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run_relation.py
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run_relation.py
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"""
This code is based on the file in SpanBERT repo: https://github.com/facebookresearch/SpanBERT/blob/master/code/run_tacred.py
"""
import argparse
import logging
import os
import random
import time
import json
import sys
import numpy as np
import torch
from torch.utils.data import DataLoader, TensorDataset
from collections import Counter
from torch.nn import CrossEntropyLoss
from transformers.file_utils import PYTORCH_PRETRAINED_BERT_CACHE, WEIGHTS_NAME, CONFIG_NAME
from relation.models import BertForRelation, AlbertForRelation
from transformers import AutoTokenizer
from transformers import AdamW, get_linear_schedule_with_warmup
from relation.utils import generate_relation_data, decode_sample_id
from shared.const import task_rel_labels, task_ner_labels
CLS = "[CLS]"
SEP = "[SEP]"
logging.basicConfig(format='%(asctime)s - %(levelname)s - %(name)s - %(message)s',
datefmt='%m/%d/%Y %H:%M:%S',
level=logging.INFO)
logger = logging.getLogger(__name__)
class InputFeatures(object):
"""A single set of features of data."""
def __init__(self, input_ids, input_mask, segment_ids, label_id, sub_idx, obj_idx):
self.input_ids = input_ids
self.input_mask = input_mask
self.segment_ids = segment_ids
self.label_id = label_id
self.sub_idx = sub_idx
self.obj_idx = obj_idx
def add_marker_tokens(tokenizer, ner_labels):
new_tokens = ['<SUBJ_START>', '<SUBJ_END>', '<OBJ_START>', '<OBJ_END>']
for label in ner_labels:
new_tokens.append('<SUBJ_START=%s>'%label)
new_tokens.append('<SUBJ_END=%s>'%label)
new_tokens.append('<OBJ_START=%s>'%label)
new_tokens.append('<OBJ_END=%s>'%label)
for label in ner_labels:
new_tokens.append('<SUBJ=%s>'%label)
new_tokens.append('<OBJ=%s>'%label)
tokenizer.add_tokens(new_tokens)
logger.info('# vocab after adding markers: %d'%len(tokenizer))
def convert_examples_to_features(examples, label2id, max_seq_length, tokenizer, special_tokens, unused_tokens=True):
"""
Loads a data file into a list of `InputBatch`s.
unused_tokens: whether use [unused1] [unused2] as special tokens
"""
def get_special_token(w):
if w not in special_tokens:
if unused_tokens:
special_tokens[w] = "[unused%d]" % (len(special_tokens) + 1)
else:
special_tokens[w] = ('<' + w + '>').lower()
return special_tokens[w]
num_tokens = 0
max_tokens = 0
num_fit_examples = 0
num_shown_examples = 0
features = []
for (ex_index, example) in enumerate(examples):
if ex_index % 10000 == 0:
logger.info("Writing example %d of %d" % (ex_index, len(examples)))
tokens = [CLS]
SUBJECT_START = get_special_token("SUBJ_START")
SUBJECT_END = get_special_token("SUBJ_END")
OBJECT_START = get_special_token("OBJ_START")
OBJECT_END = get_special_token("OBJ_END")
SUBJECT_NER = get_special_token("SUBJ=%s" % example['subj_type'])
OBJECT_NER = get_special_token("OBJ=%s" % example['obj_type'])
SUBJECT_START_NER = get_special_token("SUBJ_START=%s"%example['subj_type'])
SUBJECT_END_NER = get_special_token("SUBJ_END=%s"%example['subj_type'])
OBJECT_START_NER = get_special_token("OBJ_START=%s"%example['obj_type'])
OBJECT_END_NER = get_special_token("OBJ_END=%s"%example['obj_type'])
for i, token in enumerate(example['token']):
if i == example['subj_start']:
sub_idx = len(tokens)
tokens.append(SUBJECT_START_NER)
if i == example['obj_start']:
obj_idx = len(tokens)
tokens.append(OBJECT_START_NER)
for sub_token in tokenizer.tokenize(token):
tokens.append(sub_token)
if i == example['subj_end']:
tokens.append(SUBJECT_END_NER)
if i == example['obj_end']:
tokens.append(OBJECT_END_NER)
tokens.append(SEP)
num_tokens += len(tokens)
max_tokens = max(max_tokens, len(tokens))
if len(tokens) > max_seq_length:
tokens = tokens[:max_seq_length]
if sub_idx >= max_seq_length:
sub_idx = 0
if obj_idx >= max_seq_length:
obj_idx = 0
else:
num_fit_examples += 1
segment_ids = [0] * len(tokens)
input_ids = tokenizer.convert_tokens_to_ids(tokens)
input_mask = [1] * len(input_ids)
padding = [0] * (max_seq_length - len(input_ids))
