454, 'recall': 0.569620253164557, 'f_score': 0.5572755417956657}, 'value': {'precision': 0.671604938271605, 'recall': 0.7292225201072386, 'f_score': 0.699228791773779}, 'temporal': {'precision': 0.4620938628158845, 'recall': 0.5182186234817814, 'f_score': 0.4885496183206107}, 'person': {'precision': 0.8432835820895522, 'recall': 0.743421052631579, 'f_score': 0.7902097902097901}, 'observation': {'precision': 0.35714285714285715, 'recall': 0.1968503937007874, 'f_score': 0.25380710659898476}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}, 'mood': {'precision': 0.26666666666666666, 'recall': 0.1702127659574468, 'f_score': 0.20779220779220778}, 'device': {'precision': 0.6, 'recall': 0.6, 'f_score': 0.6}}, 'relax': {'condition': {'precision': 0.8504753673293, 'recall': 0.9309366130558183, 'f_score': 0.888888888888889}, 'drug': {'precision': 0.8805194805194805, 'recall': 0.9826086956521739, 'f_score': 0.9287671232876713}, 'procedure': {'precision': 0.6927899686520376, 'recall': 0.7836879432624113, 'f_score': 0.7354409317803661}, 'measurement': {'precision': 0.8575757575757575, 'recall': 0.8955696202531646, 'f_score': 0.8761609907120742}, 'value': {'precision': 0.8395061728395061, 'recall': 0.9115281501340483, 'f_score': 0.8740359897172237}, 'temporal': {'precision': 0.6534296028880866, 'recall': 0.7327935222672065, 'f_score': 0.6908396946564885}, 'person': {'precision': 0.8805970149253731, 'recall': 0.7763157894736842, 'f_score': 0.8251748251748251}, 'observation': {'precision': 0.4857142857142857, 'recall': 0.2677165354330709, 'f_score': 0.3451776649746193}, 'pregnancy_considerations': {'precision': 0.25301204819277107, 'recall': 1.75, 'f_score': 0.44210526315789467}, 'mood': {'precision': 0.5333333333333333, 'recall': 0.3404255319148936, 'f_score': 0.41558441558441556}, 'device': {'precision': 0.7142857142857143, 'recall': 0.7142857142857143, 'f_score': 0.7142857142857143}}}}\r\n",
" \r\n",
"2021-01-12 22:34:51 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_4999.bin\r\n",
"2021-01-12 22:34:54 - Transformer_NER - INFO - \r\n",
" Global step: 4999; \r\n",
" Epoch: 4; \r\n",
" average_train_loss: 0.7690; \r\n",
" eval_loss: 0.4406; \r\n",
" current best score: 0.6420\r\n",
"2021-01-12 22:47:56 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:47:56 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:47:56 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:48:06 - Transformer_NER - INFO - \r\n",
" Global step: 5999; \r\n",
" Epoch: 5; \r\n",
" previous best score: 0.6420; \r\n",
" new best score: 0.6448; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.8024, 'strict': {'precision': 0.6097052694254242, 'recall': 0.6842632809889743, 'f_score': 0.6448362720403022}, 'relax': {'precision': 0.7719559392676392, 'recall': 0.8663548279318409, 'f_score': 0.8164357682619647}}, 'category': {'strict': {'condition': {'precision': 0.7000895255147717, 'recall': 0.7398297067171239, 'f_score': 0.7194112235510579}, 'drug': {'precision': 0.7506426735218509, 'recall': 0.8463768115942029, 'f_score': 0.7956403269754768}, 'procedure': {'precision': 0.4585492227979275, 'recall': 0.6276595744680851, 'f_score': 0.5299401197604791}, 'measurement': {'precision': 0.5740740740740741, 'recall': 0.5886075949367089, 'f_score': 0.58125}, 'value': {'precision': 0.7061855670103093, 'recall': 0.7345844504021448, 'f_score': 0.7201051248357424}, 'temporal': {'precision': 0.4511494252873563, 'recall': 0.6356275303643725, 'f_score': 0.5277310924369747}, 'person': {'precision': 0.8321167883211679, 'recall': 0.75, 'f_score': 0.7889273356401383}, 'observation': {'precision': 0.34615384615384615, 'recall': 0.28346456692913385, 'f_score': 0.3116883116883117}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}, 'mood': {'precision': 0.2127659574468085, 'recall': 0.2127659574468085, 'f_score': 0.21276595744680848}, 'device': {'precision': 0.4878048780487805, 'recall': 0.5714285714285714, 'f_score': 0.5263157894736842}}, 'relax': {'condition': {'precision': 0.8666069829901522, 'recall': 0.9157994323557237, 'f_score': 0.890524379024839}, 'drug': {'precision': 0.8431876606683805, 'recall': 0.9507246376811594, 'f_score': 0.8937329700272479}, 'procedure': {'precision': 0.6191709844559585, 'recall': 0.8475177304964538, 'f_score': 0.715568862275449}, 'measurement': {'precision': 0.8240740740740741, 'recall': 0.8449367088607594, 'f_score': 0.8343749999999999}, 'value': {'precision': 0.884020618556701, 'recall': 0.9195710455764075, 'f_score': 0.9014454664914585}, 'temporal': {'precision': 0.6005747126436781, 'recall': 0.8461538461538461, 'f_score': 0.7025210084033614}, 'person': {'precision': 0.8613138686131386, 'recall': 0.7763157894736842, 'f_score': 0.8166089965397924}, 'observation': {'precision': 0.49038461538461536, 'recall': 0.4015748031496063, 'f_score': 0.44155844155844154}, 'pregnancy_considerations': {'precision': 0.28205128205128205, 'recall': 1.8333333333333333, 'f_score': 0.4888888888888888}, 'mood': {'precision': 0.425531914893617, 'recall': 0.425531914893617, 'f_score': 0.42553191489361697}, 'device': {'precision': 0.6829268292682927, 'recall': 0.8, 'f_score': 0.736842105263158}}}}\r\n",
" \r\n",
"2021-01-12 22:48:06 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_5999.bin\r\n",
"2021-01-12 22:48:09 - Transformer_NER - INFO - \r\n",
" Global step: 5999; \r\n",
" Epoch: 5; \r\n",
" average_train_loss: 0.6940; \r\n",
" eval_loss: 0.4611; \r\n",
" current best score: 0.6448\r\n",
"2021-01-12 22:56:08 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 22:56:08 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 22:56:08 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 22:56:21 - Transformer_NER - INFO - \r\n",
" Global step: 6999; \r\n",
" Epoch: 6; \r\n",
" previous best score: 0.6448; \r\n",
" new best score: 0.6504; \r\n",
" full evaluation metrix: {'overall': {'acc': 0.806, 'strict': {'precision': 0.6176028837488735, 'recall': 0.6869361844303374, 'f_score': 0.6504270800379627}, 'relax': {'precision': 0.7798137578852509, 'recall': 0.8673571667223522, 'f_score': 0.8212590952230309}}, 'category': {'strict': {'condition': {'precision': 0.7228915662650602, 'recall': 0.7379375591296121, 'f_score': 0.7303370786516854}, 'drug': {'precision': 0.7582697201017812, 'recall': 0.863768115942029, 'f_score': 0.8075880758807589}, 'procedure': {'precision': 0.5, 'recall': 0.5957446808510638, 'f_score': 0.5436893203883495}, 'measurement': {'precision': 0.5322128851540616, 'recall': 0.6012658227848101, 'f_score': 0.5646359583952452}, 'value': {'precision': 0.717948717948718, 'recall': 0.7506702412868632, 'f_score': 0.7339449541284403}, 'temporal': {'precision': 0.46319018404907975, 'recall': 0.611336032388664, 'f_score': 0.5270506108202443}, 'person': {'precision': 0.78, 'recall': 0.7697368421052632, 'f_score': 0.7748344370860928}, 'observation': {'precision': 0.2846715328467153, 'recall': 0.30708661417322836, 'f_score': 0.2954545454545454}, 'pregnancy_considerations': {'precision': 0.0, 'recall': 0.0, 'f_score': 0.0}, 'device': {'precision': 0.5116279069767442, 'recall': 0.6285714285714286, 'f_score': 0.5641025641025641}, 'mood': {'precision': 0.21153846153846154, 'recall': 0.23404255319148937, 'f_score': 0.2222222222222222}}, 'relax': {'condition': {'precision': 0.8878591288229842, 'recall': 0.9063386944181646, 'f_score': 0.897003745318352}, 'drug': {'precision': 0.8473282442748091, 'recall': 0.9652173913043478, 'f_score': 0.9024390243902439}, 'procedure': {'precision': 0.6785714285714286, 'recall': 0.8085106382978723, 'f_score': 0.737864077669903}, 'measurement': {'precision': 0.7983193277310925, 'recall': 0.9018987341772152, 'f_score': 0.8469539375928677}, 'value': {'precision': 0.8717948717948718, 'recall': 0.9115281501340483, 'f_score': 0.8912188728702489}, 'temporal': {'precision': 0.6134969325153374, 'recall': 0.8097165991902834, 'f_score': 0.6980802792321116}, 'person': {'precision': 0.8133333333333334, 'recall': 0.8026315789473685, 'f_score': 0.8079470198675497}, 'observation': {'precision': 0.4233576642335766, 'recall': 0.4566929133858268, 'f_score': 0.43939393939393945}, 'pregnancy_considerations': {'precision': 0.3181818181818182, 'recall': 1.75, 'f_score': 0.5384615384615383}, 'device': {'precision': 0.6744186046511628, 'recall': 0.8285714285714286, 'f_score': 0.7435897435897435}, 'mood': {'precision': 0.4230769230769231, 'recall': 0.46808510638297873, 'f_score': 0.4444444444444444}}}}\r\n",
" \r\n",
"2021-01-12 22:56:21 - Transformer_NER - INFO - save checkpoint to chia_bert_model/checkpoint_6999.bin\r\n",
"2021-01-12 22:56:23 - Transformer_NER - INFO - \r\n",
" Global step: 6999; \r\n",
" Epoch: 6; \r\n",
" average_train_loss: 0.6344; \r\n",
" eval_loss: 0.4605; \r\n",
" current best score: 0.6504\r\n",
"2021-01-12 23:04:20 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 23:04:20 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:04:20 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:04:28 - Transformer_NER - INFO - \r\n",
" Global step: 7999; \r\n",
" Epoch: 7; \r\n",
" average_train_loss: 0.5859; \r\n",
" eval_loss: 0.4847; \r\n",
" current best score: 0.6504\r\n",
"2021-01-12 23:12:29 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 23:12:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:12:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:12:39 - Transformer_NER - INFO - \r\n",
" Global step: 8999; \r\n",
" Epoch: 8; \r\n",
" average_train_loss: 0.5446; \r\n",
" eval_loss: 0.5306; \r\n",
" current best score: 0.6504\r\n",
"2021-01-12 23:20:35 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 23:20:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:20:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:20:46 - Transformer_NER - INFO - \r\n",
" Global step: 9999; \r\n",
" Epoch: 8; \r\n",
" average_train_loss: 0.5090; \r\n",
" eval_loss: 0.5179; \r\n",
" current best score: 0.6504\r\n",
"2021-01-12 23:28:40 - Transformer_NER - INFO - ***** Running evaluation on 150 number of test data *****\r\n",
"2021-01-12 23:28:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:28:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:28:51 - Transformer_NER - INFO - \r\n",
" Global step: 10999; \r\n",
" Epoch: 9; \r\n",
" average_train_loss: 0.4775; \r\n",
" eval_loss: 0.5664; \r\n",
" current best score: 0.6504\r\n",
"2021-01-12 23:31:22 - Transformer_NER - WARNING - Early stop activated; performance not improve anymore.\r\n"
]
}
],
"source": [
"cat ./chia_bert_log.txt"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"# run prediction\n",
"\n",
"! export CUDA_VISIBLE_DEVICES=0\n",
"\n",
"# use format 1 for BRAT, 2 for BioC, 0 as default for BIO\n",
"! python ./ClinicalTransformerNER/src/run_transformer_batch_prediction.py \\\n",
" --model_type bert \\\n",
" --pretrained_model ./chia_bert_model/ \\\n",
" --preprocessed_text_dir ./chia/tests \\\n",
" --output_dir ./chia_bert_results/ \\\n",
" --max_seq_length 128 \\\n",
" --do_lower_case \\\n",
" --eval_batch_size 8 \\\n",
" --log_file ./chia_bert_prediction_log.txt\\\n",
" --do_copy \\\n",
" --data_has_offset_information"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2021-01-12 23:31:26 - Transformer_NER - INFO - Task will use cuda device: GPU_0.\r\n",
"2021-01-12 23:31:26 - Transformer_NER - INFO - load checkpoint from chia_bert_model/checkpoint_6999.bin\r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'pregnant', 'or', 'lac', '##tat', '##ing', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2024, 6875, 2030, 18749, 29336, 2075, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 2, 2, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"mask: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 2, 3, 4, 4, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'participated', 'in', 'any', 'other', 'studies', 'involving', 'investigation', '##al', 'products', 'within', '30', 'days', 'prior', 'to', 'entry', 'into', 'this', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2031, 4194, 1999, 2151, 2060, 2913, 5994, 4812, 2389, 3688, 2306, 2382, 2420, 3188, 2000, 4443, 2046, 2023, 2817, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'significant', 'metabolic', 'and', 'end', '##oc', '##rine', 'diseases', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'cancer', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'healthy', 'post', '##men', '##opa', '##usa', '##l', 'women', 'with', '50', 'or', 'more', 'moderate', 'to', 'severe', 'hot', 'flush', '##es', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'between', '40', 'to', '70', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'lac', '##tat', '##ing', 'women', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ev', '##ol', '##utive', 'skin', 'disease', 'on', 'the', 'testing', 'zone', '(', 'lower', 'back', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'a', 'clinical', '##ly', 'significant', 'disease', '(', 'chronic', ',', 'rec', '##urrent', 'or', 'active', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00445029_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'both', 'groups', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'aged', 'from', '18', 'to', '65', 'years', 'old', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 5022, 4793, 2013, 2324, 2000, 3515, 2086, 2214, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'both', 'gender', '##s', 'eligible', 'for', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2119, 5907, 2015, 7792, 2005, 2817, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 2, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"segment ids: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"guards: [0, 1, 2, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-12 23:31:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-12 23:31:34 - Transformer_NER - ERROR - Traceback (most recent call last):\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 119, in <module>\r\n",
" main(global_args)\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 63, in main\r\n",
" _output_bio(args, test_example, predictions)\r\n",
" File \"/mnt/d/Clinical/ad/chia-ner/NER_tutorial/ClinicalTransformerNER/src/transformer_ner/task.py\", line 436, in _output_bio\r\n",
" assert len(tokens) == len(predicted_labels), \"Not same length sentence\\nExpect: {} {}\\nBut: {} {}\".format(\r\n",
"AssertionError: Not same length sentence\r\n",
"Expect: 6 ['\\uf0d8', 'First', 'group', ':', 'allergic', 'patients']\r\n",
"But: 5 ['O', 'O', 'O', 'B-Condition', 'O']\r\n",
"\r\n",
"2021-01-19 19:16:37 - Transformer_NER - INFO - Task will use cuda device: GPU_0.\r\n",
"2021-01-19 19:16:37 - Transformer_NER - INFO - load checkpoint from chia_bert_model/checkpoint_6999.bin\r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'pregnant', 'or', 'lac', '##tat', '##ing', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'participated', 'in', 'any', 'other', 'studies', 'involving', 'investigation', '##al', 'products', 'within', '30', 'days', 'prior', 'to', 'entry', 'into', 'this', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'undergoing', 'an', 'acute', 'withdrawal', 'syndrome', 'from', 'drugs', 'or', 'alcohol', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'provide', 'written', 'informed', 'consent', 'before', 'beginning', 'any', 'study', 'related', 'activities', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', 'able', 'to', 'speak', ',', 'read', 'and', 'write', 'english', 'and', 'follow', 'simple', 'instructions', 'for', 'completing', 'self', '-', 'rated', 'scales', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'body', 'mass', 'index', '(', 'b', '##mi', ')', 'of', '35', 'kg', '/', 'm2', 'or', 'more', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'significant', 'metabolic', 'and', 'end', '##oc', '##rine', 'diseases', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'cancer', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'healthy', 'post', '##men', '##opa', '##usa', '##l', 'women', 'with', '50', 'or', 'more', 'moderate', 'to', 'severe', 'hot', 'flush', '##es', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'between', '40', 'to', '70', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'lac', '##tat', '##ing', 'women', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ev', '##ol', '##utive', 'skin', 'disease', 'on', 'the', 'testing', 'zone', '(', 'lower', 'back', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'a', 'clinical', '##ly', 'significant', 'disease', '(', 'chronic', ',', 'rec', '##urrent', 'or', 'active', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00445029_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'both', 'groups', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'aged', 'from', '18', 'to', '65', 'years', 'old', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'both', 'gender', '##s', 'eligible', 'for', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:16:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:16:48 - Transformer_NER - ERROR - Traceback (most recent call last):\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 119, in <module>\r\n",
