transformers/examples/run_tf_ner.py

616 lines
26 KiB
Python

# coding=utf-8
import datetime
import os
import math
import glob
import re
import tensorflow as tf
import collections
import numpy as np
from seqeval import metrics
import _pickle as pickle
from absl import logging
from transformers import TF2_WEIGHTS_NAME, BertConfig, BertTokenizer, TFBertForTokenClassification
from transformers import RobertaConfig, RobertaTokenizer, TFRobertaForTokenClassification
from transformers import DistilBertConfig, DistilBertTokenizer, TFDistilBertForTokenClassification
from transformers import create_optimizer, GradientAccumulator
from utils_ner import convert_examples_to_features, get_labels, read_examples_from_file
from fastprogress import master_bar, progress_bar
from absl import flags
from absl import app
ALL_MODELS = sum(
(tuple(conf.pretrained_config_archive_map.keys()) for conf in (BertConfig, RobertaConfig, DistilBertConfig)),
())
MODEL_CLASSES = {
"bert": (BertConfig, TFBertForTokenClassification, BertTokenizer),
"roberta": (RobertaConfig, TFRobertaForTokenClassification, RobertaTokenizer),
"distilbert": (DistilBertConfig, TFDistilBertForTokenClassification, DistilBertTokenizer)
}
flags.DEFINE_string(
"data_dir", None,
"The input data dir. Should contain the .conll files (or other data files) "
"for the task.")
flags.DEFINE_string(
"model_type", None,
"Model type selected in the list: " + ", ".join(MODEL_CLASSES.keys()))
flags.DEFINE_string(
"model_name_or_path", None,
"Path to pre-trained model or shortcut name selected in the list: " + ", ".join(ALL_MODELS))
flags.DEFINE_string(
"output_dir", None,
"The output directory where the model checkpoints will be written.")
flags.DEFINE_string(
"labels", "",
"Path to a file containing all labels. If not specified, CoNLL-2003 labels are used.")
flags.DEFINE_string(
"config_name", "",
"Pretrained config name or path if not the same as model_name")
flags.DEFINE_string(
"tokenizer_name", "",
"Pretrained tokenizer name or path if not the same as model_name")
flags.DEFINE_string(
"cache_dir", "",
"Where do you want to store the pre-trained models downloaded from s3")
flags.DEFINE_integer(
"max_seq_length", 128,
"The maximum total input sentence length after tokenization. "
"Sequences longer than this will be truncated, sequences shorter "
"will be padded.")
flags.DEFINE_string(
"tpu", None,
"The Cloud TPU to use for training. This should be either the name "
"used when creating the Cloud TPU, or a grpc://ip.address.of.tpu:8470 "
"url.")
flags.DEFINE_integer(
"num_tpu_cores", 8,
"Total number of TPU cores to use.")
flags.DEFINE_boolean(
"do_train", False,
"Whether to run training.")
flags.DEFINE_boolean(
"do_eval", False,
"Whether to run eval on the dev set.")
flags.DEFINE_boolean(
"do_predict", False,
"Whether to run predictions on the test set.")
flags.DEFINE_boolean(
"evaluate_during_training", False,
"Whether to run evaluation during training at each logging step.")
flags.DEFINE_boolean(
"do_lower_case", False,
"Set this flag if you are using an uncased model.")
flags.DEFINE_integer(
"per_device_train_batch_size", 8,
"Batch size per GPU/CPU/TPU for training.")
flags.DEFINE_integer(
"per_device_eval_batch_size", 8,
"Batch size per GPU/CPU/TPU for evaluation.")
flags.DEFINE_integer(
"gradient_accumulation_steps", 1,
"Number of updates steps to accumulate before performing a backward/update pass.")
flags.DEFINE_float(
"learning_rate", 5e-5,
"The initial learning rate for Adam.")
flags.DEFINE_float(
"weight_decay", 0.0,
"Weight decay if we apply some.")
