def decode(hp):
tokenizer = BertTokenizer.from_pretrained(hp.bert_model_dir, do_lower_case=False)
if hp.dataset == "lm_raw_data_finance":
dict_file = "../data/dataset_finance/annual_report_entity_list"
elif hp.dataset == "lm_raw_data_novel":
dict_file = "../data/dataset_book9/entity_book9"
entity_dict = EntityDict(hp.dataset, dict_file)
entity_dict.load(os.path.join(hp.bert_model_dir, 'entity.dict'))
device = 'cuda' if torch.cuda.is_available() else 'cpu'
ner_label = NerLabel([hp.decodeset])
if os.path.exists(os.path.join(hp.logdir, 'dict.pt')):
ner_label.load(os.path.join(hp.logdir, 'dict.pt'))
else:
print('dict.pt is not exit')
exit()
decode_dataset = NerDataset(hp.decodeset, ner_label, tokenizer, entity_dict)
model = Net(hp.bert_model_dir, hp.top_rnns, len(ner_label.VOCAB), entity_dict.entity_num, device, hp.finetuning).to(device)
model = nn.DataParallel(model)
## Load the model parameters
if os.path.exists(os.path.join(hp.logdir, 'model.pt')):
model.load_state_dict(torch.load(os.path.join(hp.logdir, 'model.pt')))
else:
print("the pretrianed model path does not exist! ")
exit()
decode_iter = data.DataLoader(dataset=decode_dataset,
batch_size=hp.batch_size,
shuffle=True,
num_workers=4,
collate_fn=pad)
fname = os.path.join(hp.logdir, '_')
precision, recall, f1 = evaluate(model, decode_iter, fname, ner_label, verbose=False)
if __name__=="__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--batch_size", type=int, default=128)
parser.add_argument("--lr", type=float, default=0.0001)
parser.add_argument("--n_epochs", type=int, default=30)
parser.add_argument("--finetuning", dest="finetuning", action="store_true")
parser.add_argument("--explainable", dest="explainable", action="store_true")
parser.add_argument("--top_rnns", dest="top_rnns", action="store_true")
parser.add_argument("--logdir", type=str, default="checkpoints/01")
parser.add_argument("--trainset", type=str, default="conll2003/train.txt")
parser.add_argument("--validset", type=str, default="conll2003/valid.txt")
hp = parser.parse_args()
device = 'cuda' if torch.cuda.is_available() else 'cpu'
train_dataset = NerDataset(hp.trainset)
eval_dataset = NerDataset(hp.validset)
if hp.explainable:
print('WARNING: use EXPLAINABLE mode')
maxlen = max(train_dataset.maxlen, eval_dataset.maxlen)
_pad = partial(pad, maxlen=maxlen)
model = Net(top_rnns=hp.top_rnns, vocab_size=len(VOCAB), device=device, finetuning=hp.finetuning,
explainable=hp.explainable).to(device)
model.init_tf(maxlen=maxlen)
#model = nn.DataParallel(model)
else:
model = Net(hp.top_rnns, len(VOCAB), device, hp.finetuning).to(device)
model = nn.DataParallel(model)
_pad = pad
def train(hp):
tokenizer = BertTokenizer.from_pretrained(hp.bert_model_dir, do_lower_case=False)
if hp.dataset == "lm_raw_data_finance":
dict_file = "../data/dataset_finance/raw_data/annual_report_entity_list"
elif hp.dataset == "lm_raw_data_novel":
dict_file = "../data/dataset_book9/raw_data/entity_book9"
elif hp.dataset == "lm_raw_data_thuner":
dict_file = "../data/dataset_thuner/raw_data/thu_entity.txt"
entity_dict = EntityDict(hp.dataset, dict_file)
entity_dict.load(os.path.join(hp.bert_model_dir, 'entity.dict'))
device = 'cuda' if torch.cuda.is_available() else 'cpu'
ner_label = NerLabel([hp.trainset, hp.validset])
fname = os.path.join(hp.logdir, 'dict.pt')
ner_label.save(fname)
train_dataset = NerDataset(hp.trainset, ner_label, tokenizer, entity_dict)
eval_dataset = NerDataset(hp.validset, ner_label, tokenizer, entity_dict)
test_dataset = NerDataset(hp.testset, ner_label, tokenizer, entity_dict)
model = Net(hp.bert_model_dir, hp.top_rnns, len(ner_label.VOCAB), entity_dict.entity_num, device, hp.finetuning).to(device)
device_ids = [0, 1]
model = nn.DataParallel(model, device_ids=device_ids)
train_iter = data.DataLoader(dataset=train_dataset,
batch_size=hp.batch_size,
shuffle=True,
num_workers=4,
collate_fn=pad)
eval_iter = data.DataLoader(dataset=eval_dataset,
batch_size=hp.batch_size,
shuffle=False,
num_workers=4,
collate_fn=pad)
test_iter = data.DataLoader(dataset=test_dataset,
batch_size=hp.batch_size,
shuffle=False,
num_workers=4,
collate_fn=pad)
optimizer = optim.Adam(model.parameters(), lr=hp.lr)
criterion = nn.CrossEntropyLoss(ignore_index=0)
## train the model
best_eval = -10
for epoch in range(1, hp.n_epochs + 1):
train_epoch(model, train_iter, optimizer, criterion, tokenizer)
print(f"=========eval at epoch={epoch}=========")
if not os.path.exists(hp.logdir): os.makedirs(hp.logdir)
fname = os.path.join(hp.logdir, 'model')
precision, recall, f1 = evaluate(model, eval_iter, fname, ner_label, verbose=False)