" main(global_args)\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 63, in main\r\n",
" _output_bio(args, test_example, predictions)\r\n",
" File \"/mnt/d/Clinical/ad/chia-ner/ClinicalTransformerNER/ClinicalTransformerNER/src/transformer_ner/task.py\", line 440, in _output_bio\r\n",
" assert len(tokens) == len(predicted_labels), \"Not same length sentence\\nExpect: {} {}\\nBut: {} {}\".format(\r\n",
"AssertionError: Not same length sentence\r\n",
"Expect: 6 ['\\uf0d8', 'First', 'group', ':', 'allergic', 'patients']\r\n",
"But: 5 ['O', 'O', 'O', 'B-Condition', 'O']\r\n",
"\r\n",
"2021-01-19 19:17:09 - Transformer_NER - INFO - Task will use cuda device: GPU_0.\r\n",
"2021-01-19 19:17:09 - Transformer_NER - INFO - load checkpoint from chia_bert_model/checkpoint_6999.bin\r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'pregnant', 'or', 'lac', '##tat', '##ing', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'participated', 'in', 'any', 'other', 'studies', 'involving', 'investigation', '##al', 'products', 'within', '30', 'days', 'prior', 'to', 'entry', 'into', 'this', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2031, 4194, 1999, 2151, 2060, 2913, 5994, 4812, 2389, 3688, 2306, 2382, 2420, 3188, 2000, 4443, 2046, 2023, 2817, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'undergoing', 'an', 'acute', 'withdrawal', 'syndrome', 'from', 'drugs', 'or', 'alcohol', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2024, 14996, 2019, 11325, 10534, 8715, 2013, 5850, 2030, 6544, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:15 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', 'between', 'age', '18', 'and', '55', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', 'able', 'to', 'speak', ',', 'read', 'and', 'write', 'english', 'and', 'follow', 'simple', 'instructions', 'for', 'completing', 'self', '-', 'rated', 'scales', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'body', 'mass', 'index', '(', 'b', '##mi', ')', 'of', '35', 'kg', '/', 'm2', 'or', 'more', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'significant', 'metabolic', 'and', 'end', '##oc', '##rine', 'diseases', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'cancer', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'healthy', 'post', '##men', '##opa', '##usa', '##l', 'women', 'with', '50', 'or', 'more', 'moderate', 'to', 'severe', 'hot', 'flush', '##es', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'between', '40', 'to', '70', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'lac', '##tat', '##ing', 'women', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ev', '##ol', '##utive', 'skin', 'disease', 'on', 'the', 'testing', 'zone', '(', 'lower', 'back', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'a', 'clinical', '##ly', 'significant', 'disease', '(', 'chronic', ',', 'rec', '##urrent', 'or', 'active', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00445029_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'both', 'groups', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'aged', 'from', '18', 'to', '65', 'years', 'old', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:17:16 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:17:16 - Transformer_NER - ERROR - Traceback (most recent call last):\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 119, in <module>\r\n",
" main(global_args)\r\n",
" File \"./ClinicalTransformerNER/src/run_transformer_batch_prediction.py\", line 63, in main\r\n",
" _output_bio(args, test_example, predictions)\r\n",
" File \"/mnt/d/Clinical/ad/chia-ner/ClinicalTransformerNER/ClinicalTransformerNER/src/transformer_ner/task.py\", line 440, in _output_bio\r\n",
" assert len(tokens) == len(predicted_labels), \"Not same length sentence\\nExpect: {} {}\\nBut: {} {}\".format(\r\n",
"AssertionError: Not same length sentence\r\n",
"Expect: 6 ['\\uf0d8', 'First', 'group', ':', 'allergic', 'patients']\r\n",
"But: 5 ['O', 'O', 'O', 'B-Condition', 'O']\r\n",
"\r\n",
"2021-01-19 19:23:22 - Transformer_NER - INFO - Task will use cuda device: GPU_0.\r\n",
"2021-01-19 19:23:22 - Transformer_NER - INFO - load checkpoint from chia_bert_model/checkpoint_6999.bin\r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'pregnant', 'or', 'lac', '##tat', '##ing', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'participated', 'in', 'any', 'other', 'studies', 'involving', 'investigation', '##al', 'products', 'within', '30', 'days', 'prior', 'to', 'entry', 'into', 'this', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'are', 'undergoing', 'an', 'acute', 'withdrawal', 'syndrome', 'from', 'drugs', 'or', 'alcohol', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:28 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'provide', 'written', 'informed', 'consent', 'before', 'beginning', 'any', 'study', 'related', 'activities', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', 'between', 'age', '18', 'and', '55', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', 'able', 'to', 'speak', ',', 'read', 'and', 'write', 'english', 'and', 'follow', 'simple', 'instructions', 'for', 'completing', 'self', '-', 'rated', 'scales', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00122070_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'body', 'mass', 'index', '(', 'b', '##mi', ')', 'of', '35', 'kg', '/', 'm2', 'or', 'more', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'significant', 'metabolic', 'and', 'end', '##oc', '##rine', 'diseases', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'cancer', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'healthy', 'post', '##men', '##opa', '##usa', '##l', 'women', 'with', '50', 'or', 'more', 'moderate', 'to', 'severe', 'hot', 'flush', '##es', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'between', '40', 'to', '70', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00317148_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00445029_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'both', 'groups', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'aged', 'from', '18', 'to', '65', 'years', 'old', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'both', 'gender', '##s', 'eligible', 'for', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00445029_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inadequate', 'bone', 'marrow', 'reserve', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'poorly', 'controlled', 'hyper', '##tension', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00502567_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'his', '##to', '##logical', '##ly', 'confirmed', 'meta', '##static', 'cancer', 'that', 'is', 'not', 'am', '##ena', '##ble', 'to', 'surgery', 'or', 'radiation', 'therapy', 'with', 'cu', '##rative', 'intent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'me', '##asurable', 'les', '##ion', 'by', 'ct', 'or', 'other', 'techniques', 'according', 'to', 'rec', '##ist', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:29 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00502567_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'other', 'respiratory', 'disorders', 'or', 'signs', 'for', 'other', 'respiratory', 'disorders', '(', 'e', '.', 'g', '.', 'asthma', ',', 'lung', 'cancer', ',', 'sar', '##co', '##ido', '##sis', ',', 'tuberculosis', ',', 'lung', 'fi', '##bro', '##sis', ',', 'cy', '##stic', 'fi', '##bro', '##sis', ',', 'bro', '##nch', '##oe', '##cta', '##sis', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'history', 'of', 'significant', 'inflammatory', 'disease', ',', 'other', 'than', 'cop', '##d', '(', 'e', '.', 'g', '.', 'r', '##he', '##uma', '##to', '##id', 'arthritis', 'and', 'systemic', 'lu', '##pus', 'er', '##ythe', '##mat', '##os', '##us', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2124, 2381, 1997, 3278, 20187, 4295, 1010, 2060, 2084, 8872, 2094, 1006, 1041, 1012, 1043, 1012, 1054, 5369, 12248, 3406, 3593, 27641, 1998, 22575, 11320, 12207, 9413, 26688, 18900, 2891, 2271, 1007, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10, 11, 12, 12, 12, 12, 13, 13, 13, 13, 13, 14, 15, 16, 17, 17, 18, 18, 18, 18, 18, 19, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'to', 'be', 'severely', 'alpha', '-', '1', '-', 'anti', '##try', '##ps', '##in', 'def', '##icient', '(', 'pi', 's', '##z', 'or', 'z', '##z', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2124, 2000, 2022, 8949, 6541, 1011, 1015, 1011, 3424, 11129, 4523, 2378, 13366, 20132, 1006, 14255, 1055, 2480, 2030, 1062, 2480, 1007, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 7, 8, 9, 9, 10, 11, 11, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:29 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00527826_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'must', 'have', 'a', 'diagnosis', 'of', 'cop', '##d', 'based', 'on', 'the', 'american', 'thor', '##ac', '##ic', 'society', '(', 'at', '##s', ')', '/', 'european', 'respiratory', 'society', '(', 'er', '##s', ')', 'criteria', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3395, 2442, 2031, 1037, 11616, 1997, 8872, 2094, 2241, 2006, 1996, 2137, 15321, 6305, 2594, 2554, 1006, 2012, 2015, 1007, 1013, 2647, 16464, 2554, 1006, 9413, 2015, 1007, 9181, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'male', 'or', 'female', 'subjects', ',', 'aged', '>', '=', '40', 'years', '.', 'females', 'must', 'be', 'of', 'non', 'child', 'bearing', 'potential', '.', 'the', 'definition', 'of', 'non', 'child', 'bearing', 'potential', 'is', 'as', 'following', ':', 'females', ',', 'regardless', 'of', 'their', 'age', ',', 'with', 'functioning', 'o', '##var', '##ies', 'and', 'who', 'have', 'a', 'current', 'documented', 'tuba', '##l', 'liga', '##tion', 'or', 'h', '##yst', '##ere', '##ct', '##omy', ',', 'or', 'females', 'who', 'are', 'post', '-', 'men', '##opa', '##usa', '##l', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3287, 2030, 2931, 5739, 1010, 4793, 1028, 1027, 2871, 2086, 1012, 3801, 2442, 2022, 1997, 2512, 2775, 7682, 4022, 1012, 1996, 6210, 1997, 2512, 2775, 7682, 4022, 2003, 2004, 2206, 1024, 3801, 1010, 7539, 1997, 2037, 2287, 1010, 2007, 12285, 1051, 10755, 3111, 1998, 2040, 2031, 1037, 2783, 8832, 29242, 2140, 8018, 3508, 2030, 1044, 27268, 7869, 6593, 16940, 1010, 2030, 3801, 2040, 2024, 2695, 1011, 2273, 29477, 10383, 2140, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'diagnosed', 'cop', '##d', 'stage', 'iii', 'or', 'iv', 'according', 'to', 'gold', 'criteria', ':', 'a', 'baseline', 'post', '-', 'bro', '##nch', '##od', '##ila', '##tor', 'forced', 'ex', '##pi', '##rator', '##y', 'volume', ',', 'measured', 'at', '1', 'second', '(', 'fe', '##v', '##1', ')', '<', '50', '%', 'of', 'predicted', 'normal', 'and', 'a', 'baseline', 'post', '-', 'bro', '##nch', '##od', '##ila', '##tor', 'fe', '##v', '##1', '/', 'ins', '##pi', '##rator', '##y', 'vital', 'capacity', '(', 'iv', '##c', ')', 'ratio', '<', '70', '%', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00527826_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'contra', '##ind', '##ication', 'to', 'cl', '##op', '##ido', '##gre', '##l', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'smoking', '(', 'current', 'smoke', '##rs', 'and', 'patients', 'who', 'quit', 'smoking', 'less', 'than', 'six', 'months', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mali', '##gnan', '##cy', '(', 'diagnosed', 'or', 'under', 'investigation', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00728156_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 't', '##2', '##dm', 'and', 'cas', 'as', 'defined', 'below', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'clinical', 'definitions', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 't', '##2', '##dm', ':', 'diagnosed', 'according', 'to', 'the', 'who', 'criteria', '[', '53', ']', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00728156_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'asa', '3', '+', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'severely', 'car', '##ious', 'teeth', 'resulting', 'in', 'inability', 'to', 'isolate', 'for', 'procedure', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00806273_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'asa', '1', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'asa', '2', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pts', 'have', 'current', 'treatment', 'plan', 'at', 'oh', '##su', 'for', 'extraction', 'of', 'some', 'or', 'all', 'of', 'remaining', 'teeth', 'and', 'scheduled', 'for', 'delivery', 'of', 'a', 're', '##movable', 'app', '##lian', '##ce', 'post', 'extraction', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00806273_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'are', 'pregnant', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'is', 'unable', 'to', 'perform', 'tasks', 'associated', 'with', 'study', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00926523_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'are', 'at', 'least', '18', 'years', 'of', 'age', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'has', 'confirmed', 'pulmonary', 'hyper', '##tension', 'and', 'inter', '##sti', '##tial', 'lung', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'are', 'able', 'to', 'complete', 'study', 'procedures', ',', 'such', 'as', 'sp', '##iro', '##metry', ',', 'and', 'pulmonary', 'exercise', 'test', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00926523_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mali', '##gnan', '##cy', 'and', 'other', 'significant', 'medical', 'conditions', 'that', 'will', 'impact', 'follow', 'up', 'within', 'this', 'program', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'those', 'less', 'than', '18', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'con', '##com', '##itan', '##t', 'inter', '##sti', '##tial', 'lung', 'disease', ',', 'sar', '##co', '##ido', '##sis', ',', 'other', 'significant', 'lung', 'disease', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00954850_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'adults', '(', '18', 'and', 'older', ')', 'with', 'physiological', '##ly', 'confirmed', 'sa', 'or', 'mild', '-', 'moderate', 'asthma', 'and', 'followed', 'by', 'an', 'asthma', 'specialist', 'for', 'at', 'least', '6', 'months', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'must', 'agree', 'to', 'have', 'regular', 'clinic', 'visits', '(', 'minimum', '3', '-', '4', 'per', 'year', 'for', 'sa', ',', '1', '-', '2', 'for', 'mild', '-', 'moderate', 'asthma', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'must', 'have', 'good', 'compliance', 'with', 'medications', 'patients', 'with', 'asthma', 'and', 'cop', '##d', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:30 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00954850_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'sy', '##sto', '##lic', 'blood', 'pressure', '<', '100', 'mm', '##hg', 'or', 'basal', 'heart', 'rate', '<', '60', '/', 'min', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'portal', 'vein', 'th', '##rom', '##bos', '##is', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'un', '##con', '##tro', '##lled', 'as', '##cite', '##s', 'or', 'he', '##pati', '##c', 'en', '##ce', '##pha', '##lo', '##pathy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:30 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00965900_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'liver', 'ci', '##rr', '##hosis', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'es', '##op', '##ha', '##ge', '##al', 'var', '##ices', 'with', 'high', 'bleeding', 'risk', ':', 'more', 'than', 'f', '##2', 'and', 'red', 'color', 