input_ids += padding
input_mask += padding
segment_ids += padding
label_id = label2id[example['relation']]
assert len(input_ids) == max_seq_length
assert len(input_mask) == max_seq_length
assert len(segment_ids) == max_seq_length
if num_shown_examples < 20:
if (ex_index < 5) or (label_id > 0):
num_shown_examples += 1
logger.info("*** Example ***")
logger.info("guid: %s" % (example['id']))
logger.info("tokens: %s" % " ".join(
[str(x) for x in tokens]))
logger.info("input_ids: %s" % " ".join([str(x) for x in input_ids]))
logger.info("input_mask: %s" % " ".join([str(x) for x in input_mask]))
logger.info("segment_ids: %s" % " ".join([str(x) for x in segment_ids]))
logger.info("label: %s (id = %d)" % (example['relation'], label_id))
logger.info("sub_idx, obj_idx: %d, %d" % (sub_idx, obj_idx))
features.append(
InputFeatures(input_ids=input_ids,
input_mask=input_mask,
segment_ids=segment_ids,
label_id=label_id,
sub_idx=sub_idx,
obj_idx=obj_idx))
logger.info("Average #tokens: %.2f" % (num_tokens * 1.0 / len(examples)))
logger.info("Max #tokens: %d"%max_tokens)
logger.info("%d (%.2f %%) examples can fit max_seq_length = %d" % (num_fit_examples,
num_fit_examples * 100.0 / len(examples), max_seq_length))
return features
def simple_accuracy(preds, labels):
return (preds == labels).mean()
def compute_f1(preds, labels, e2e_ngold):
n_gold = n_pred = n_correct = 0
for pred, label in zip(preds, labels):
if pred != 0:
n_pred += 1
if label != 0:
n_gold += 1
if (pred != 0) and (label != 0) and (pred == label):
n_correct += 1
if n_correct == 0:
return {'precision': 0.0, 'recall': 0.0, 'f1': 0.0}
else:
prec = n_correct * 1.0 / n_pred
recall = n_correct * 1.0 / n_gold
if prec + recall > 0:
f1 = 2.0 * prec * recall / (prec + recall)
else:
f1 = 0.0
if e2e_ngold is not None:
e2e_recall = n_correct * 1.0 / e2e_ngold
e2e_f1 = 2.0 * prec * e2e_recall / (prec + e2e_recall)
else:
e2e_recall = e2e_f1 = 0.0
return {'precision': prec, 'recall': e2e_recall, 'f1': e2e_f1, 'task_recall': recall, 'task_f1': f1,
'n_correct': n_correct, 'n_pred': n_pred, 'n_gold': e2e_ngold, 'task_ngold': n_gold}
def evaluate(model, device, eval_dataloader, eval_label_ids, num_labels, e2e_ngold=None, verbose=True):
model.eval()
eval_loss = 0
nb_eval_steps = 0
preds = []
reps = []
for input_ids, input_mask, segment_ids, label_ids, sub_idx, obj_idx in eval_dataloader:
input_ids = input_ids.to(device)
input_mask = input_mask.to(device)
segment_ids = segment_ids.to(device)
label_ids = label_ids.to(device)
sub_idx = sub_idx.to(device)
obj_idx = obj_idx.to(device)
with torch.no_grad():
logits, rep = model(input_ids, segment_ids, input_mask, labels=None, sub_idx=sub_idx, obj_idx=obj_idx)
loss_fct = CrossEntropyLoss()
tmp_eval_loss = loss_fct(logits.view(-1, num_labels), label_ids.view(-1))
eval_loss += tmp_eval_loss.mean().item()
nb_eval_steps += 1
if len(preds) == 0:
preds.append(logits.detach().cpu().numpy())
reps.append(rep.detach().cpu().numpy())
else:
preds[0] = np.append(
preds[0], logits.detach().cpu().numpy(), axis=0)
reps[0] = np.append(
reps[0], rep.detach().cpu().numpy(), axis=0)
eval_loss = eval_loss / nb_eval_steps
reps = reps[0]
#reps_dict = {k:reps[k] for k in range(len(reps))}
#labels_dict = {k:eval_label_ids[k] for k in range(len(eval_label_ids))}
#with open("train_datastore.json", "w") as f:
# json.dump(reps_dict, f)
#with open("train_labels.json", "w") as f:
# json.dump(labels_dict, f)
logits = preds[0]
preds = np.argmax(preds[0], axis=1)
result = compute_f1(preds, eval_label_ids.numpy(), e2e_ngold=e2e_ngold)
result['accuracy'] = simple_accuracy(preds, eval_label_ids.numpy())
result['eval_loss'] = eval_loss
if verbose:
logger.info("***** Eval results *****")
for key in sorted(result.keys()):
logger.info(" %s = %s", key, str(result[key]))
return preds, result, logits
def print_pred_json(eval_data, eval_examples, preds, id2label, output_file):
rels = dict()
for ex, pred in zip(eval_examples, preds):
doc_sent, sub, obj = decode_sample_id(ex['id'])
if doc_sent not in rels:
rels[doc_sent] = []
if pred != 0:
rels[doc_sent].append([sub[0], sub[1], obj[0], obj[1], id2label[pred]])
