with open(label_file) as f:
return [line.strip() for line in f]
return ['B-GPE', 'I-GPE', 'O', 'B-PER', 'I-PER',
'B-ORG', 'I-ORG', 'B-LOC', 'I-LOC', 'B-TTL', 'I-TTL',
'I-FAC', 'B-FAC', 'B-VEH', 'I-VEH', 'B-WEA', 'I-WEA']
num_labels = len(get_labels())
tokenizer = BertTokenizer.from_pretrained('bert-base-cased',
do_lower_case=False, do_basic_tokenize=False)
model_dir = '../KBP_19_bert_ner_5e-5'
output_model_file = os.path.join(model_dir, WEIGHTS_NAME)
output_config_file = os.path.join(model_dir, CONFIG_NAME)
config = BertConfig(output_config_file)
model = BertForTokenClassification(config, num_labels=num_labels)
model.load_state_dict(torch.load(output_model_file))
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model.to(device)
def pred_ner(sent):
eval_examples = read_sent(sent)
label_list = get_labels()
eval_features = convert_examples_to_features(
eval_examples, label_list, 300, tokenizer)
all_input_ids = torch.tensor([f.input_ids for f in eval_features], dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in eval_features], dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in eval_features], dtype=torch.long)
all_label_ids = torch.tensor([f.label_id for f in eval_features], dtype=torch.long)
all_label_masks = torch.tensor([f.label_mask for f in eval_features], dtype=torch.long)
eval_data = TensorDataset(all_input_ids, all_input_mask,
all_segment_ids, all_label_ids, all_label_masks)
# Run prediction for full data
class NERPredictor:
def __init__(self,
model_dir,
batch_size,
epoch,
max_seq_length=128,
local_rank=-1,
no_cuda=False):
self._batch_size = batch_size
self._local_rank = local_rank
self._max_seq_length = max_seq_length
self._device, self._n_gpu = get_device(no_cuda=no_cuda)
self._model_config = json.load(
open(os.path.join(model_dir, "model_config.json"), "r"))
self._label_to_id = self._model_config['label_map']
self._label_map = {
v: k
for k, v in self._model_config['label_map'].items()
}
self._bert_tokenizer = \
BertTokenizer.from_pretrained(model_dir,
do_lower_case=self._model_config['do_lower'])
output_config_file = os.path.join(model_dir, CONFIG_NAME)
output_model_file = os.path.join(
model_dir, "pytorch_model_ep{}.bin".format(epoch))
config = BertConfig(output_config_file)
self._model = BertForTokenClassification(config,
num_labels=len(
self._label_map))
self._model.load_state_dict(
torch.load(output_model_file,
map_location=lambda storage, loc: storage
if no_cuda else None))
self._model.to(self._device)
self._model.eval()
return
def classify_text(self, sentences):
examples = NerProcessor.create_examples(sentences, 'test')
features = [
fe for ex in examples for fe in convert_examples_to_features(
ex, self._label_to_id, self._max_seq_length,
self._bert_tokenizer)
]
data_loader = NerProcessor.make_data_loader(None,
self._batch_size,
self._local_rank,
self._label_to_id,
self._max_seq_length,
self._bert_tokenizer,
features=features,
sequential=True)
prediction_tmp = model_predict(data_loader, self._device,
self._label_map, self._model)
assert len(prediction_tmp) == len(features)
prediction = []
prev_guid = None
for fe, pr in zip(features, prediction_tmp):