'sign', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT00965900_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'an', 'underlying', 'infectious', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ch', '##rom', '##osomal', 'abnormal', '##ity', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01098383_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'a', 'signed', 'parental', 'consent', 'form', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01098383_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'meets', 'criteria', 'for', 'major', 'de', '##pressive', 'episode', ',', 'by', 'diagnostic', 'statistical', 'manual', 'of', 'mental', 'disorder', '-', 'iv', '(', 'tr', ')', 'criteria', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 6010, 9181, 2005, 2350, 2139, 27484, 2792, 1010, 2011, 16474, 7778, 6410, 1997, 5177, 8761, 1011, 4921, 1006, 19817, 1007, 9181, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'clinical', '##ly', 'significant', 'agitation', '/', 'aggression', 'for', 'which', 'either', '1', ')', 'the', 'frequency', 'of', 'agitation', '/', 'aggression', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'very', 'frequently', \"'\", ',', 'or', '2', ')', 'the', 'frequency', 'of', 'agitation', '/', 'aggression', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'frequently', \"'\", 'and', 'the', 'severity', 'of', 'the', 'agitation', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'moderate', \"'\", ',', 'or', \"'\", 'marked', \"'\", '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 6612, 2135, 3278, 22356, 1013, 14974, 2005, 2029, 2593, 1015, 1007, 1996, 6075, 1997, 22356, 1013, 14974, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 2200, 4703, 1005, 1010, 2030, 1016, 1007, 1996, 6075, 1997, 22356, 1013, 14974, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 4703, 1005, 1998, 1996, 18976, 1997, 1996, 22356, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 8777, 1005, 1010, 2030, 1005, 4417, 1005, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 2, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 1, 2, 3, 4, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 15, 16, 17, 18, 19, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 37, 38, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'clinical', '##ly', 'significant', 'del', '##usions', 'for', 'which', 'either', '1', ')', 'the', 'frequency', 'of', 'del', '##usions', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'very', 'frequently', \"'\", ',', 'or', '2', ')', 'the', 'frequency', 'of', 'del', '##usions', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'frequently', \"'\", 'and', 'the', 'severity', 'of', 'the', 'del', '##usions', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'moderate', \"'\", ',', 'or', \"'\", 'marked', \"'\", '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 6612, 2135, 3278, 3972, 22016, 2005, 2029, 2593, 1015, 1007, 1996, 6075, 1997, 3972, 22016, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 2200, 4703, 1005, 1010, 2030, 1016, 1007, 1996, 6075, 1997, 3972, 22016, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 4703, 1005, 1998, 1996, 18976, 1997, 1996, 3972, 22016, 2004, 14155, 2011, 1996, 27937, 2072, 2003, 1005, 8777, 1005, 1010, 2030, 1005, 4417, 1005, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 2, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 3 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01117181_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'possible', 'or', 'probable', 'alzheimer', \"'\", 's', 'disease', '(', 'national', 'institute', 'of', 'neurological', 'and', 'com', '##mun', '##icative', 'disorders', 'and', 'stroke', '-', 'alzheimer', \"'\", 's', 'disease', 'and', 'related', 'disorders', 'association', '(', 'ni', '##nc', '##ds', '-', 'ad', '##rda', ')', 'criteria', ')', ',', 'with', 'mini', '-', 'mental', 'state', 'exam', '(', 'mm', '##se', ')', 'score', 'of', '10', '-', '26', 'inclusive', ';', 'mm', '##se', 'scores', 'above', '26', 'in', 'those', 'who', 'nevertheless', 'meet', 'criteria', 'for', 'ad', 'may', 'be', 'allowed', 'with', 'steering', 'committee', 'approval', 'on', 'a', 'case', 'by', 'case', 'basis', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"label: [1, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 13, 13, 14, 15, 16, 17, 18, 19, 19, 20, 21, 22, 23, 24, 25, 26, 26, 26, 27, 28, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'clinical', '##ly', 'significant', 'ap', '##athy', 'for', 'at', 'least', 'four', 'weeks', 'for', 'which', 'either', '1', ')', 'the', 'frequency', 'of', 'ap', '##athy', 'as', 'assessed', 'by', 'the', 'ne', '##uro', '##psy', '##chia', '##tric', 'inventory', '(', 'np', '##i', ')', 'is', \"'\", 'very', 'frequently', \"'\", ',', 'or', '2', ')', 'the', 'frequency', 'of', 'ap', '##athy', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'frequently', \"'\", 'or', \"'\", 'often', \"'\", 'and', 'the', 'severity', 'of', 'ap', '##athy', 'as', 'assessed', 'by', 'the', 'np', '##i', 'is', \"'\", 'moderate', \"'\", 'or', \"'\", 'marked', \"'\", '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'a', 'medication', 'for', 'ap', '##athy', 'is', 'appropriate', ',', 'in', 'the', 'opinion', 'of', 'the', 'study', 'physician', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01117181_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inability', 'to', 'provide', 'informed', 'consent', 'or', 'to', 'comply', 'with', 'study', 'assessments', '(', 'e', '.', 'g', '.', 'due', 'to', 'cognitive', 'impairment', 'or', 'geographic', 'distance', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '=', '17', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', '##ergy', 'to', 'po', '##vid', '##one', 'io', '##dine', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:31 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01175044_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:31 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01175044_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'current', 'pregnancy', 'or', 'lac', '##tation', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'liver', 'disease', 'or', 'elevated', 'liver', 'enzymes', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'established', 'diagnosis', 'of', 'diabetes', 'mel', '##lit', '##us', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01483118_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'aged', 'greater', 'than', '18', 'years', 'of', 'age', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ability', 'to', 'understand', 'and', 'willingness', 'to', 'comply', 'with', 'the', 'study', 'protocol', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'written', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01483118_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'any', 'other', 'variety', 'of', 'lal', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'chronic', 'liver', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01491763_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'ph', '(', 'bc', '##r', '/', 'ab', '##l', ')', 'positive', 'de', 'novo', '<', '55', 'years', 'old', '(', 'it', 'is', 'ad', '##vis', '##able', 'to', 'include', 'patients', 'over', '55', 'years', 'lal', '##0', '##7', '##op', '##h', 'protocol', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'performance', 'status', '0', '-', '2', '(', 'appendix', 'b', ')', 'may', 'include', 'patients', 'with', 'performance', 'status', '>', '2', 'at', '##tri', '##bu', '##table', 'to', 'lal', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 130).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Patients without functional impairment of organs : liver function : total bilirubin , AST , ALT , alfa - GT and alkaline phosphatase less than 3 times the upper limit of normal laboratory renal function : serum creatinine < 2 mg / dL or clearance creatinine > 30 ml / min ( except renal function attributable to LAL ) cardiac function ( Appendix B ) normal : ventricular EF > 50 % , absence of severe chronic respiratory disease . In the event that alterations are secondary to the disease is at the discretion of the investigator to determine if the patient can be included in the trial .\r\n",
"\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'without', 'functional', 'impairment', 'of', 'organs', ':', 'liver', 'function', ':', 'total', 'bi', '##li', '##ru', '##bin', ',', 'as', '##t', ',', 'alt', ',', 'alfa', '-', 'gt', 'and', 'al', '##kali', '##ne', 'ph', '##os', '##pha', '##tase', 'less', 'than', '3', 'times', 'the', 'upper', 'limit', 'of', 'normal', 'laboratory', 'renal', 'function', ':', 'serum', 'cr', '##ea', '##tin', '##ine', '<', '2', 'mg', '/', 'dl', 'or', 'clearance', 'cr', '##ea', '##tin', '##ine', '>', '30', 'ml', '/', 'min', '(', 'except', 'renal', 'function', 'at', '##tri', '##bu', '##table', 'to', 'lal', ')', 'cardiac', 'function', '(', 'appendix', 'b', ')', 'normal', ':', 'vent', '##ric', '##ular', 'e', '##f', '>', '50', '%', ',', 'absence', 'of', 'severe', 'chronic', 'respiratory', 'disease', '.', 'in', 'the', 'event', 'that', 'alterations', 'are', 'secondary', 'to', 'the', 'disease', 'is', 'at', 'the', 'discretion', 'of', 'the', 'investigator', 'to', 'determine', 'if', 'the', 'patient', 'can', 'be', '[NEXT]', '[SEP]']\r\n",
"input ids: [101, 5022, 2302, 8360, 25172, 1997, 11595, 1024, 11290, 3853, 1024, 2561, 12170, 3669, 6820, 8428, 1010, 2004, 2102, 1010, 12456, 1010, 22989, 1011, 14181, 1998, 2632, 28613, 2638, 6887, 2891, 21890, 18260, 2625, 2084, 1017, 2335, 1996, 3356, 5787, 1997, 3671, 5911, 25125, 3853, 1024, 20194, 13675, 5243, 7629, 3170, 1026, 1016, 11460, 1013, 21469, 2030, 14860, 13675, 5243, 7629, 3170, 1028, 2382, 19875, 1013, 8117, 1006, 3272, 25125, 3853, 2012, 18886, 8569, 10880, 2000, 21348, 1007, 15050, 3853, 1006, 22524, 1038, 1007, 3671, 1024, 18834, 7277, 7934, 1041, 2546, 1028, 2753, 1003, 1010, 6438, 1997, 5729, 11888, 16464, 4295, 1012, 1999, 1996, 2724, 2008, 16705, 2024, 3905, 2000, 1996, 4295, 2003, 2012, 1996, 19258, 1997, 1996, 14064, 2000, 5646, 2065, 1996, 5776, 2064, 2022, 100, 102]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01491763_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ca', '##uda', 'e', '##quin', '##a', 'or', 'con', '##us', 'les', '##ion', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'currently', 'use', 'vent', '##ila', '##tor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2747, 2224, 18834, 11733, 4263, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'col', '##ost', '##omy', ',', 'or', 'do', 'not', 'perform', 'regular', 'bow', '##el', 'care', 'for', 'any', 'reason', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 1, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 10, 11, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01567605_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'traumatic', 'spinal', 'cord', 'injury', 'at', 'least', 'one', 'year', 'ago', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'regular', 'bow', '##el', 'care', 'routine', '(', 'at', 'least', 'four', 'weeks', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01567605_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', 'less', 'than', '14', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'estimated', 'life', 'expect', '##ancy', '(', 'due', 'to', 'como', '##rb', '##idi', '##ties', ')', 'less', 'than', '90', 'days', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01639664_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'patients', 'admitted', 'to', 'the', 'ic', '##u', 'in', 'sept', '##ic', 'shock', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'patients', 'that', 'develop', 'sept', '##ic', 'shock', 'while', 'in', 'the', 'ic', '##u', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:32 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01639664_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'meta', '##static', 'tumor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'locally', 'un', '##res', '##ect', '##able', 'tumor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'previous', 'gas', '##tric', 'res', '##ection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3025, 3806, 12412, 24501, 18491, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:32 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01642875_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'primary', 'per', '##iam', '##pu', '##llary', 'tumor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'r', '##0', ',', 'r', '##1', 'res', '##ection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01642875_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'prior', 'chemotherapy', 'prior', 'treatment', 'with', 'ge', '##fi', '##tin', '##ib', ',', 'er', '##lot', '##ini', '##b', ',', 'or', 'other', 'drugs', 'that', 'target', 'e', '##gf', '##r', 'patients', 'must', 'not', 'be', 'receiving', 'any', 'other', 'investigation', '##al', 'agents', 'any', 'evidence', 'of', 'inter', '##sti', '##tial', 'lung', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01665417_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01665417_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'for', 'subjects', 'in', 'co', '##hort', 'a', ':', 'previous', 'therapy', 'for', 'more', 'than', '48', 'hours', 'with', 'any', 'parent', '##eral', 'anti', '##biotic', 'with', 'activity', 'against', 's', '.', 'au', '##reus', 'within', '72', 'hours', 'of', 'positive', 'blood', 'culture', 'results', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 18, 19, 19, 20, 21, 22, 23, 23, 24, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'for', 'subjects', 'in', 'co', '##hort', 'b', ':', 'previous', 'therapy', 'for', 'more', 'than', '48', 'hours', 'with', 'any', 'parent', '##eral', 'anti', '##biotic', 'with', 'activity', 'against', 'mrs', '##a', ',', 'except', 'van', '##com', '##y', '##cin', 'and', '/', 'or', 'da', '##pt', '##omy', '##cin', ',', 'within', '72', 'hours', 'of', 'positive', 'blood', 'culture', 'results', 'confirming', 'persistence', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'previous', 'episode', 'of', 's', '.', 'au', '##reus', 'ba', '##cter', '##emia', 'within', '3', 'months', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01701219_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'presence', 'of', 'ba', '##cter', '##emia', 'due', 'solely', 'to', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 's', '.', 'au', '##reus', 'on', 'at', 'least', '1', 'blood', 'culture', 'within', '72', 'hours', 'of', 'beginning', 'study', 'drug', '(', 'co', '##hort', 'a', ')', 'or', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mrs', '##a', 'on', 'a', 'baseline', 'blood', 'culture', 'and', 'on', 'at', 'least', '1', 'additional', 'blood', 'culture', 'after', 'at', 'least', '72', 'hours', 'of', 'van', '##com', '##y', '##cin', 'and', '/', 'or', 'da', '##pt', '##omy', '##cin', 'treatment', '(', 'co', '##hort', 'b', ')', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 21, 21, 21, 22, 22, 22, 23, 23, 23, 23, 24, 25, 26, 26, 27, 28, 29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01701219_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'refusal', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', 'less', 'than', '40', 'or', 'over', '80', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01715584_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'treated', 'hyper', '##tension', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01715584_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'younger', 'than', '18', 'years', 'old', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'h', '##bs', '##ag', 'negative', 'at', 'baseline', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'lac', '##tat', '##ing', 'women', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01768195_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'treatment', '-', 'naive', 'patients', 'with', 'b', '-', 'cell', 'l', '##ym', '##ph', '##oma', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'h', '##bs', '##ag', 'positive', 'at', 'baseline', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'treated', 'with', 'ri', '##tu', '##xi', '##ma', '##b', '-', 'based', 'im', '##mun', '##oche', '##mot', '##her', '##ap', '##y', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01768195_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'any', 