js = eval_data.js
for doc in js:
doc['predicted_relations'] = []
for sid in range(len(doc['sentences'])):
k = '%s@%d'%(doc['doc_key'], sid)
doc['predicted_relations'].append(rels.get(k, []))
logger.info('Output predictions to %s..'%(output_file))
with open(output_file, 'w') as f:
f.write('\n'.join(json.dumps(doc) for doc in js))
def setseed(seed):
random.seed(seed)
np.random.seed(args.seed)
torch.manual_seed(seed)
if torch.cuda.is_available():
torch.cuda.manual_seed_all(seed)
def save_trained_model(output_dir, model, tokenizer):
if not os.path.exists(output_dir):
os.mkdir(output_dir)
logger.info('Saving model to %s'%output_dir)
model_to_save = model.module if hasattr(model, 'module') else model
output_model_file = os.path.join(output_dir, WEIGHTS_NAME)
output_config_file = os.path.join(output_dir, CONFIG_NAME)
torch.save(model_to_save.state_dict(), output_model_file)
model_to_save.config.to_json_file(output_config_file)
tokenizer.save_vocabulary(output_dir)
def main(args):
if 'albert' in args.model:
RelationModel = AlbertForRelation
args.add_new_tokens = True
else:
RelationModel = BertForRelation
device = torch.device("cuda" if torch.cuda.is_available() and not args.no_cuda else "cpu")
n_gpu = torch.cuda.device_count()
# train set
if args.do_train:
train_dataset, train_examples, train_nrel = generate_relation_data(args.task,args.train_file, use_gold=True, context_window=args.context_window)
# dev set
if (args.do_eval and args.do_train) or (args.do_eval and not(args.eval_test)):
eval_dataset, eval_examples, eval_nrel = generate_relation_data(args.task,os.path.join(args.entity_output_dir, args.entity_predictions_dev), use_gold=args.eval_with_gold, context_window=args.context_window)
# test set
if args.eval_test:
test_dataset, test_examples, test_nrel = generate_relation_data(args.task,os.path.join(args.entity_output_dir, args.entity_predictions_test), use_gold=args.eval_with_gold, context_window=args.context_window)
setseed(args.seed)
if not args.do_train and not args.do_eval:
raise ValueError("At least one of `do_train` or `do_eval` must be True.")
if not os.path.exists(args.output_dir):
os.makedirs(args.output_dir)
if args.do_train:
logger.addHandler(logging.FileHandler(os.path.join(args.output_dir, "train.log"), 'w'))
else:
logger.addHandler(logging.FileHandler(os.path.join(args.output_dir, "eval.log"), 'w'))
logger.info(sys.argv)
logger.info(args)
logger.info("device: {}, n_gpu: {}".format(
device, n_gpu))
# get label_list
if os.path.exists(os.path.join(args.output_dir, 'label_list.json')):
with open(os.path.join(args.output_dir, 'label_list.json'), 'r') as f:
label_list = json.load(f)
else:
label_list = [args.negative_label] + task_rel_labels[args.task]
with open(os.path.join(args.output_dir, 'label_list.json'), 'w') as f:
json.dump(label_list, f)
label2id = {label: i for i, label in enumerate(label_list)}
id2label = {i: label for i, label in enumerate(label_list)}
num_labels = len(label_list)
tokenizer = AutoTokenizer.from_pretrained(args.model, do_lower_case=args.do_lower_case)
if args.add_new_tokens:
add_marker_tokens(tokenizer, task_ner_labels[args.task])
if os.path.exists(os.path.join(args.output_dir, 'special_tokens.json')):
with open(os.path.join(args.output_dir, 'special_tokens.json'), 'r') as f:
special_tokens = json.load(f)
else:
special_tokens = {}
if args.do_eval and (args.do_train or not(args.eval_test)):
eval_features = convert_examples_to_features(
eval_examples, label2id, args.max_seq_length, tokenizer, special_tokens, unused_tokens=not(args.add_new_tokens))
logger.info("***** Dev *****")
logger.info(" Num examples = %d", len(eval_examples))
logger.info(" Batch size = %d", args.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)
all_sub_idx = torch.tensor([f.sub_idx for f in eval_features], dtype=torch.long)
all_obj_idx = torch.tensor([f.obj_idx for f in eval_features], dtype=torch.long)
eval_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids, all_sub_idx, all_obj_idx)
eval_dataloader = DataLoader(eval_data, batch_size=args.eval_batch_size)
eval_label_ids = all_label_ids
