import os
import sys
import torch
import numpy as np
from transformers import AutoTokenizer, AutoModel, AutoConfig
from tqdm import tqdm
import faiss
import random
import string
import time
import pickle
import gc
batch_size = 64
device = torch.device("cuda:0")
def get_bert_embed(phrase_list, m, tok, normalize=True, summary_method="CLS", tqdm_bar=False):
input_ids = []
for phrase in phrase_list:
input_ids.append(tok.encode_plus(
phrase, max_length=32, add_special_tokens=True,
truncation=True, pad_to_max_length=True)['input_ids'])
# print(len(input_ids))
m.eval()
count = len(input_ids)
now_count = 0
output_list = []
with torch.no_grad():
if tqdm_bar:
pbar = tqdm(total=count)
while now_count < count:
input_gpu_0 = torch.LongTensor(input_ids[now_count:min(
now_count + batch_size, count)]).to(device)
if summary_method == "CLS":
embed = m(input_gpu_0)[1]
if summary_method == "MEAN":
embed = torch.mean(m(input_gpu_0)[0], dim=1)
if normalize:
embed_norm = torch.norm(
embed, p=2, dim=1, keepdim=True).clamp(min=1e-12)
embed = embed / embed_norm
if now_count % 1000000 == 0:
if now_count != 0:
output_list.append(output.cpu().numpy())
del output
torch.cuda.empty_cache()
output = embed
else:
output = torch.cat((output, embed), dim=0)
if tqdm_bar:
pbar.update(min(now_count + batch_size, count) - now_count)
now_count = min(now_count + batch_size, count)
del input_gpu_0
torch.cuda.empty_cache()
if tqdm_bar:
pbar.close()
output_list.append(output.cpu().numpy())
del output
torch.cuda.empty_cache()
return np.concatenate(output_list, axis=0)
def get_KNN(embeddings, k, use_multi_gpu=True):
if use_multi_gpu:
d = embeddings.shape[1]
index = faiss.IndexFlatIP(d)
gpu_index = faiss.index_cpu_to_all_gpus(index)
gpu_index.add(embeddings)
else:
d = embeddings.shape[1]
res = faiss.StandardGpuResources()
index = faiss.IndexFlatIP(d)
gpu_index = faiss.index_cpu_to_gpu(res, 0, index)
gpu_index.add(embeddings)
print(gpu_index.ntotal)
similarity, indices = gpu_index.search(embeddings.astype(np.float32), k)
del gpu_index
gc.collect()
return similarity, indices
def find_new_index(new_CODER_path, output_path, similarity_path, idx2string_path='data/idx2string.pkl', ori_CODER_path='GanjinZero/UMLSBert_ENG', use_multi_gpu=True):
print('start finding new index...')
config = AutoConfig.from_pretrained(ori_CODER_path)
tokenizer = AutoTokenizer.from_pretrained(ori_CODER_path)
print('start loading phrases...')
with open('data/idx2string.pkl', 'rb') as f:
phrase_list = list(pickle.load(f).values())
print('done loading phrases')
model = torch.load(new_CODER_path).to(device)
embeddings = get_bert_embed(phrase_list, model, tokenizer, summary_method="MEAN", tqdm_bar=True)
del model
torch.cuda.empty_cache()
print('start knn')
similarity, indices = get_KNN(embeddings, 30, use_multi_gpu)
# similarity = np.zeros((len(phrase_list), 30))
# indices = similarity
with open(output_path, 'wb') as f:
np.save(f, indices)
with open(similarity_path, 'wb') as f:
np.save(f, similarity)
print('done knn')
return None
if __name__ == "__main__":
filename = "GanjinZero/UMLSBert_ENG"
config = AutoConfig.from_pretrained(filename)
tokenizer = AutoTokenizer.from_pretrained(filename)
print('start loading phrases...')
with open('data/idx2string.pkl', 'rb') as f:
phrase_list = list(pickle.load(f).values())
print('done loading phrases')
# model = AutoModel.from_pretrained(
# filename,
# config=config).to(device)
model = torch.load('output_testttt/last_model.pth').to(device)
start = time.time()
print('start testing...')
embeddings = get_bert_embed(phrase_list[:100], model, tokenizer, summary_method="MEAN", tqdm_bar=True)
print(embeddings.shape)
# with open('data/embeddings.npy', 'wb') as f:
# np.save(f, embeddings)
# print('done testing')
# del model
# torch.cuda.empty_cache()
# embeddings = np.load('data/embeddings.npy')
# print('start knn...')
# similarity, indices = get_KNN(embeddings, 30, use_multi_gpu=True)
# with open('data/similarity.npy', 'wb') as f:
# np.save(f, similarity)
# with open('data/indices.npy', 'wb') as f:
# np.save(f, indices)
# print('done knn')
# end = time.time()
# print(end - start, 's')