'neurological', 'conditions', 'other', 'than', 'pd', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'significant', 'mu', '##scu', '##los', '##kel', '##eta', '##l', 'or', 'card', '##io', '##pu', '##lm', '##ona', '##ry', 'diseases', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:33 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01799681_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:33 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01799681_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'deny', 'to', 'sign', 'the', 'informed', 'consent', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'type', '1', 'diabetes', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'family', 'history', 'of', 'hyper', '##tri', '##gly', '##cer', '##ide', '##mia', 'or', 'fast', '##ing', 'tri', '##gly', '##cer', '##ide', '>', '4', '.', '56', 'mm', '##ol', '/', 'l', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01857167_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'fast', '##ing', 'glucose', '>', '7', '.', '0', 'or', 'have', 'diabetes', 'medication', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01857167_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hc', '##v', ',', 'hiv', ',', 'or', 'hd', '##v', 'coin', '##fect', '##ion', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hc', '##c', 'or', 'other', 'mali', '##gnan', '##cy', 'within', '3', 'years', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01907230_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT01907230_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'use', 'of', 'any', 'investigation', '##al', 'or', 'non', '-', 'registered', 'drug', 'or', 'vaccine', 'product', 'within', '30', 'days', 'preceding', 'the', 'administration', 'of', 'the', 'study', 'vaccine', 'or', 'planned', 'use', 'within', 'the', 'first', 'six', 'weeks', 'of', 'the', 'study', 'period', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'has', 'received', 'any', 'licensed', 'or', 'other', 'investigation', '##al', 'influenza', 'vaccine', 'within', '3', 'months', 'prior', 'to', 'enrollment', 'in', 'this', 'study', 'or', 'expected', 'receipt', 'of', 'any', 'influenza', 'va', '##cci', '##nation', 'before', 'the', 'day', '21', 'blood', 'collection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 25, 25, 26, 27, 28, 29, 30, 31, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'excessive', 'alcohol', 'use', ',', 'drug', 'abuse', 'or', 'significant', 'psychiatric', 'illness', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2381, 1997, 11664, 6544, 2224, 1010, 4319, 6905, 2030, 3278, 13691, 7355, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 3 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02015494_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'males', 'and', 'females', 'aged', '18', '-', '40', 'years', 'of', 'age', 'at', 'the', 'time', 'of', 'va', '##cci', '##nation', 'in', 'good', 'health', 'as', 'determined', 'by', 'medical', 'history', ',', 'physical', 'exam', ',', 'laboratory', 'assessments', 'and', 'the', 'clinical', 'judgment', 'of', 'the', 'principal', 'investigator', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'able', 'to', 'provide', 'informed', 'consent', 'indicating', 'that', 'they', 'understand', 'the', 'purpose', 'of', 'this', 'study', 'and', 'are', 'willing', 'to', 'adhere', 'to', 'the', 'procedures', 'described', 'in', 'this', 'protocol', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02015494_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ne', '##ph', '##rot', '##ic', 'range', 'protein', '##uria', '(', 'ur', '##ina', '##ry', 'protein', '>', '3', '.', '5', 'gm', '/', 'day', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02046395_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'type', '2', 'diabetes', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hyper', '##tension', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'estimated', 'g', '##lom', '##er', '##ular', 'fi', '##lt', '##ration', 'rate', '(', 'e', '##gf', '##r', ')', '>', '30', 'ml', '/', 'min', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:34 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02046395_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diabetes', 'mel', '##lit', '##us', 'or', 'plasma', 'glucose', '>', '11', ',', '1', 'at', 'admission', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 2, 2, 3, 4, 5, 6, 7, 7, 7, 8, 9, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'receiving', 'ste', '##roids', 'at', 'the', 'time', 'of', 'transplant', '##ation', 'or', 'likely', 'to', 'need', 'ste', '##roids', 'after', 'transplant', '##ation', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'multi', '##org', '##an', 'transplant', '##s', 'and', '/', 'or', 'previously', 'transplant', '##ed', 'with', 'any', 'other', 'organ', 'than', 'kidney', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 4800, 21759, 2319, 22291, 2015, 1998, 1013, 2030, 3130, 22291, 2098, 2007, 2151, 2060, 5812, 2084, 14234, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:34 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02083991_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'first', 'or', 'second', 'single', 'kidney', '(', 'cad', '##aver', '##ic', 'or', 'living', 'donors', ')', 'transplant', 'recipients', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'considered', 'for', 'a', 'standard', 'im', '##mun', '##os', '##up', '##pressive', 'protocol', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02083991_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'breast', '##fe', '##eding', 'patients', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'with', 'a', 'history', 'of', 'hyper', '##sen', '##sit', '##ivity', 'to', 'coli', '##sti', '##n', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02117986_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'hospitalized', 'in', 'critical', 'care', 'units', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'infected', 'by', 'multi', 'drug', 'resistant', 'gram', 'negative', 'bacteria', 'su', '##sc', '##ept', '##ibly', 'only', 'to', 'coli', '##sti', '##n', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'source', 'of', 'infection', ':', 'blood', ',', 'respiratory', ',', 'intra', 'abdominal', 'or', 'ur', '##ina', '##ry', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3120, 1997, 8985, 1024, 2668, 1010, 16464, 1010, 26721, 21419, 2030, 24471, 3981, 2854, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02117986_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'lifetime', 'history', 'of', 'bipolar', 'disorder', ',', 'dementia', ',', 'autism', 'spectrum', 'disorder', ',', 'schizophrenia', ',', 'or', 'any', 'other', 'psychotic', 'disorder', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'psychotic', 'symptoms', 'occurring', 'at', 'any', 'time', 'during', 'the', 'current', 'major', 'de', '##pressive', 'episode', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'current', '(', 'past', '12', 'months', ')', 'diagnosis', 'of', 'panic', 'disorder', ',', 'ob', '##ses', '##sive', 'com', '##pu', '##ls', '##ive', 'disorder', ',', 'post', '##tra', '##umatic', 'stress', 'disorder', ',', 'an', '##ore', '##xia', 'ne', '##r', '##vos', '##a', ',', 'or', 'bu', '##lim', '##ia', 'ne', '##r', '##vos', '##a', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 3 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02137369_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'men', 'or', 'women', 'aged', '18', '-', '60', 'years', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'primary', 'psychiatric', 'diagnosis', 'of', 'major', 'de', '##pressive', 'disorder', ',', 'without', 'psychotic', 'features', ',', 'confirmed', 'via', 'sci', '##d', '-', 'iv', 'structured', 'diagnostic', 'interview', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02137369_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02186600_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'who', 'are', 'in', 'their', 'first', '5', 'years', 'of', 'men', '##opa', '##use', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10, 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'a', 't', 'score', 'between', '-', '1', 'and', '-', '2', '.', '49', 'at', 'the', 'fe', '##moral', 'neck', ',', 'total', 'hip', ',', 'or', 'l', '##1', '-', 'l', '##4', 'spine', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2031, 1037, 1056, 3556, 2090, 1011, 1015, 1998, 1011, 1016, 1012, 4749, 2012, 1996, 10768, 22049, 3300, 1010, 2561, 5099, 1010, 2030, 1048, 2487, 1011, 1048, 2549, 8560, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'be', '19', 'years', 'of', 'age', 'or', 'older', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2022, 2539, 2086, 1997, 2287, 2030, 3080, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02186600_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '<', '20', 'or', '>', '35', 'years', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02186782_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'une', '##x', '##pl', '##aine', '##d', 'in', '##fer', '##tility', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:35 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02186782_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', '##ergy', 'to', 'ce', '##ft', '##ria', '##xon', '##e', 'or', 'macro', '##lide', '##s', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'major', 'ty', '##ph', '##oid', 'fever', '-', 'associated', 'complications', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inability', 'to', 'swallow', 'oral', 'medication', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:35 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02224040_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'blood', 'culture', '-', 'proven', 'ty', '##ph', '##oid', 'fever', '(', 's', '.', 'ty', '##phi', 'or', 's', '.', 'para', '##ty', '##phi', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'signed', 'informed', 'consent', 'to', 'participate', 'in', 'the', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02224040_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'justification', ':', 'stroke', 'or', 'head', 'trauma', 'can', 'lower', 'the', 'seizure', 'threshold', ',', 'and', 'are', 'therefore', 'contra', '-', 'indications', 'for', 't', '##ms', '.', 'faint', '##ing', 'episodes', 'or', 'sync', '##ope', 'of', 'unknown', 'cause', 'could', 'indicate', 'an', 'und', '##ia', '##gno', '##sed', 'condition', 'associated', 'with', 'seizures', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'screening', 'tool', ':', 't', '##ms', 'adult', 'safety', 'question', '##naire', ',', 'medical', 'history', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 5 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02231892_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subjects', 'must', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'be', 'able', 'to', 'give', 'valid', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'be', '18', '55', 'years', 'of', 'age', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1016, 1012, 2022, 2324, 4583, 2086, 1997, 2287, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 225).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"2 . Screening tools : Medical Assessment , Medical History and Physical Examination . Medical assessments include : Vital Signs , EKG , oral HIV test , height / weight measurements , urinalysis and blood sample . Tests on the blood sample include CBC , complete metabolic profile , TSH , ESR , STS and HIV ( if needed to confirm a positive salivary test for HIV ) . The following individual laboratory results will independently disqualify individuals : Cholesterol > 250 mg / dl , Hemoglobin < 10.5 g / dl , WBC < 2400 / microl , LFTs > 3Xnormal , HCG positive , Casual serum glucose > 200 mg / dl , Urine protein > 1 + . The MAI will retain discretion to exclude at less extreme values , depending on the clinical presentation . ( Serum glucose over 140 mg / dl will be followed up with a fasting serum glucose assessment . Those with fasting glucose below 100 mg / dl may be considered for the protocol . Others will be rejected and referred for work - up . ) MAI will make the final judgment on any questionable lab results .\r\n",
"\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02231892_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'undergoing', 'caesar', '##ean', 'section', 'at', 'less', 'than', '37', 'weeks', 'of', 'ge', '##station', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2308, 14996, 11604, 11219, 2930, 2012, 2625, 2084, 4261, 3134, 1997, 16216, 20100, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hyper', '##tension', 'with', 'pregnancy', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'cardiac', 'and', 'corona', '##ry', 'diseases', 'with', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02277041_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'with', 'a', 'singleton', 'pregnancy', 'undergoing', 'cesare', '##an', 'section', 'after', '37', 'weeks', 'of', 'ge', '##station', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:36 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02277041_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'smoke', '##rs', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'under', 'chronic', 'use', 'of', 'medications', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'neurological', 'diseases', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:36 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02295202_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'metabolic', 'syndrome', '(', 'atp', 'iii', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'moderate', 'to', 'severe', 'os', '##a', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02295202_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'moderate', 'or', 'severe', 'end', '##ome', '##tri', '##osis', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 4, 4, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hydro', '##sal', '##pin', '##x', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ut', '##erine', 'abnormalities', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 21183, 24226, 28828, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 2, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02312076_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'subjected', 'to', 'ic', '##si', 'through', 'controlled', 'o', '##var', '##ian', 'hyper', '##sti', '##mu', '##lation', '(', 'co', '##h', ')', 'with', 'pit', '##uit', '##ary', 'down', '##re', '##gul', '##ation', 'by', 'g', '##nr', '##ha', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2308, 13532, 2000, 24582, 5332, 2083, 4758, 1051, 10755, 2937, 23760, 16643, 12274, 13490, 1006, 2522, 2232, 1007, 2007, 6770, 14663, 5649, 2091, 2890, 24848, 3370, 2011, 1043, 16118, 3270, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 2, 3, 3, 3, 2, 2, 3, 2, 2, 2, 3, 3, 2, 3, 3, 3, 2, 2, 3, 2, 2, 2, 3, 3, 2, 2, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 5, 6, 7, 7, 7, 8, 8, 8, 8, 9, 10, 10, 11, 12, 13, 13, 13, 14, 14, 14, 14, 15, 16, 16, 16, 17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02312076_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - \r\n",
"Sentence after tokenization is too long (expect less than 126 but got 135).\r\n",
"You have to increase max_seq_length to make sure every sentence after tokenization is not longer than the max_seq_length.\r\n",
"Or you can further split you long sentences into shorter ones. We will defaultly segment the sentence to two or more seqs with length as (~max_seq_len * n + rest).\r\n",
"The extra long sentence: \r\n",
"Contraindication for hepatectomy , including gastrointestinal hemorrhage , severe hemorrhagic disorders , explicit acute nonspecific infectious lesion , overt ascites , Child - Pugh Score C , indocyanine green retention rate at 15min ( ICGR15)＞30%(12 ) , serum hepatitis B virus ( HBV)-DNA＞126 copies / ml and serum alanine aminotransferase ( ALT ) ＞ 2×ULN , serum triglycerides＞2.0 mmol / L , circulatory shock , stroke , acute myocardial infarction , renal failure , coma of unknown cause\r\n",