with open(os.path.join(args.output_dir, 'special_tokens.json'), 'w') as f:
json.dump(special_tokens, f)
if args.do_train:
train_features = convert_examples_to_features(
train_examples, label2id, args.max_seq_length, tokenizer, special_tokens, unused_tokens=not(args.add_new_tokens))
if args.train_mode == 'sorted' or args.train_mode == 'random_sorted':
train_features = sorted(train_features, key=lambda f: np.sum(f.input_mask))
else:
random.shuffle(train_features)
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)
all_sub_idx = torch.tensor([f.sub_idx for f in train_features], dtype=torch.long)
all_obj_idx = torch.tensor([f.obj_idx for f in train_features], dtype=torch.long)
train_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids, all_sub_idx, all_obj_idx)
train_dataloader = DataLoader(train_data, batch_size=args.train_batch_size)
train_batches = [batch for batch in train_dataloader]
num_train_optimization_steps = len(train_dataloader) * args.num_train_epochs
logger.info("***** Training *****")
logger.info(" Num examples = %d", len(train_examples))
logger.info(" Batch size = %d", args.train_batch_size)
logger.info(" Num steps = %d", num_train_optimization_steps)
best_result = None
eval_step = max(1, len(train_batches) // args.eval_per_epoch)
lr = args.learning_rate
model = RelationModel.from_pretrained(
args.model, cache_dir=str(PYTORCH_PRETRAINED_BERT_CACHE), num_rel_labels=num_labels)
if hasattr(model, 'bert'):
model.bert.resize_token_embeddings(len(tokenizer))
elif hasattr(model, 'albert'):
model.albert.resize_token_embeddings(len(tokenizer))
else:
raise TypeError("Unknown model class")
model.to(device)
if n_gpu > 1:
model = torch.nn.DataParallel(model)
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 = AdamW(optimizer_grouped_parameters, lr=lr, correct_bias=not(args.bertadam))
scheduler = get_linear_schedule_with_warmup(optimizer, int(num_train_optimization_steps * args.warmup_proportion), num_train_optimization_steps)
start_time = time.time()
global_step = 0
tr_loss = 0
nb_tr_examples = 0
nb_tr_steps = 0
for epoch in range(int(args.num_train_epochs)):
model.train()
logger.info("Start epoch #{} (lr = {})...".format(epoch, lr))
if args.train_mode == 'random' or args.train_mode == 'random_sorted':
random.shuffle(train_batches)
for step, batch in enumerate(train_batches):
batch = tuple(t.to(device) for t in batch)
input_ids, input_mask, segment_ids, label_ids, sub_idx, obj_idx = batch
loss = model(input_ids, segment_ids, input_mask, label_ids, sub_idx, obj_idx)
if n_gpu > 1:
loss = loss.mean()
loss.backward()
tr_loss += loss.item()
nb_tr_examples += input_ids.size(0)
nb_tr_steps += 1
optimizer.step()
scheduler.step()
optimizer.zero_grad()
global_step += 1
if (step + 1) % eval_step == 0:
logger.info('Epoch: {}, Step: {} / {}, used_time = {:.2f}s, loss = {:.6f}'.format(
epoch, step + 1, len(train_batches),
time.time() - start_time, tr_loss / nb_tr_steps))
save_model = False
if args.do_eval:
preds, result, logits = evaluate(model, device, eval_dataloader, eval_label_ids, num_labels, e2e_ngold=eval_nrel)
model.train()
result['global_step'] = global_step
result['epoch'] = epoch
result['learning_rate'] = lr
result['batch_size'] = args.train_batch_size
if (best_result is None) or (result[args.eval_metric] > best_result[args.eval_metric]):
best_result = result
logger.info("!!! Best dev %s (lr=%s, epoch=%d): %.2f" %
(args.eval_metric, str(lr), epoch, result[args.eval_metric] * 100.0))
save_trained_model(args.output_dir, model, tokenizer)
evaluation_results = {}
if args.do_eval:
logger.info(special_tokens)
if args.eval_test:
eval_dataset = test_dataset
eval_examples = test_examples
eval_features = convert_examples_to_features(
test_examples, label2id, args.max_seq_length, tokenizer, special_tokens, unused_tokens=not(args.add_new_tokens))
eval_nrel = test_nrel
logger.info(special_tokens)
logger.info("***** Test *****")
logger.info(" Num examples = %d", len(test_examples))
logger.info(" Batch size = %d", args.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)
all_sub_idx = torch.tensor([f.sub_idx for f in eval_features], dtype=torch.long)
