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b/docproduct/models.py |
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from __future__ import absolute_import, division, print_function, unicode_literals |
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import os |
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import pandas as pd |
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from sklearn.model_selection import train_test_split |
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import numpy as np |
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import tensorflow as tf |
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import tensorflow.keras.backend as K |
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from tensorflow import keras |
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from docproduct.bert import build_model_from_config |
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from keras_bert.loader import load_model_weights_from_checkpoint |
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class FFN(tf.keras.layers.Layer): |
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def __init__( |
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self, |
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hidden_size=768, |
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dropout=0.2, |
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residual=True, |
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name='FFN', |
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**kwargs): |
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"""Simple Dense wrapped with various layers |
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""" |
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super(FFN, self).__init__(name=name, **kwargs) |
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self.hidden_size = hidden_size |
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self.dropout = dropout |
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self.residual = residual |
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self.ffn_layer = tf.keras.layers.Dense( |
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units=hidden_size, |
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use_bias=True |
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) |
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def call(self, inputs): |
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ffn_embedding = self.ffn_layer(inputs) |
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ffn_embedding = tf.keras.layers.ReLU()(ffn_embedding) |
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if self.dropout > 0: |
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ffn_embedding = tf.keras.layers.Dropout( |
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self.dropout)(ffn_embedding) |
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if self.residual: |
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ffn_embedding += inputs |
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return ffn_embedding |
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class MedicalQAModel(tf.keras.Model): |
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def __init__(self, name=''): |
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super(MedicalQAModel, self).__init__(name=name) |
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self.q_ffn = FFN(name='q_ffn', input_shape=(768,)) |
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self.a_ffn = FFN(name='a_ffn', input_shape=(768,)) |
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def call(self, inputs): |
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q_bert_embedding, a_bert_embedding = tf.unstack(inputs, axis=1) |
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q_embedding, a_embedding = self.q_ffn( |
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q_bert_embedding), self.a_ffn(a_bert_embedding) |
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return tf.stack([q_embedding, a_embedding], axis=1) |
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class MedicalQAModelwithBert(tf.keras.Model): |
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def __init__( |
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self, |
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hidden_size=768, |
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dropout=0.2, |
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residual=True, |
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config_file=None, |
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checkpoint_file=None, |
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bert_trainable=True, |
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layer_ind=-1, |
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name=''): |
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super(MedicalQAModelwithBert, self).__init__(name=name) |
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build = checkpoint_file != None |
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self.biobert, config = build_model_from_config( |
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config_file=config_file, |
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training=False, |
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trainable=bert_trainable, |
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build=build) |
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if checkpoint_file is not None: |
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load_model_weights_from_checkpoint( |
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model=self.biobert, config=config, checkpoint_file=checkpoint_file, training=False) |
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self.q_ffn_layer = FFN( |
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hidden_size=hidden_size, |
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dropout=dropout, |
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residual=residual, |
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name='q_ffn') |
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self.a_ffn_layer = FFN( |
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hidden_size=hidden_size, |
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dropout=dropout, |
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residual=residual, |
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name='a_ffn') |
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self.layer_ind = layer_ind |
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def call(self, inputs): |
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if 'q_input_ids' in inputs: |
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with_question = True |
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else: |
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with_question = False |
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if 'a_input_ids' in inputs: |
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with_answer = True |
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else: |
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with_answer = False |
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# according to USE, the DAN network average embedding across tokens |
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if with_question: |
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q_bert_embedding = self.biobert( |
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(inputs['q_input_ids'], inputs['q_segment_ids'], inputs['q_input_masks']))[self.layer_ind] |
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q_bert_embedding = tf.reduce_mean(q_bert_embedding, axis=1) |
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if with_answer: |
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a_bert_embedding = self.biobert( |
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(inputs['a_input_ids'], inputs['a_segment_ids'], inputs['a_input_masks']))[self.layer_ind] |
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a_bert_embedding = tf.reduce_mean(a_bert_embedding, axis=1) |
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if with_question: |
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q_embedding = self.q_ffn_layer(q_bert_embedding) |
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output = q_embedding |
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if with_answer: |
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a_embedding = self.a_ffn_layer(a_bert_embedding) |
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output = a_embedding |
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if with_question and with_answer: |
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output = tf.stack([q_embedding, a_embedding], axis=1) |
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return output |