"\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'contra', '##ind', '##ication', 'for', 'he', '##pate', '##ct', '##omy', ',', 'including', 'gas', '##tro', '##int', '##estinal', 'hem', '##or', '##rh', '##age', ',', 'severe', 'hem', '##or', '##rh', '##agi', '##c', 'disorders', ',', 'explicit', 'acute', 'non', '##sp', '##ec', '##ific', 'infectious', 'les', '##ion', ',', 'over', '##t', 'as', '##cite', '##s', ',', 'child', '-', 'pu', '##gh', 'score', 'c', ',', 'indo', '##cy', '##ani', '##ne', 'green', 'retention', 'rate', 'at', '15', '##min', '(', 'ic', '##gr', '##15', ')', '[UNK]', '%', '(', '12', ')', ',', 'serum', 'hepatitis', 'b', 'virus', '(', 'h', '##b', '##v', ')', '-', '[UNK]', 'copies', '/', 'ml', 'and', 'serum', 'alan', '##ine', 'amino', '##tra', '##ns', '##fera', '##se', '(', 'alt', ')', '[UNK]', '2', '##×', '##ul', '##n', ',', 'serum', '[UNK]', '.', '0', 'mm', '##ol', '/', 'l', ',', 'ci', '##rc', '##ulator', '##y', 'shock', ',', 'stroke', ',', 'acute', 'my', '##oca', '##rdial', '[NEXT]', '[SEP]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '[UNK]', '[UNK]', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02321202_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'the', 'ci', '##rr', '##hot', '##ic', 'mal', '##no', '##uri', '##shed', 'patients', 'who', 'were', 'diagnosed', 'as', 'liver', 'cancer', 'pre', '##oper', '##ative', '##ly', 'and', 'underwent', 'he', '##pate', '##ct', '##omy', 'were', 'consecutive', '##ly', 'enrolled', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02321202_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'current', 'or', 'past', 'dia', '##gno', '##ses', 'of', 'other', 'axis', 'i', 'psychiatric', 'disorders', ',', 'except', 'for', 'generalized', 'anxiety', 'disorder', '(', 'ga', '##d', ')', 'symptoms', 'occurring', 'during', 'a', 'de', '##pressive', 'episode', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'alcohol', 'or', 'drug', 'dependence', 'or', 'abuse', 'in', 'the', 'last', 'three', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"input tokens: ['[CLS]', 'history', 'of', 'developmental', 'disorder', 'or', 'iq', 'score', '<', '70', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02332291_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '60', 'years', 'or', 'older', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02332291_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02385448_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'good', 'general', 'health', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'older', 'than', 'the', 'age', 'of', 'legal', 'consent', '(', 'i', '.', 'e', '.', '18', 'years', 'old', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'son', '##ographic', 'diagnosis', 'of', 'o', '##var', '##ian', 'end', '##ome', '##tri', '##oma', 'with', 'diameter', 'at', 'least', '4', 'cm', 'on', '2', 'separate', 'scans', 'at', 'least', '6', 'weeks', 'apart', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02385448_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'documented', 'cl', '##otti', '##ng', '/', 'coa', '##gul', '##ation', 'disorder', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'cancer', '(', 'within', 'the', 'last', 'year', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'any', 'diagnosis', 'requiring', 'anti', '-', 'coa', '##gul', '##ation', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:37 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02406885_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'men', 'or', 'women', ',', '18', 'to', '65', 'years', 'old', 'with', 'a', 'b', '##mi', 'of', '35', 'kg', '/', 'm2', 'or', 'greater', 'who', 'will', 'be', 'undergoing', 'bari', '##at', '##ric', 'surgery', '(', 'vs', '##g', 'and', 'ry', '##gb', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 24, 24, 25, 26, 27, 27, 28, 29, 29, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'signed', 'written', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'of', 'child', '##be', '##aring', 'potential', '(', 'wo', '##cb', '##p', ')', 'must', 'have', 'a', 'negative', 'serum', 'or', 'urine', 'pregnancy', 'test', '(', 'minimum', 'sensitivity', '25', 'i', '##u', '/', 'l', 'or', 'equivalent', 'units', 'of', 'hc', '##g', ')', 'within', '24', 'hours', 'prior', 'to', 'the', 'start', 'of', 'study', 'drug', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:37 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02406885_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ad', '##ju', '##vant', 'radio', '##therapy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'evident', 'intra', '-', 'abdominal', 'inflammation', '(', 'diagnosed', 'by', 'imaging', 'and', '/', 'or', 'laboratory', 'results', ',', 'including', 'an', 'abs', '##ces', '##s', 'or', 'cho', '##le', '##cy', '##sti', '##tis', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'chronic', 'pan', '##cre', '##ati', '##tis', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02425774_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'undergoing', 'partial', 'or', 'full', 'res', '##ection', 'of', 'the', 'pan', '##cre', '##as', 'due', 'to', 'a', 'benign', 'or', 'mali', '##gnant', 'tumor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02425774_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'active', 'op', '##io', '##id', 'dependence', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'acute', 'or', 'chronic', 'pain', 'requiring', 'op', '##io', '##id', 'treatment', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'acute', 'liver', 'injury', '(', 'liver', 'amino', '##tra', '##ns', '##fera', '##se', 'concentrations', '>', '5', 'times', 'the', 'upper', 'limit', 'of', 'normal', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 11325, 11290, 4544, 1006, 11290, 13096, 6494, 3619, 27709, 3366, 14061, 1028, 1019, 2335, 1996, 3356, 5787, 1997, 3671, 1007, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 6, 6, 6, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02445339_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'english', 'or', 'spanish', 'speaking', '*', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'emergency', 'department', 'patient', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'aged', '18', '-', '80', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 4793, 2324, 1011, 3770, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02445339_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'did', 'not', 'have', 'breast', 'cancer', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'do', 'not', 'use', 'tam', '##ox', '##ife', '##n', 'or', 'aroma', '##tase', 'inhibitor', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'not', 'in', 'men', '##opa', '##use', 'and', 'not', 'have', 'hot', 'flashes', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2025, 1999, 2273, 29477, 8557, 1998, 2025, 2031, 2980, 16121, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02467686_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'men', '##opa', '##usa', '##l', 'women', 'with', 'breast', 'cancer', 'treated', 'and', 'using', 'tam', '##ox', '##ife', '##n', 'or', 'aroma', '##tase', 'inhibitor', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'with', 'hot', 'flashes', 'and', 'with', 'or', 'without', 'active', 'sexual', 'life', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02467686_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'vi', '##tre', '##ct', '##omy', 'surgery', ',', 'sub', '##mac', '##ular', 'surgery', ',', 'or', 'other', 'surgical', 'intervention', 'for', 'rv', '##o', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'o', '##cular', 'disorders', 'in', 'the', 'study', 'eye', 'that', 'may', 'con', '##fo', '##und', 'interpretation', 'of', 'study', 'results', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02478515_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'signed', 'informed', 'consent', 'form', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mac', '##ula', 'ed', '##ema', 'secondary', 'to', 'br', '##vo', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'bc', '##va', 'of', '77', 'to', '20', 'letters', 'assessed', 'with', 'the', 'use', 'of', 'et', '##dr', '##s', 'charts', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02478515_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'prior', 'treatment', 'with', 'cis', '##pl', '##atin', 'before', 'random', '##ization', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'un', '##con', '##tro', '##lled', 'concurrent', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02481518_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '>', '18', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'eastern', 'cooperative', 'on', '##cology', 'group', 'score', '0', '-', '2', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'first', 'diagnosed', 'head', 'and', 'neck', 'cancer', 'and', 'plan', 'for', 'treatment', 'with', 'cis', '##pl', '##atin', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:38 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:38 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02481518_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'newborn', '##s', 'of', 'substance', 'abu', '##sing', 'mothers', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'newborn', '##s', 'with', 'any', 'contra', '##ind', '##ication', '##s', 'to', 'routine', 'ci', '##rc', '##um', '##cision', ',', 'anatomical', 'or', 'hem', '##ato', '##logic', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02498483_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ap', '##gar', 'score', 'at', '5', 'minutes', '>', '7', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'birth', '##weight', 'greater', 'than', '2', '.', '4', 'kg', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', 'of', 'at', 'least', '10', 'hours', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2287, 1997, 2012, 2560, 2184, 2847, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02498483_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'minors', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'on', 'a', 'legal', 'protection', 'regime', 'type', 'guardians', '##hip', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'respiratory', 'path', '##ologies', ',', 'cardiovascular', ',', 'renal', ',', 'diabetes', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02529475_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'informed', 'consent', 'signed', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'medical', 'examination', 'performed', 'prior', 'to', 'participation', 'in', 'research', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02529475_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'aged', 'under', '18', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'lack', 'of', 'informed', 'consent', 'signed', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'radio', '##fr', '##e', '##que', '##ncy', 'treatment', 'history', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 3 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02558504_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', 'over', '18', 'years', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 3 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02558504_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'the', 'patient', 'is', 'unwilling', 'to', 'provide', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02566928_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'fluent', 'in', 'english', 'or', 'spanish', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:39 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02566928_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '<', '37', 'weeks', 'ge', '##station', ',', 'h', '/', 'o', 'cesare', '##an', 'section', ',', 'multiple', 'ge', '##station', ',', 'pre', '-', 'ec', '##lam', '##ps', '##ia', ',', 'narcotics', 'within', '3', 'hours', 'prior', 'to', 'labor', 'ep', '##id', '##ural', 'placement', ',', 'chronic', 'pain', '(', 'as', 'defined', 'by', 'chronic', 'op', '##iate', 'consumption', ')', ',', 'women', 'who', 'are', 'participating', 'in', 'another', 'study', 'that', 'will', 'impact', 'protocol', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1026, 4261, 3134, 16216, 20100, 1010, 1044, 1013, 1051, 26708, 2319, 2930, 1010, 3674, 16216, 20100, 1010, 3653, 1011, 14925, 10278, 4523, 2401, 1010, 27290, 2306, 1017, 2847, 3188, 2000, 4450, 4958, 3593, 11137, 11073, 1010, 11888, 3255, 1006, 2004, 4225, 2011, 11888, 6728, 13143, 8381, 1007, 1010, 2308, 2040, 2024, 8019, 1999, 2178, 2817, 2008, 2097, 4254, 8778, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 2, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 5, 6, 7, 8, 9, 9, 10, 11, 12, 13, 13, 14, 15, 16, 17, 17, 17, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 26, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:39 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02573597_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'asa', 'i', '&', 'ii', ',', 'null', '##ip', '##aro', '##us', 'and', 'multi', '##par', '##ous', ',', 'spontaneous', '/', 'induced', '/', 'augmented', 'labor', ',', 'early', 'active', 'labor', '(', 'ce', '##r', '##vi', '##x', '<', '5', 'cm', '(', 'if', 'known', ')', ')', ',', 'pain', '(', 'vp', '##s', ')', '>', '3', ',', '18', '-', '45', 'years', 'of', 'age', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 17306, 1045, 1004, 2462, 1010, 19701, 11514, 10464, 2271, 1998, 4800, 19362, 3560, 1010, 17630, 1013, 10572, 1013, 19335, 4450, 1010, 2220, 3161, 4450, 1006, 8292, 2099, 5737, 2595, 1026, 1019, 4642, 1006, 2065, 2124, 1007, 1007, 1010, 3255, 1006, 21210, 2015, 1007, 1028, 1017, 1010, 2324, 1011, 3429, 2086, 1997, 2287, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 6, 6, 6, 7, 8, 8, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 21, 21, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02573597_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'will', 'not', 'be', 'included', 'if', 'they', 'have', 'reached', 'a', 'stable', 'dose', 'of', 'war', '##far', '##in', ',', 'liver', 'dysfunction', ',', 'alcoholism', ',', 'use', 'of', 'another', 'anti', '##co', '##ag', '##ula', '##nt', ',', 'use', 'of', 'chemotherapy', ',', 'or', 'if', 'they', 'do', 'not', 'meet', 'the', 'inclusion', 'criteria', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 5022, 2097, 2025, 2022, 2443, 2065, 2027, 2031, 2584, 1037, 6540, 13004, 1997, 2162, 14971, 2378, 1010, 11290, 28466, 1010, 25519, 1010, 2224, 1997, 2178, 3424, 3597, 8490, 7068, 3372, 1010, 2224, 1997, 27144, 1010, 2030, 2065, 2027, 2079, 2025, 3113, 1996, 10502, 9181, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 24, 24, 24, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02592980_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'only', 'patients', 'with', 'at', '##rial', 'fi', '##bri', '##llation', ',', 'above', '18', 'years', ',', 'and', 'with', 'tt', '##r', '<', '50', '%', 'based', 'on', 'the', 'last', 'three', 'values', 'of', 'in', '##r', 'will', 'be', 'included', 'in', 'this', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2069, 5022, 2007, 2012, 14482, 10882, 23736, 20382, 1010, 2682, 2324, 2086, 1010, 1998, 2007, 23746, 2099, 1026, 2753, 1003, 2241, 2006, 1996, 2197, 2093, 5300, 1997, 1999, 2099, 2097, 2022, 2443, 1999, 2023, 2817, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 2, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 5, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 24, 25, 26, 27, 28, 29, 30, 31, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02592980_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'a', 'medical', 'condition', ',', 'other', 'than', 'p', '##bc', ',', 'that', 'in', 'the', 'investigator', \"'\", 's', 'opinion', 'would', 'pre', '##cl', '##ude', 'full', 'participation', 'in', 'the', 'study', 'or', 'con', '##fo', '##und', 'its', 'results', '(', 'e', '.', 'g', '.', ',', 'cancer', 'on', 'active', 'treatment', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 18, 18, 19, 20, 21, 22, 23, 24, 25, 25, 25, 26, 27, 28, 29, 29, 29, 29, 30, 31, 32, 33, 34, 35, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'as', '##t', 'or', 'alt', '>', '3', '×', 'ul', '##n', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'total', 'bi', '##li', '##ru', '##bin', '>', '2', '×', 'ul', '##n', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02609048_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'must', 'have', 'given', 'written', 'informed', 'consent', '(', 'signed', 'and', 'dated', ')', 'and', 'any', 'authorization', '##s', 'required', 'by', 