if f1 > best_eval:
best_eval = f1
print("epoch{} get the best eval f-score:{}".format(epoch, best_eval))
torch.save(model.state_dict(), f"{fname}.pt")
print(f"weights were saved to {fname}.pt")
print(f"=========test at epoch={epoch}=========")
if not os.path.exists(hp.logdir): os.makedirs(hp.logdir)
fname = os.path.join(hp.logdir, str(epoch))
precision, recall, f1 = evaluate(model, test_iter, fname, ner_label, verbose=False)
hp = parser.parse_args()
device = 'cuda' if torch.cuda.is_available() else 'cpu'
print("=========build model=========")
model = Net(hp.top_rnns, len(VOCAB), device, hp.finetuning).cuda()
# model=1
print("=========parallel=========")
model = nn.DataParallel(model)
df_case = pd.read_csv('df_case.csv')
# make_ner_txt(df_case.inf,hp.testset)
print("=========load data=========")
test_dataset = NerDataset(hp.testset)
test_iter = data.DataLoader(dataset=test_dataset,
batch_size=hp.batch_size,
shuffle=False,
num_workers=4,
collate_fn=pad)
optimizer = optim.Adam(model.parameters(), lr=hp.lr)
criterion = nn.CrossEntropyLoss(ignore_index=0)
# f1_best=0
# fname = os.path.join(hp.logdir, 'model')
# print("=========ner=========")
# test_model=Net(hp.top_rnns, len(VOCAB), device, hp.finetuning)
# test_model = nn.DataParallel(test_model)
torch.set_rng_state(state['torch_rng_state'])
torch.cuda.set_rng_state(state['cuda_rng_state']),
torch.cuda.set_rng_state_all(state['cuda_rng_state_all']),
np.random.set_state(state['np_rng_state'])
random.setstate(state['random_rng_state'])
if state.get('model') is not None and model is not None:
model.load_state_dict(state['model'])
if __name__ == "__main__":
for fold_iter_idx in range(args.fold_num):
if args.do_train:
Fold_iter_idx = fold_iter_idx
# Prepare Documents
if args.task.lower() == 'bc2gm':
train_dataset = NerDataset(f"../{args.task}/train.tsv",
args.task, args.pretrain_dir)
eval_dataset = NerDataset(f"../{args.task}/test.tsv",
args.task, args.pretrain_dir)
elif args.task.lower() == 'bc6pm':
if args.do_cross_valid:
if fold_iter_idx == 0:
if args.train_withGNP:
train_data_dir = os.path.join(
os.environ.get('BC6PM_dir'), 'GNormPlus',
'withAnn-Result',
'PMtask_Relations_TrainingSet_r.json')
else:
train_data_dir = os.path.join(
os.environ.get('BC6PM_dir'), 'json',
'PMtask_Relations_TrainingSet.json')
with open(train_data_dir) as f:
fout.write(f"precision={score[0]}\n")
fout.write(f"recall={score[1]}\n")
fout.write(f"f1={score[2]}\n")
os.remove(f)
print("precision=%.2f" % score[0])
print("recall=%.2f" % score[1])
print("f1=%.2f" % score[2])
return score[0], score[1], score[2]
if __name__ == "__main__":
train_dataset = NerDataset("Data/train.tsv", 'i2b2')
eval_dataset = NerDataset("Data/test.tsv", 'i2b2')
# Define model
config = BertConfig(
vocab_size_or_config_json_file=parameters.BERT_CONFIG_FILE)
model = Net(config=config,
bert_state_dict=model_state_dict,
vocab_len=len(hp.VOCAB),
device=hp.device)
# 'bc5cdr': ('<PAD>', 'B-Chemical', 'O', 'B-Disease' , 'I-Disease', 'I-Chemical'),
class_sample_count = [
10, 1, 20, 3, 4
] # dataset has 10 class-1 samples, 1 class-2 samples, etc.
fout.write(f"precision={precision}\n")
fout.write(f"recall={recall}\n")
fout.write(f"f1={f1}\n")
os.remove(f)
print("precision=%.2f" % precision)
print("recall=%.2f" % recall)
print("f1=%.2f" % f1)
return precision, recall, f1
if __name__ == "__main__":
train_dataset = NerDataset("data/train.tsv",
'bc5cdr') # here bc5cdr is dataset type
eval_dataset = NerDataset("data/test.tsv", 'bc5cdr')
hp = HParams('bc5cdr')
# Define model
config = BertConfig(
vocab_size_or_config_json_file=parameters.BERT_CONFIG_FILE)
model = Net(config=config,
bert_state_dict=state_dict,
vocab_len=len(hp.VOCAB),
device=hp.device)
if torch.cuda.is_available():
model.cuda()
model.train()
# update with already pretrained weight
fout.write(f"precision={precision}\n")
fout.write(f"recall={recall}\n")
fout.write(f"f1={f1}\n")
os.remove(f)
print("precision=%.2f"%precision)
print("recall=%.2f"%recall)
print("f1=%.2f"%f1)
return precision, recall, f1
if __name__=="__main__":
model = Net(training=False)
model.to('cuda')
train_dataset = NerDataset("conll2003/train.txt")
eval_dataset = NerDataset("conll2003/valid.txt")
train_iter = data.DataLoader(dataset=train_dataset,
batch_size=hp.batch_size,
shuffle=True,
num_workers=4,
collate_fn=pad)
eval_iter = data.DataLoader(dataset=eval_dataset,
batch_size=hp.batch_size,
shuffle=False,
num_workers=4,
collate_fn=pad)
optimizer = optim.Adam(model.parameters(), lr = hp.lr)
# optimizer = optim.SGD(model.parameters(), lr=0.0001, momentum=0.9)