all_obj_idx = torch.tensor([f.obj_idx for f in eval_features], dtype=torch.long)
eval_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids, all_sub_idx, all_obj_idx)
eval_dataloader = DataLoader(eval_data, batch_size=args.eval_batch_size)
eval_label_ids = all_label_ids
model = RelationModel.from_pretrained(args.output_dir, num_rel_labels=num_labels)
model.to(device)
preds, result, logits = evaluate(model, device, eval_dataloader, eval_label_ids, num_labels, e2e_ngold=eval_nrel)
logger.info('*** Evaluation Results ***')
for key in sorted(result.keys()):
logger.info(" %s = %s", key, str(result[key]))
print_pred_json(eval_dataset, eval_examples, preds, id2label, os.path.join(args.output_dir, args.prediction_file))
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--model", default=None, type=str, required=True)
parser.add_argument("--output_dir", default=None, type=str, required=True,
help="The output directory where the model predictions and checkpoints will be written.")
parser.add_argument("--eval_per_epoch", default=10, type=int,
help="How many times it evaluates on dev set per epoch")
parser.add_argument("--max_seq_length", default=128, type=int,
help="The maximum total input sequence length after WordPiece tokenization. \n"
"Sequences longer than this will be truncated, and sequences shorter \n"
"than this will be padded.")
parser.add_argument("--negative_label", default="no_relation", type=str)
parser.add_argument("--do_train", action='store_true', help="Whether to run training.")
parser.add_argument("--train_file", default=None, type=str, help="The path of the training data.")
parser.add_argument("--train_mode", type=str, default='random_sorted', choices=['random', 'sorted', 'random_sorted'])
parser.add_argument("--do_eval", action='store_true', help="Whether to run eval on the dev set.")
parser.add_argument("--do_lower_case", action='store_true', help="Set this flag if you are using an uncased model.")
parser.add_argument("--eval_test", action="store_true", help="Whether to evaluate on final test set.")
parser.add_argument("--eval_with_gold", action="store_true", help="Whether to evaluate the relation model with gold entities provided.")
parser.add_argument("--train_batch_size", default=32, type=int,
help="Total batch size for training.")
parser.add_argument("--eval_batch_size", default=8, type=int,
help="Total batch size for eval.")
parser.add_argument("--eval_metric", default="f1", type=str)
parser.add_argument("--learning_rate", default=None, type=float,
help="The initial learning rate for Adam.")
parser.add_argument("--num_train_epochs", default=3.0, type=float,
help="Total number of training epochs to perform.")
parser.add_argument("--warmup_proportion", default=0.1, type=float,
help="Proportion of training to perform linear learning rate warmup for. "
"E.g., 0.1 = 10%% of training.")
parser.add_argument("--no_cuda", action='store_true',
help="Whether not to use CUDA when available")
parser.add_argument('--seed', type=int, default=0,
help="random seed for initialization")
parser.add_argument("--bertadam", action="store_true", help="If bertadam, then set correct_bias = False")
parser.add_argument("--entity_output_dir", type=str, default=None, help="The directory of the prediction files of the entity model")
parser.add_argument("--entity_predictions_dev", type=str, default="ent_pred_dev.json", help="The entity prediction file of the dev set")
parser.add_argument("--entity_predictions_test", type=str, default="ent_pred_test.json", help="The entity prediction file of the test set")
parser.add_argument("--prediction_file", type=str, default="predictions.json", help="The prediction filename for the relation model")
parser.add_argument('--task', type=str, default=None, required=True, choices=['ace04', 'ace05', 'scierc', 'wiki80','i2b2','tacred'])
parser.add_argument('--context_window', type=int, default=0)
parser.add_argument('--add_new_tokens', action='store_true',
help="Whether to add new tokens as marker tokens instead of using [unusedX] tokens.")
args = parser.parse_args()
main(args)