'local', 'law', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02609048_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02609425_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'patients', 'with', 'es', '##op', '##ha', '##ge', '##al', 'cancer', 'who', 'are', 'deemed', 'candidates', 'for', 'minimal', '##ly', 'invasive', 'robot', 'assisted', 'ivo', '##r', 'lewis', 'es', '##op', '##ha', '##go', '##gas', '##tre', '##ct', '##omy', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 4, 4, 4, 5, 6, 7, 8, 9, 10, 11, 11, 12, 13, 14, 15, 15, 16, 17, 17, 17, 17, 17, 17, 17, 17, 18, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'who', 'provide', 'written', 'informed', 'consent', 'for', 'the', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02609425_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'im', '##mun', '##os', '##up', '##pres', '##ant', 'host', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'chronic', 'cardiovascular', '/', 'pulmonary', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hospital', 'acquired', 'infection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02618057_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'evidence', 'of', 'my', '##co', '##pl', '##as', '##ma', 'pneumonia', '##e', 'infection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'lo', '##bar', 'pneumonia', 'or', 'pneumonia', '##e', 'with', 'pl', '##eur', '##al', 'e', '##ff', '##usion', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02618057_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'na', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:40 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02620904_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'intra', '##uter', '##ine', 'fetal', 'death', 'as', 'confirmed', 'by', 'absence', 'of', 'cardiac', 'motion', 'on', 'ultrasound', 'by', 'attending', 'physician', 'at', 'the', 'time', 'of', 'admission', 'to', 'the', 'hospital', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'estimated', 'ge', '##station', '##al', 'age', 'greater', 'than', '20', 'weeks', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hem', '##od', '##yna', '##mic', '##ally', 'stable', 'and', 'appropriate', 'for', 'induction', 'of', 'labor', 'as', 'per', 'primary', 'clinical', 'health', 'team', 'in', 'house', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 19610, 7716, 18279, 7712, 3973, 6540, 1998, 6413, 2005, 15946, 1997, 4450, 2004, 2566, 3078, 6612, 2740, 2136, 1999, 2160, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:40 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02620904_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'type', '1', 'diabetes', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'peripheral', 'artery', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'liver', 'enzymes', 'equal', 'or', 'more', 'than', '1', '.', '5', 'times', 'the', 'upper', 'limit', 'of', 'normal', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02624908_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'use', 'of', 'basal', '-', 'bo', '##lus', 'insulin', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'onset', 'of', 'diabetes', 'after', 'age', '30', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'b', '##mi', 'less', 'than', '35', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02624908_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ps', '##oria', '##sis', 'or', 'ps', '##oria', '##sis', 'art', '##hr', '##opa', '##thy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inflammatory', 'bow', '##el', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'unwilling', '##ness', 'to', 'participate', 'in', 'the', 'study', 'with', 'additional', 'imaging', 'protocols', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02634541_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'axial', 'sp', '##ond', '##yl', '##oa', '##rth', '##rit', '##is', '(', 'asa', '##s', 'criteria', ')', 'and', 'radio', '##logic', 'sac', '##roi', '##li', '##itis', 'as', 'detected', 'either', 'by', 'mri', 'or', 'x', '-', 'ray', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 26819, 11867, 15422, 8516, 10441, 15265, 14778, 2483, 1006, 17306, 2015, 9181, 1007, 1998, 2557, 27179, 17266, 26692, 3669, 13706, 2004, 11156, 2593, 2011, 27011, 2030, 1060, 1011, 4097, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 2, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 3, 3, 2, 3, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 5, 6, 7, 8, 8, 9, 9, 9, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02634541_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'decrease', 'in', 'size', 'of', 'the', 'designated', 'target', 'ul', '##cer', '(', 's', ')', 'by', '≥', '30', '%', 'during', 'the', '7', '-', 'day', 'screening', 'period', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1015, 1012, 9885, 1999, 2946, 1997, 1996, 4351, 4539, 17359, 17119, 1006, 1055, 1007, 2011, 1609, 2382, 1003, 2076, 1996, 1021, 1011, 2154, 11326, 2558, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10, 10, 10, 11, 12, 13, 14, 15, 16, 17, 18, 18, 18, 19, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'can', 'not', 'tolerate', 'or', 'comply', 'with', 'compression', 'therapy', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1016, 1012, 2064, 2025, 19242, 2030, 14037, 2007, 13379, 7242, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'an', 'ul', '##cer', 'which', 'shows', 'signs', 'of', 'severe', 'clinical', 'infection', ',', 'defined', 'as', 'pu', '##s', 'o', '##oz', '##ing', 'from', 'the', 'ul', '##cer', 'site', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1017, 1012, 2019, 17359, 17119, 2029, 3065, 5751, 1997, 5729, 6612, 8985, 1010, 4225, 2004, 16405, 2015, 1051, 18153, 2075, 2013, 1996, 17359, 17119, 2609, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 2, 2, 3, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 16, 16, 17, 18, 19, 19, 20, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 4 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:41 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02652572_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'age', '18', 'years', 'or', 'older', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'diagnosis', 'of', 've', '##nous', 'leg', 'ul', '##cer', '(', 's', ')', ',', 'as', 'clinical', '##ly', 'determined', 'by', 'the', 'investigator', 'by', 'a', 'positive', 've', '##nous', 'ref', '##lux', 'test', '(', 've', '##nous', 'ref', '##ill', '##ing', '<', '20', 'seconds', ')', 'using', 'do', '##pp', '##ler', 'ultrasound', 'for', 'at', 'least', '4', 'weeks', 'prior', 'to', 'screening', 'day', ',', 'which', 'have', 'not', 'adequately', 'responded', 'to', 'conventional', 'ul', '##cer', 'therapy', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'designated', 've', '##nous', 'leg', 'ul', '##cer', 'meets', 'the', 'following', 'criteria', 'at', 'both', 'the', 'screening', 'and', 'baseline', 'visits', '.', 'if', 'the', 'patient', 'has', 'multiple', 'ul', '##cer', '##s', ',', 'at', 'least', 'one', 'ul', '##cer', 'must', 'meet', 'the', 'following', 'criteria', 'at', 'both', 'the', 'screening', 'and', 'baseline', 'visits', ':', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1017, 1012, 4351, 2310, 18674, 4190, 17359, 17119, 6010, 1996, 2206, 9181, 2012, 2119, 1996, 11326, 1998, 26163, 7879, 1012, 2065, 1996, 5776, 2038, 3674, 17359, 17119, 2015, 1010, 2012, 2560, 2028, 17359, 17119, 2442, 3113, 1996, 2206, 9181, 2012, 2119, 1996, 11326, 1998, 26163, 7879, 1024, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:41 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02652572_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'un', '##con', '##tro', '##lled', 'medical', 'problems', 'including', 'pulmonary', ',', 'cardiovascular', 'or', 'or', '##th', '##oped', '##ic', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'any', 'de', '##bil', '##itating', 'disease', 'prior', 'to', 'the', 'sci', 'that', 'caused', 'exercise', 'into', '##ler', '##ance', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'prem', '##or', '##bid', ',', 'ongoing', 'major', 'depression', 'or', 'psycho', '##sis', ',', 'altered', 'cognitive', 'status', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02701777_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'male', 'and', 'females', 'between', 'ages', '18', '-', '85', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'right', 'handed', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02701777_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'evidence', 'of', 'deco', '##mp', '##ens', '##ated', 'liver', 'disease', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02734173_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hc', '##v', 'rna', 'evidence', 'of', 'hc', '##v', 'infection', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'documented', 'history', 'of', 'chronic', 'hc', '##v', 'rna', 'infection', 'with', 'gen', '##otype', '1', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'able', 'to', 'provide', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02734173_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'liver', 'ci', '##rr', '##hosis', ',', 'he', '##pa', '##to', '##cellular', 'car', '##cino', '##ma', 'or', 'other', 'mali', '##gnan', '##cies', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'other', 'factors', 'causing', 'liver', 'diseases', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'and', 'lac', '##tat', '##ing', 'women', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02745704_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hepatitis', 'b', 'e', 'antigen', '(', 'h', '##be', '##ag', ')', '-', 'negative', 'and', 'anti', '-', 'h', '##be', '##ag', 'positive', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hepatitis', 'b', 'surface', 'antigen', '(', 'h', '##bs', '##ag', ')', 'positive', 'and', '<', '1500', 'i', '##u', '/', 'ml', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:42 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02745704_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'refusal', 'of', 'village', 'chief', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:42 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02754583_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'community', 'in', 'a', 'school', 'district', 'that', 'is', 'within', 'the', 'study', 'area', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'area', 'within', 'each', 'school', 'district', 'that', 'is', 'in', 'need', 'of', 'a', 'well', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02754583_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'current', 'w', '##hee', '##ze', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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},
{
"name": "stdout",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'severe', 'mal', '##nut', '##rit', '##ion', '(', 'weight', '-', 'for', '-', 'height', 'z', '-', 'score', '<', '-', '3', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02783859_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02783859_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'and', '/', 'or', 'nursing', 'mothers', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', '##ergy', 'to', 'bu', '##pi', '##vac', '##aine', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'drug', '/', 'alcohol', 'abuse', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02805504_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'undergoing', 'ur', '##olo', '##gic', 'surgery', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02805504_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'the', 'use', 'of', 'weight', '-', 'lowering', 'drugs', ',', 'any', 'investigation', '##al', 'blood', '-', 'glucose', 'or', 'lip', '##id', '-', 'lowering', 'agent', '(', 'other', 'than', 'stat', '##ins', 'or', 'e', '##ze', '##ti', '##mi', '##be', ')', 'within', 'the', 'past', '3', 'months', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 20, 21, 22, 22, 23, 24, 24, 24, 24, 24, 25, 26, 27, 28, 29, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'previous', 'treatment', 'with', 'systemic', 'co', '##rti', '##cos', '##ter', '##oids', 'or', 'a', 'change', 'in', 'dos', '##age', 'of', 'thyroid', 'hormones', 'in', 'the', 'previous', '6', 'weeks', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'the', 'use', 'of', 'insulin', 'within', 'the', '3', 'months', 'prior', 'to', 'screening', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1996, 2224, 1997, 22597, 2306, 1996, 1017, 2706, 3188, 2000, 11326, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02823808_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'type', '2', 'diabetes', 'mel', '##lit', '##us', 'patients', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2828, 1016, 14671, 11463, 15909, 2271, 5022, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'who', 'had', 'been', 'diagnosed', 'within', 'the', 'previous', '12', 'months', 'with', 'h', '##ba', '##1', '##c', 'levels', 'of', '8', '.', '0', '-', '12', '.', '0', '%', ',', 'did', 'not', 'have', 'a', 'medical', 'history', 'related', 'to', 'diabetes', ',', 'and', 'did', 'not', 'display', 'pro', '##life', '##rative', 're', '##tino', '##pathy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02823808_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'dual', 'organ', 'transplant', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02883400_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'liver', 'transplant', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02883400_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'human', 'im', '##mun', '##ode', '##fi', '##ciency', 'virus', '(', 'hiv', ')', '-', 'infected', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'baseline', 'ser', '##ology', 'showed', 'a', 'non', '##rea', '##ctive', 'r', '##pr', 'test', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'follow', '-', 'up', 'is', 'inadequate', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02884115_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'early', 'sy', '##phi', '##lis', 'cases', 'determined', 'to', 'be', 'ser', '##of', '##ast', 'at', '6', 'months', 'after', 'initial', 'treatment', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02884115_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', 'less', 'than', 'one', 'year', 'or', 'age', 'greater', 'than', '/', 'equals', 'to', '18', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'previous', 'treatment', 'with', 'cy', '##to', '##to', '##xi', '##c', 'agents', 'or', 'high', '-', 'dose', 'ste', '##roids', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mixed', 'ph', '##eno', '##type', 'acute', 'leukemia', '(', 'mp', '##al', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:43 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02894645_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'confirmed', 'diagnosis', 'of', 'non', '-', 'bu', '##rk', '##itt', 'b', '-', 'lineage', 'all', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', 'to', '17', 'years', 'of', 'age', '(', 'before', '18th', 'birthday', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:43 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02894645_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'or', 'breast', '##fe', '##eding', 'woman', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subject', 'una', '##ffi', '##lia', '##ted', 'insurance', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02901106_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', '18', 'years', 'old', 'and', 'more', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'with', 'multiple', 'sc', '##ler', '##osis', 'according', 'to', 'the', 'criteria', 'of', 'mac', 'donald', '2010', ':', 're', '##la', '##ps', '##ing', '-', 're', '##mit', '##ting', '(', 'rr', ')', ',', 'secondary', '-', 'progressive', '(', 'sp', ')', 'or', 'primary', '-', 'progressive', '(', 'pp', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 3, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 13, 13, 13, 14, 15, 15, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'which', 'treatment', 'with', 'dime', '##thy', '##l', '-', 'fu', '##mara', '##te', 'has', 'been', 'prescribed', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2005, 2029, 3949, 2007, 27211, 16921, 2140, 1011, 11865, 28225, 2618, 