# longer sentences might have been processed in several steps
# therefore we have to glue them together. This can be done on the basis of the guid.
if prev_guid != fe.guid:
prediction.append((fe.tokens[1:-1], pr))
else:
prediction[-1] = (prediction[-1][0] + fe.tokens[1:-1],
prediction[-1][1] + pr)
prev_guid = fe.guid
try:
assert len(sentences) == len(prediction)
except AssertionError:
print('Sentences:\n')
print(sentences)
print('\n\nPrediciton:\n')
print(prediction)
return prediction
def train_and_evaluate(OUTPUT_DIR, do_train=True, do_eval=True):
""" Train and evaluate a BERT NER Model"""
BATCH_SIZE = 32
LEARNING_RATE = 2e-5
NUM_TRAIN_EPOCHS = 5.0
#in this steps lr will be low and training will be slow
WARMUP_PROPORTION = 0.1
if os.path.exists(OUTPUT_DIR) and os.listdir(OUTPUT_DIR) and do_train:
raise ValueError(
"Output directory ({}) already exists and is not empty.".format(
OUTPUT_DIR))
if not os.path.exists(OUTPUT_DIR):
os.makedirs(OUTPUT_DIR)
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
tokenizer = BertTokenizer.from_pretrained("bert-base-uncased",
do_lower_case=True)
if do_train:
train_examples, num_train_examples = create_datasets("AGE/train.txt")
num_train_steps = int(
math.ceil(num_train_examples / BATCH_SIZE * NUM_TRAIN_EPOCHS))
num_warmup_steps = int(num_train_steps * WARMUP_PROPORTION)
model = BertForTokenClassification.from_pretrained(
"bert-base-uncased", num_labels=num_labels)
model.to(device)
param_optimizer = list(model.named_parameters())
no_decay = ['bias', 'LayerNorm.bias', 'LayerNorm.weight']
optimizer_grouped_parameters = [{
'params': [
p for n, p in param_optimizer
if not any(nd in n for nd in no_decay)
],
'weight_decay':
0.01
}, {
'params':
[p for n, p in param_optimizer if any(nd in n for nd in no_decay)],
'weight_decay':
0.0
}]
optimizer = BertAdam(optimizer_grouped_parameters,
lr=LEARNING_RATE,
warmup=WARMUP_PROPORTION,
t_total=num_train_steps)
global_step = 0
nb_tr_steps = 0
tr_loss = 0
train_features = convert_examples_to_features(train_examples,
label_list,
MAX_SEQ_LENGTH,
tokenizer)
logger.info("***** Running training *****")
logger.info(" Num examples = %d", num_train_examples)
logger.info(" Batch size = %d", BATCH_SIZE)
logger.info(" Num steps = %d", num_train_steps)
all_input_ids = torch.tensor([f.input_ids for f in train_features],
dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in train_features],
dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in train_features],
dtype=torch.long)
all_label_ids = torch.tensor([f.label_id for f in train_features],
dtype=torch.long)
train_data = TensorDataset(all_input_ids, all_input_mask,
all_segment_ids, all_label_ids)
train_sampler = RandomSampler(train_data)
train_dataloader = DataLoader(train_data,
sampler=train_sampler,
batch_size=BATCH_SIZE)
model.train()
# for name, param in model.named_parameters():
# if param.requires_grad:
# print(name)
# return
for _ in trange(int(NUM_TRAIN_EPOCHS), desc="Epoch"):
tr_loss = 0
nb_tr_examples, nb_tr_steps = 0, 0
for step, batch in enumerate(
tqdm(train_dataloader, desc="Iteration")):
batch = tuple(t.to(device) for t in batch)
input_ids, input_mask, segment_ids, label_ids = batch
loss = model(input_ids, segment_ids, input_mask, label_ids)
loss.backward()
tr_loss += loss.item()
nb_tr_examples += input_ids.size(0)
nb_tr_steps += 1
optimizer.step()
optimizer.zero_grad()
global_step += 1
print(tr_loss)
# Save a trained model and the associated configuration
model_to_save = model.module if hasattr(
model, 'module') else model # Only save the model it-self
output_model_file = os.path.join(OUTPUT_DIR, WEIGHTS_NAME)
torch.save(model_to_save.state_dict(), output_model_file)
output_config_file = os.path.join(OUTPUT_DIR, CONFIG_NAME)
with open(output_config_file, 'w') as f:
f.write(model_to_save.config.to_json_string())
label_map = {i: label for i, label in enumerate(label_list, 1)}