2038, 2042, 16250, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02901106_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'spinal', 'cord', 'ste', '##nosis', 'or', 'clinical', 'symptoms', 'of', 'lu', '##mba', '##r', 'ra', '##dic', '##ulo', '##pathy', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'or', 'onset', 'neurological', 'diseases', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'generalized', 'pain', 'or', 'fi', '##bro', '##my', '##al', '##gia', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02904785_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'clinical', 'and', 'radio', '##logic', 'diagnosis', 'of', 'primary', 'knee', 'os', '##te', '##oa', '##rth', '##rit', '##is', '(', 'ke', '##ll', '##gren', '&', 'lawrence', 'i', ',', 'ii', 'or', 'iii', ')', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'capability', 'to', 'understand', 'the', 'informed', 'consent', 'form', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'chronic', 'pain', 'for', 'at', 'least', '3', 'months', 'prior', 'to', 'inclusion', ',', 'measured', 'by', 'va', '##s', '.', '(', 'va', '##s', '4', 'or', 'above', ')', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02904785_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'currently', 'pregnant', 'or', 'using', 'a', 'reliable', 'contra', '##ception', '(', 'e', '.', 'g', '.', 'in', '##ject', '##able', '##s', ',', 'intra', '##uter', '##ine', 'devices', ',', 'implant', ',', 'oral', 'contra', '##ceptive', 'pills', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'des', '##iring', 'pregnancy', 'in', 'the', 'next', 'year', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'tuba', '##l', 'liga', '##tion', 'or', 'h', '##yst', '##ere', '##ct', '##omy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02905890_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'b', '##v', 'positive', 'by', 'nu', '##gent', 'score', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'hiv', 'negative', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'capable', 'of', 'providing', 'written', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02905890_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ile', '##us', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'or', 'suspected', 'bow', '##el', 'obstruction', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'active', 'bow', '##el', 'inflammation', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02908919_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'subjects', 'referred', 'to', 'diagnostic', 'or', 'therapeutic', 'colon', '##os', '##co', '##py', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02908919_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'na', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02953873_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'at', 'least', '18', 'years', 'of', 'age', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'signed', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'african', 'american', 'race', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3060, 2137, 2679, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:44 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02953873_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'into', '##ler', '##ance', 'to', 'l', '##m', '##w', '##hs', 'during', 'hd', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'receiving', 'war', '##far', '##in', 'or', 'other', 'oral', 'anti', '##co', '##ag', '##ula', '##nt', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnant', 'patients', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:44 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02957877_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '>', '=', '18', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02957877_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'breast', 'car', '##cino', '##ma', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02959580_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'id', '##io', '##pathic', 'gran', '##ulo', '##mat', '##ous', 'mast', '##itis', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02959580_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'having', 'experienced', 'severe', 'all', '##er', '##gies', ',', 'trauma', 'history', 'and', '/', 'or', 'operation', 'history', 'within', '3', 'months', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'with', 'a', 'history', 'of', 'mental', 'illness', 'and', '/', 'or', 'family', 'history', 'of', 'mental', 'illness', 'limb', 'disabled', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'taking', 'medicine', 'within', 'one', 'month', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02990403_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'woman', 'who', 'had', '2', 'mis', '##carriage', 'before', '12', '(', 'th', ')', 'week', 'of', 'ge', '##station', '.', 'the', 'patient', 'who', 'is', 'diagnosed', 'as', 'th', '##rom', '##bo', '##phi', '##lia', 'with', 'rec', '##urrent', 'pregnancy', 'loss', '.', 'signed', 'consent', 'form', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02990403_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '<', '45', 'or', '>', '80', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', '##er', '##gies', 'to', 'medications', 'used', 'in', 'the', 'study', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'renal', 'diseases', ',', 'a', 'coa', '##gul', '##ation', 'abnormal', '##ity', ',', 'a', 'he', '##pati', '##c', 'disease', ',', 'or', 'drug', 'abuse', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2381, 1997, 25125, 7870, 1010, 1037, 28155, 24848, 3370, 19470, 3012, 1010, 1037, 2002, 24952, 2278, 4295, 1010, 2030, 4319, 6905, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02992028_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'rot', '##ator', 'cuff', 'tear', 'patients', 'undergoing', 'art', '##hr', '##os', '##copic', 'rot', '##ator', 'cuff', 'tear', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT02992028_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'prior', 'treatment', 'with', 'en', '##zal', '##uta', '##mide', 'or', 'ab', '##ira', '##ter', '##one', 'ace', '##tate', 'for', '>', '14', 'days', 'prior', 'to', 'enrollment', 'and', 'completion', 'of', 'baseline', 'tests', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'receipt', 'of', 'chemotherapy', 'for', 'prostate', 'or', 'other', 'cancer', 'within', 'the', 'past', '12', 'months', 'with', 'residual', 'cognitive', 'deficit', '##s', ',', 'or', 'receipt', 'of', 'chemotherapy', 'for', 'mc', '##rp', '##c', '.', 'patients', '/', 'physicians', 'planning', 'treatment', 'with', 'chemotherapy', 'during', 'the', '12', 'month', 'period', 'of', 'the', 'investigation', 'are', 'also', 'ineligible', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 24306, 1997, 27144, 2005, 25086, 2030, 2060, 4456, 2306, 1996, 2627, 2260, 2706, 2007, 21961, 10699, 15074, 2015, 1010, 2030, 24306, 1997, 27144, 2005, 11338, 14536, 2278, 1012, 5022, 1013, 11572, 4041, 3949, 2007, 27144, 2076, 1996, 2260, 3204, 2558, 1997, 1996, 4812, 2024, 2036, 22023, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 17, 18, 19, 20, 21, 22, 23, 24, 24, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'history', 'of', 'cognitive', 'impairment', 'or', 'dysfunction', ',', 'including', 'a', 'history', 'of', 'dementia', ',', 'alzheimer', \"'\", 's', 'disease', ',', 'stroke', 'with', 'residual', 'cognitive', 'deficit', '##s', ',', 'cognitive', 'dysfunction', 'related', 'to', 'alcohol', 'or', 'substance', 'abuse', ',', 'or', 'cognitive', 'dysfunction', 'related', 'to', 'prior', 'treatment', 'for', 'any', 'cancer', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2381, 1997, 10699, 25172, 2030, 28466, 1010, 2164, 1037, 2381, 1997, 28767, 1010, 21901, 1005, 1055, 4295, 1010, 6909, 2007, 21961, 10699, 15074, 2015, 1010, 10699, 28466, 3141, 2000, 6544, 2030, 9415, 6905, 1010, 2030, 10699, 28466, 3141, 2000, 3188, 3949, 2005, 2151, 4456, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 15, 16, 17, 18, 19, 20, 21, 22, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03016741_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'have', 'diagnosis', 'of', 'prostate', 'cancer', 'and', 'have', 'received', 'treatment', 'with', 'g', '##nr', '##h', 'ago', '##nist', 'or', 'antagonist', 'therapy', 'for', 'at', 'least', '1', 'month', 'prior', 'to', 'enrollment', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'willing', 'and', 'able', 'to', 'complete', 'survey', 'question', '##naire', '##s', 'in', 'english', 'without', 'assistance', 'through', 'the', 'duration', 'of', 'the', 'study', '.', 'this', 'st', '##ip', '##ulation', 'is', 'in', 'place', 'because', 'not', 'all', 'of', 'the', 'proposed', 'quality', 'of', 'life', 'or', 'cognitive', 'tests', 'are', 'available', 'or', 'valid', '##ated', 'in', 'other', 'languages', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '=', '18', 'years', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:45 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03016741_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:45 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03043495_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'undergoing', 'surge', '##ries', 'in', 'the', 'upper', 'limb', '(', 'arm', ',', 'forearm', 'or', 'hand', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03043495_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'unable', 'to', 'am', '##bula', '##te', 'at', 'least', '150', 'feet', 'prior', 'to', 'stroke', ',', 'or', 'experienced', 'intermittent', 'cl', '##aud', '##ication', 'while', 'walking', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', '.', 'history', 'of', 'cong', '##est', '##ive', 'heart', 'failure', ',', 'unstable', 'cardiac', 'ar', '##rh', '##yt', '##hmi', '##as', ',', 'hyper', '##tro', '##phic', 'card', '##iom', '##yo', '##pathy', ',', 'severe', 'ao', '##rti', '##c', 'ste', '##nosis', ',', 'ang', '##ina', 'or', 'd', '##ys', '##p', '##nea', 'at', 'rest', 'or', 'during', 'ad', '##l', \"'\", 's', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'history', 'of', 'oxygen', 'dependence', ';', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1017, 1012, 2381, 1997, 7722, 18642, 1025, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03056287_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', ')', 'age', '50', '-', '70', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '2', ')', 'stroke', 'within', 'the', 'past', '6', 'to', '60', 'months', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', ')', 'major', 'de', '##pressive', 'disorder', '(', 'ph', '##q', '-', '9', '>', '10', ')', 'and', 'diagnosed', 'using', 'the', 'structured', 'clinical', 'interview', 'for', 'depression', '(', 'sci', '##d', ')', 'according', 'to', 'the', 'diagnostic', 'and', 'statistical', 'manual', 'of', 'mental', 'disorders', ',', 'fourth', 'edition', '(', 'ds', '##m', '-', 'iv', ')', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 1017, 1007, 2350, 2139, 27484, 8761, 1006, 6887, 4160, 1011, 1023, 1028, 2184, 1007, 1998, 11441, 2478, 1996, 14336, 6612, 4357, 2005, 6245, 1006, 16596, 2094, 1007, 2429, 2000, 1996, 16474, 1998, 7778, 6410, 1997, 5177, 10840, 1010, 2959, 3179, 1006, 16233, 2213, 1011, 4921, 1007, 1010, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03056287_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'patient', 'or', 'relatives', 'unable', 'or', 'unwilling', 'to', 'give', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03056391_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '1', '.', 'patient', 'age', '≥', '12', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '3', '.', 'temperature', '>', '38', '##c', 'on', 'admission', 'or', 'fever', 'during', 'the', 'preceding', '48', 'hours', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03056391_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'na', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:46 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03077204_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '>', '18', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'the', 'capacity', 'to', 'provide', 'informed', 'consent', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ***** Running evaluation on 4 number of test data *****\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:46 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03077204_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mo', '##lar', 'teeth', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'mill', '##ler', 'class', '4', 'recession', 'defects', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', '(', 'self', '-', 'reported', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03124329_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'male', 'and', 'female', 'individuals', 'between', 'ages', 'of', '18', 'to', '70', 'years', 'old', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'multiple', 'contiguous', 'gin', '##gi', '##val', 'recession', 'defects', 'on', 'a', 'minimum', 'of', 'two', 'adjacent', 'teeth', ',', 'exhibiting', '3', 'mm', 'or', 'more', 'recession', 'on', 'at', 'least', 'one', 'of', 'those', 'teeth', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 3674, 25177, 18353, 5856, 10175, 19396, 18419, 2006, 1037, 6263, 1997, 2048, 5516, 4091, 1010, 22922, 1017, 3461, 2030, 2062, 19396, 2006, 2012, 2560, 2028, 1997, 2216, 4091, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 3, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'no', 'prior', 'surgical', 'treatment', 'in', 'the', 'sites', 'planned', 'for', 'therapy', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2053, 3188, 11707, 3949, 1999, 1996, 4573, 3740, 2005, 7242, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03124329_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '<', '18', 'years', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 2287, 1026, 2324, 2086, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'previous', 'history', 'of', 'ro', '##ux', '-', 'en', '-', 'y', 'gas', '##tric', 'bypass', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'undergoing', 'other', 'bari', '##at', '##ric', 'procedures', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03187379_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'bari', '##at', '##ric', 'surgery', 'patients', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'lap', '##aro', '##scopic', 'ro', '##ux', '-', 'en', '-', 'y', 'gas', '##tric', 'bypass', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'use', 'of', 'ee', '##a', 'staple', '##r', 'ana', '##sto', '##mos', '##is', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03187379_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'lifetime', 'personal', 'history', 'of', 'diagnosis', 'of', 'major', 'de', '##pressive', 'disorder', 'according', 'to', 'the', 'ds', '##m', '-', 'v', '(', 'american', 'psychiatric', 'association', ',', '2013', ')', 'using', 'the', 'structured', 'clinical', 'interview', 'for', 'ds', '##m', '-', 'v', 'axis', 'i', 'disorders', ',', 'research', 'version', ',', 'non', '-', 'patient', 'edition', '(', 'sci', '##d', '-', '5', '-', 'rv', 'for', 'ds', '##m', '-', 'v', ';', 'first', 'et', 'al', '.', ',', '2015', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'a', 'history', 'of', 'suicidal', 'idea', '##tion', 'and', 'behaviour', ',', 'including', 'self', '-', 'harm', 'and', '/', 'or', 'harm', 'to', 'others', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'a', 'history', 'of', 'substance', 'abuse', 'and', '/', 'or', 'dependence', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 4 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03249311_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'male', 'participants', 'between', '18', 'and', '40', 'years', '-', 'old', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'written', 'informed', 'consent', 'signed', 'by', 'the', 'participant', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03249311_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'known', 'hyper', '##sen', '##sit', '##ivity', 'to', 'stat', '##in', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'treatment', 'with', 'stat', '##ins', 'during', 'the', 'past', 'month', 'prior', 'to', 'study', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'serum', 'cr', '##ea', '##tin', '##ine', '>', '3', 'mg', '/', 'dl', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:47 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03255044_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosed', 'with', 'stable', 'chronic', 'heart', 'failure', 'ny', '##ha', 'class', 'ii', '-', 'iii', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'e', '##ject', '##ion', 'fraction', '<', '40', '%', 'as', 'assessed', 'by', '2d', 'echo', '##card', '##iography', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:47 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03255044_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'with', 'history', 'of', 'all', '##ergy', 'in', 'any', 'kind', 'an', '##est', '##hetic', 'drug', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'who', 'pregnant', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'who', 'sign', 'for', 'single', 'port', 'g', '##yne', '##col', '##og', '##ic', 'lap', '##aro', '##scopic', 'surgery', 'or', 'note', 'surgery', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03259243_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'who', 'undergoing', 'g', '##yne', '##col', '##og', '##ic', 'lap', '##aro', '##scopic', 'surgery', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'who', 'agrees', 'to', 'participate', 'in', 'this', 'study', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patient', 'able', 'to', 'speak', 'and', 'understand', 'thai', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03259243_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'american', 'association', 'of', 'an', '##est', '##hes', '##iology', 'class', '1', '-', '3', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'american', 'heart', 'association', 'class', '>', '3', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'b', '##mi', '>', '37', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03336801_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'scheduled', 'back', 'surgery', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03336801_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inability', 'to', 'understand', 'and', 'comply', 'with', 'the', 'instructions', 'of', 'the', 'study', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03337503_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'written', 'informed', 'consent', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'adult', 'patients', '(', 'older', 'than', '18', 'years', 'of', 'age', ')', ',', 'male', 'and', 'female', ',', 'with', 'chronic', 'non', '-', 'cancer', 'and', 'cancer', 'pain', '(', 'at', 'least', '3', 'months', 'in', 'duration', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 4639, 5022, 1006, 3080, 2084, 2324, 2086, 1997, 2287, 1007, 1010, 3287, 1998, 2931, 1010, 2007, 11888, 2512, 1011, 4456, 1998, 4456, 3255, 1006, 2012, 2560, 1017, 2706, 1999, 9367, 1007, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'experiencing', 'an', 'average', 'weekly', 'pain', 'intensity', 'score', 'greater', 'than', '4', 'on', 'a', '11', 'points', 'nr', '##s', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 5022, 13417, 2019, 2779, 4882, 3255, 8015, 3556, 3618, 2084, 1018, 2006, 1037, 2340, 2685, 17212, 2015, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03337503_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'that', 'do', 'not', 'have', 'a', 'valid', 'ontario', 'health', 'insurance', 'plan', '(', 'oh', '##ip', ')', 'number', 'at', 'time', 'of', 'first', 'trans', '##fusion', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'that', 'require', 'emerge', '##nt', 'release', 'of', 'a', 'rb', '##c', 'trans', '##fusion', 'and', 'in', 'whom', 'emergency', 'random', '##ization', 'could', 'not', 'be', 'completed', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 'complex', 'antibody', 'profile', 'in', 'which', 'it', 'is', 'impossible', 'to', 'match', 'rb', '##c', 'units', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03344887_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'patients', '(', 'excluding', 'neon', '##ates', ')', 'requiring', 'one', 'or', 'more', 'all', '##ogen', '##ei', '##c', 'rb', '##c', 'trans', '##fusion', '##s', 'for', 'the', 'treatment', 'of', 'an', '##emia', 'will', 'be', 'included', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03344887_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'co', '-', 'infected', 'with', 'hc', '##v', ',', 'hiv', 'or', 'other', 'viral', 'hepatitis', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'hc', '##c', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:48 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03356834_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'chronic', 'hepatitis', 'b', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'anti', '##vira', '##l', 'experienced', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'currently', 'on', 'long', 'term', 'td', '##f', 'anti', '-', 'h', '##b', '##v', 'treatment', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:48 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03356834_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'women', 'pregnant', 'or', 'lac', '##tat', '##ing', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'persons', 'with', 'terminal', 'illness', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03431831_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'over', '##weight', '/', 'obe', '##se', 'adult', 'patients', '(', 'age', '19', 'years', '-', '65', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'eligible', 'based', 'on', 'wal', '##i', 'screening', 'tool', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03431831_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', '##ergy', 'to', 'do', '##xy', '##cy', '##cl', '##ine', 'or', 'methyl', '##pre', '##d', '##nis', '##olo', '##ne', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'pregnancy', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03479502_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', '18', 'years', 'of', 'age', 'and', 'older', ',', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'stage', 'ii', 'ad', '##hesive', 'caps', '##uli', '##tis', 'as', 'determined', 'by', 'clinical', 'examination', 'of', 'the', 'treating', 'physician', ',', 'and', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'absence', 'of', 'abnormal', 'findings', 'on', 'x', '-', 'ray', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03479502_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'form', 'of', 'diagnosed', 'ps', '##oria', '##sis', 'other', 'than', 'chronic', 'plaque', 'ps', '##oria', '##sis', '(', 'i', '.', 'e', '.', 'gut', '##tate', ',', 'er', '##yt', '##hr', '##oder', '##mic', ',', 'pu', '##st', '##ular', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 4, 4, 5, 6, 7, 8, 9, 9, 9, 10, 11, 11, 11, 11, 12, 12, 13, 14, 14, 14, 14, 14, 15, 16, 16, 16, 17, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'other', 'active', ',', 'ongoing', 'skin', 'diseases', 'or', 'skin', 'infections', 'that', 'may', 'interfere', 'with', 'examination', 'of', 'ps', '##oria', '##sis', 'lesions', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 11616, 1997, 2060, 3161, 1010, 7552, 3096, 7870, 2030, 3096, 15245, 2008, 2089, 15115, 2007, 7749, 1997, 8827, 11069, 6190, 22520, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ongoing', 'use', 'of', 'other', 'ps', '##oria', '##sis', 'treatment', 'including', 'but', 'not', 'limited', 'to', 'topical', 'or', 'systemic', 'co', '##rti', '##cos', '##ter', '##oids', ',', 'other', 'topical', 'medications', '(', 'i', '.', 'e', '.', 'coal', 'tar', ')', ',', 'oral', 'or', 'bio', '##logic', 'medications', 'for', 'the', 'treatment', 'of', 'ps', '##oria', '##sis', ',', 'and', 'uv', 'therapy', '.', 'the', 'following', 'wash', '##out', 'periods', 'will', 'be', 'required', ':', '2', 'weeks', 'for', 'topical', 'therapy', ';', '2', 'weeks', 'for', 'photo', '##therapy', ';', '12', 'weeks', 'for', 'bio', '##logic', 'or', 'targeted', 'the', '##ra', '##pies', ';', '4', 'weeks', 'for', 'other', 'systemic', 'the', '##ra', '##pies', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 7552, 2224, 1997, 2060, 8827, 11069, 6190, 3949, 2164, 2021, 2025, 3132, 2000, 25665, 2030, 22575, 2522, 28228, 13186, 3334, 17086, 1010, 2060, 25665, 20992, 1006, 1045, 1012, 1041, 1012, 5317, 16985, 1007, 1010, 8700, 2030, 16012, 27179, 20992, 2005, 1996, 3949, 1997, 8827, 11069, 6190, 1010, 1998, 23068, 7242, 1012, 1996, 2206, 9378, 5833, 6993, 2097, 2022, 3223, 1024, 1016, 3134, 2005, 25665, 7242, 1025, 1016, 3134, 2005, 6302, 20900, 1025, 2260, 3134, 2005, 16012, 27179, 2030, 9416, 1996, 2527, 13046, 1025, 1018, 3134, 2005, 2060, 22575, 1996, 2527, 13046, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"label: [1, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 3, 3, 3, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03506477_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'provide', 'written', ',', 'signed', 'and', 'dated', 'informed', 'consent', 'prior', 'to', 'initiating', 'any', 'study', '-', 'related', 'activities', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'male', 'or', 'female', '>', '18', 'years', 'of', 'age', 'at', 'the', 'time', 'of', 'screening', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'fitzpatrick', 'skin', 'photo', '##type', 'iv', '-', 'vi', ',', 'non', '-', 'white', 'race', '/', 'ethnicity', ',', 'including', 'but', 'not', 'limited', 'to', '-', '-', '-', 'african', 'americans', ',', 'asian', '##s', ',', 'pacific', 'islanders', 'and', 'hispanic', '##s', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
"input ids: [101, 26249, 3096, 6302, 13874, 4921, 1011, 6819, 1010, 2512, 1011, 2317, 2679, 1013, 18240, 1010, 2164, 2021, 2025, 3132, 2000, 1011, 1011, 1011, 3060, 4841, 1010, 4004, 2015, 1010, 3534, 16422, 1998, 6696, 2015, 1012, 102, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
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"guards: [0, 1, 2, 3, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 21, 21, 22, 23, 24, 24, 25, 26, 27, 28, 29, 29, 30, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03506477_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'in', '##patient', 'status', ',', 'air', '##way', 'abnormalities', ',', 'all', '##ergy', 'to', 'any', 'study', 'medications', ',', 'eggs', 'and', 'soy', ',', 'and', 'mitochondrial', 'disorders', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'subjects', 'with', 'any', 'cardiac', 'disease', 'or', 'history', 'of', 'cardiac', 'ar', '##rh', '##yt', '##hmi', '##as', 'will', 'be', 'excluded', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"guards: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 11, 11, 11, 11, 12, 13, 14, 15, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]\r\n",
"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03513757_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'all', 'children', 'scheduled', 'for', 'out', '##patient', 'mri', 'scans', 'with', 'expected', 'duration', 'of', 'scan', 'between', '30', 'minutes', 'and', '75', 'minutes', '.', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:49 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03513757_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosis', 'of', 'primary', 'progressive', 'ms', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'inability', 'to', 'complete', 'an', 'mri', '(', 'contra', '##ind', '##ication', '##s', 'for', 'mri', 'include', 'but', 'are', 'not', 'restricted', 'to', 'weight', '=', '140', 'kg', ',', 'pace', '##maker', ',', 'co', '##ch', '##lea', '##r', 'implant', '##s', ',', 'presence', 'of', 'foreign', 'substances', 'in', 'the', 'eye', ',', 'intra', '##cr', '##anial', 'vascular', 'clips', ',', 'surgery', 'within', '6', 'weeks', 'of', 'entry', 'into', 'the', 'study', ',', 'corona', '##ry', 'ste', '##nt', 'implant', '##ed', 'within', '8', 'weeks', 'prior', 'to', 'the', 'time', 'of', 'the', 'intended', 'mri', ',', 'etc', '…', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'ga', '##do', '##lini', '##um', 'into', '##ler', '##ance', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ***** Running evaluation on 2 number of test data *****\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:49 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03589105_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'age', '>', '/', '=', '18', 'years', 'at', 'screening', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'with', 're', '##la', '##ps', '##ing', 'forms', 'of', 'multiple', 'sc', '##ler', '##osis', '(', 'rms', ')', 'with', 'active', 'disease', 'defined', 'by', 'clinical', 'or', 'imaging', 'features', ':', '(', 'i', ')', 'at', 'least', 'one', 'clinical', 're', '##la', '##pse', 'over', 'a', '6', '-', 'month', 'period', 'prior', 'to', 'screening', ';', '(', 'ii', ')', 'and', '/', 'or', 'at', 'least', 'one', 't', '##1', 'ga', '##do', '##lini', '##um', '-', 'enhancing', 'les', '##ion', 'or', 'new', 'and', '/', 'or', 'en', '##lar', '##ging', 't', '##2', 'les', '##ion', 'as', 'detected', 'by', 'brain', 'magnetic', 'resonance', 'imaging', '(', 'mri', ')', 'performed', 'over', 'a', '3', 'months', 'period', 'prior', 'to', 'screening', 'with', 'no', 'change', 'of', 'disease', '-', 'modifying', 'treatment', '(', 's', ')', '(', 'd', '##mt', ')', 'compared', 'to', 'a', 'previous', 'mri', 'performed', 'within', '24', 'months', 'before', 'screening', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'for', 'women', 'of', 'child', '##be', '##aring', 'potential', ':', 'agreement', 'to', 'use', 'an', 'acceptable', 'birth', 'control', 'method', 'during', 'the', 'treatment', 'period', 'and', 'for', 'at', 'least', '12', 'months', 'after', 'the', 'last', 'dose', 'of', 'o', '##cre', '##li', '##zu', '##ma', '##b', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03589105_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'na', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03620526_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'presence', 'of', 'typical', 'h', '##f', 'symptoms', 'and', 'signs', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'l', '##v', 'e', '##ject', '##ion', 'fraction', '=', '50', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'elevated', 'levels', 'of', 'nt', '-', 'pro', '##bn', '##p', '(', 'at', 'least', '>', '125', 'pg', '/', 'ml', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03620526_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'legally', 'inc', '##omp', '##ete', '##nt', 'or', 'mentally', 'impaired', '(', 'e', '.', 'g', '.', ',', 'minors', ',', 'alzheimer', \"'\", 's', 'subjects', ',', 'dementia', ',', 'etc', '.', ')', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'younger', 'than', '18', 'years', 'of', 'age', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03631355_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'patients', 'undergoing', 'ti', '##bial', 'tube', '##rcle', 'os', '##te', '##oto', '##my', '(', 'tt', '##o', ')', 'with', 'or', 'without', 'medial', 'patel', '##lo', '-', 'fe', '##moral', 'ligament', '(', 'mp', '##fl', ')', 'reconstruction', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03631355_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diagnosed', 'advanced', 'heart', ',', 'kidney', 'or', 'liver', 'failure', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03639545_exc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - \r\n",
"************** Example ************\r\n",
"input tokens: ['[CLS]', 'diabetes', 'mel', '##lit', '##us', 'type', '1', '[SEP]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]', '[PAD]']\r\n",
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"***********************************\r\n",
" \r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ***** Running evaluation on 1 number of test data *****\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - Instantaneous batch size per GPU = 8\r\n",
"2021-01-19 19:23:50 - Transformer_NER - INFO - ******************************\r\n",
"2021-01-19 19:23:50 - Transformer_NER - WARNING - The output file is ./chia_bert_results/NCT03639545_inc.bio.txt, we recommend to use suffix as .bio.txt or .txt. \r\n",
" You can directly use formatter coverter tool in this package.\r\n"
]
}
],
"source": [
"cat ./chia_bert_prediction_log.txt"
]
}
],
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