model_config = {
"bert_model": "bert-base-uncased",
"do_lower": True,
"max_seq_length": MAX_SEQ_LENGTH,
"num_labels": len(label_list) + 1,
"label_map": label_map
}
json.dump(model_config,
open(os.path.join(OUTPUT_DIR, "model_config.json"), "w"))
else:
output_config_file = os.path.join(OUTPUT_DIR, CONFIG_NAME)
output_model_file = os.path.join(OUTPUT_DIR, WEIGHTS_NAME)
config = BertConfig(output_config_file)
model = BertForTokenClassification(config, num_labels=num_labels)
model.load_state_dict(torch.load(output_model_file))
model.to(device)
if do_eval:
EVAL_BATCH_SIZE = 32
eval_examples, num_eval_examples = create_datasets("AGE/valid.txt")
eval_features = convert_examples_to_features(eval_examples, label_list,
MAX_SEQ_LENGTH, tokenizer)
logger.info("***** Running evaluation *****")
logger.info(" Num examples = %d", num_eval_examples)
logger.info(" Batch size = %d", EVAL_BATCH_SIZE)
all_input_ids = torch.tensor([f.input_ids for f in eval_features],
dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in eval_features],
dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in eval_features],
dtype=torch.long)
all_label_ids = torch.tensor([f.label_id for f in eval_features],
dtype=torch.long)
eval_data = TensorDataset(all_input_ids, all_input_mask,
all_segment_ids, all_label_ids)
# # Run prediction for full data
eval_sampler = SequentialSampler(eval_data)
eval_dataloader = DataLoader(eval_data,
sampler=eval_sampler,
batch_size=EVAL_BATCH_SIZE)
model.eval()
eval_loss, eval_accuracy = 0, 0
nb_eval_steps, nb_eval_examples = 0, 0
y_true = []
y_pred = []
label_map = {i: label for i, label in enumerate(label_list, 1)}
for input_ids, input_mask, segment_ids, label_ids in tqdm(
eval_dataloader, desc="Evaluating"):
input_ids = input_ids.to(device)
input_mask = input_mask.to(device)
segment_ids = segment_ids.to(device)
label_ids = label_ids.to(device)
with torch.no_grad():
logits = model(input_ids, segment_ids, input_mask)
logits = torch.argmax(F.log_softmax(logits, dim=2), dim=2)
logits = logits.detach().cpu().numpy()
label_ids = label_ids.to('cpu').numpy()
input_mask = input_mask.to('cpu').numpy()
for i, mask in enumerate(input_mask):
temp_1 = []
temp_2 = []
for j, m in enumerate(mask):
if j == 0:
continue
if m:
if label_map[label_ids[i][j]] != "X":
temp_1.append(label_map[label_ids[i][j]])
temp_2.append(label_map[logits[i][j]])
else:
temp_1.pop()
temp_2.pop()
break
y_true.append(temp_1)
y_pred.append(temp_2)
report = classification_report(y_true, y_pred)
output_eval_file = os.path.join(OUTPUT_DIR, "eval_results.txt")
with open(output_eval_file, "w") as writer:
logger.info("***** Eval results *****")
logger.info("\n%s", report)
writer.write(report)
def predict(OUTPUT_DIR, in_sentences):
""" predict a bert model
OUTPUT_DIR :: contains pretrained models
in_sentences :: is a list of sentences on which tagging has to be performed
"""
PRED_BATCH_SIZE = 64
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
model_config = os.path.join(OUTPUT_DIR, "model_config.json")
model_config = json.load(open(model_config))
output_config_file = os.path.join(OUTPUT_DIR, CONFIG_NAME)
output_model_file = os.path.join(OUTPUT_DIR, WEIGHTS_NAME)
config = BertConfig(output_config_file)
model = BertForTokenClassification(config,
num_labels=model_config["num_labels"])
model.load_state_dict(torch.load(output_model_file))
model.to(device)
tokenizer = BertTokenizer.from_pretrained(
model_config["bert_model"], do_lower_case=model_config["do_lower"])
in_examples = [
InputExample(guid="",
text_a=x,
text_b=None,
label=["O"] * len(x.split(" "))) for x in in_sentences
]
in_features = convert_examples_to_features(in_examples, label_list,
MAX_SEQ_LENGTH, tokenizer)
all_input_ids = torch.tensor([f.input_ids for f in in_features],
dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in in_features],
dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in in_features],
dtype=torch.long)
pred_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids)
# # Run prediction for full data
pred_sampler = SequentialSampler(pred_data)
pred_dataloader = DataLoader(pred_data,
sampler=pred_sampler,
batch_size=PRED_BATCH_SIZE,
drop_last=False)
model.eval()
preds = []
label_map = model_config["label_map"]
for input_ids, input_mask, segment_ids in tqdm(pred_dataloader,
desc="Predicting"):
input_ids = input_ids.to(device)
input_mask = input_mask.to(device)
segment_ids = segment_ids.to(device)
with torch.no_grad():
logits = model(input_ids, segment_ids, input_mask)
logits = torch.argmax(F.log_softmax(logits, dim=2), dim=2)
logits = logits.detach().cpu().numpy()
pred_batch = []
for i, mask in enumerate(input_mask):
temp_1 = []
for j, m in enumerate(mask):
if j == 0:
continue
if m:
if label_map[str(logits[i][j])] != "X":
temp_1.append(label_map[str(logits[i][j])])
else:
temp_1.pop()
break
pred_batch.append(temp_1)
preds.extend(pred_batch)
return [(sentence, pred) for sentence, pred in zip(in_sentences, preds)]
def model_eval(batch_size,
label_map,
processor,
device,
num_train_epochs=1,
output_dir=None,
model=None,
local_rank=-1,
no_cuda=False,
dry_run=False):
output_eval_file = None
if output_dir is not None:
output_eval_file = os.path.join(output_dir,
processor.get_evaluation_file())
logger.info('Write evaluation results to: {}'.format(output_eval_file))
dataloader = processor.get_dev_examples(batch_size, local_rank)
logger.info("***** Running evaluation *****")
logger.info(" Num examples = %d", len(dataloader))
logger.info(" Batch size = %d", batch_size)
results = list()
output_config_file = None
if output_dir is not None:
output_config_file = os.path.join(output_dir, CONFIG_NAME)
for ep in trange(1, int(num_train_epochs) + 1, desc="Epoch"):
if dry_run and ep > 1:
logger.info("Dry run. Stop.")
break
if output_config_file is not None:
# Load a trained model and config that you have fine-tuned
output_model_file = os.path.join(
output_dir, "pytorch_model_ep{}.bin".format(ep))
if not os.path.exists(output_model_file):
logger.info(
"Stopping at epoch {} since model file is missing.".format(
ep))
break
config = BertConfig(output_config_file)
model = BertForTokenClassification(config,
num_labels=len(label_map))
model.load_state_dict(
torch.load(output_model_file,
map_location=lambda storage, loc: storage
if no_cuda else None))
model.to(device)
if model is None:
raise ValueError('Model required for evaluation.')
model.eval()
y_pred, y_true = model_predict_compare(dataloader, device, label_map,
model, dry_run)
lines = [
'empty ' + 'XXX ' + v + ' ' + p for yt, yp in zip(y_true, y_pred)
for v, p in zip(yt, yp)
]
res = conll_eval(lines)
# print(res)
evals = \
pd.concat([pd.DataFrame.from_dict(res['overall']['evals'], orient='index', columns=['ALL']),
pd.DataFrame.from_dict(res['slots']['LOC']['evals'], orient='index', columns=['LOC']),
pd.DataFrame.from_dict(res['slots']['PER']['evals'], orient='index', columns=['PER']),
pd.DataFrame.from_dict(res['slots']['ORG']['evals'], orient='index', columns=['ORG']),
], axis=1).T
stats = \
pd.concat(
[pd.DataFrame.from_dict(res['overall']['stats'], orient='index', columns=['ALL']),
pd.DataFrame.from_dict(res['slots']['LOC']['stats'], orient='index', columns=['LOC']),
pd.DataFrame.from_dict(res['slots']['PER']['stats'], orient='index', columns=['PER']),
pd.DataFrame.from_dict(res['slots']['ORG']['stats'], orient='index', columns=['ORG'])],
axis=1, sort=True).T
evals['epoch'] = ep
stats['epoch'] = ep
results.append(
pd.concat([
evals.reset_index().set_index(['index', 'epoch']),
stats.reset_index().set_index(['index', 'epoch'])
],
axis=1))
if output_eval_file is not None:
pd.concat(results).to_pickle(output_eval_file)
results = pd.concat(results)
print(results)
return results