flags.DEFINE_float(
"adam_epsilon", 1e-8,
"Epsilon for Adam optimizer.")
flags.DEFINE_float(
"max_grad_norm", 1.0,
"Max gradient norm.")
flags.DEFINE_integer(
"num_train_epochs", 3,
"Total number of training epochs to perform.")
flags.DEFINE_integer(
"max_steps", -1,
"If > 0: set total number of training steps to perform. Override num_train_epochs.")
flags.DEFINE_integer(
"warmup_steps", 0,
"Linear warmup over warmup_steps.")
flags.DEFINE_integer(
"logging_steps", 50,
"Log every X updates steps.")
flags.DEFINE_integer(
"save_steps", 50,
"Save checkpoint every X updates steps.")
flags.DEFINE_boolean(
"eval_all_checkpoints", False,
"Evaluate all checkpoints starting with the same prefix as model_name ending and ending with step number")
flags.DEFINE_boolean(
"no_cuda", False,
"Avoid using CUDA when available")
flags.DEFINE_boolean(
"overwrite_output_dir", False,
"Overwrite the content of the output directory")
flags.DEFINE_boolean(
"overwrite_cache", False,
"Overwrite the cached training and evaluation sets")
flags.DEFINE_integer(
"seed", 42,
"random seed for initialization")
flags.DEFINE_boolean(
"fp16", False,
"Whether to use 16-bit (mixed) precision instead of 32-bit")
flags.DEFINE_string(
"gpus", "0",
"Comma separated list of gpus devices. If only one, switch to single "
"gpu strategy, if None takes all the gpus available.")
def train(args, strategy, train_dataset, tokenizer, model, num_train_examples, labels, train_batch_size, pad_token_label_id):
if args['max_steps'] > 0:
num_train_steps = args['max_steps'] * args['gradient_accumulation_steps']
args['num_train_epochs'] = 1
else:
num_train_steps = math.ceil(num_train_examples / train_batch_size) // args['gradient_accumulation_steps'] * args['num_train_epochs']
writer = tf.summary.create_file_writer("/tmp/mylogs")
with strategy.scope():
loss_fct = tf.keras.losses.SparseCategoricalCrossentropy(reduction=tf.keras.losses.Reduction.NONE)
optimizer = create_optimizer(args['learning_rate'], num_train_steps, args['warmup_steps'])
if args['fp16']:
optimizer = tf.keras.mixed_precision.experimental.LossScaleOptimizer(optimizer, 'dynamic')
loss_metric = tf.keras.metrics.Mean(name='loss', dtype=tf.float32)
gradient_accumulator = GradientAccumulator()
logging.info("***** Running training *****")
logging.info(" Num examples = %d", num_train_examples)
logging.info(" Num Epochs = %d", args['num_train_epochs'])
logging.info(" Instantaneous batch size per device = %d", args['per_device_train_batch_size'])
logging.info(" Total train batch size (w. parallel, distributed & accumulation) = %d",
train_batch_size * args['gradient_accumulation_steps'])
logging.info(" Gradient Accumulation steps = %d", args['gradient_accumulation_steps'])
logging.info(" Total training steps = %d", num_train_steps)
model.summary()
@tf.function
def apply_gradients():
grads_and_vars = []
for gradient, variable in zip(gradient_accumulator.gradients, model.trainable_variables):
if gradient is not None:
scaled_gradient = gradient / (args['n_device'] * args['gradient_accumulation_steps'])
grads_and_vars.append((scaled_gradient, variable))
else:
grads_and_vars.append((gradient, variable))
optimizer.apply_gradients(grads_and_vars, args['max_grad_norm'])
gradient_accumulator.reset()
@tf.function
def train_step(train_features, train_labels):
def step_fn(train_features, train_labels):
inputs = {'attention_mask': train_features['input_mask'], 'training': True}
if args['model_type'] != "distilbert":
inputs["token_type_ids"] = train_features['segment_ids'] if args['model_type'] in ["bert", "xlnet"] else None
with tf.GradientTape() as tape:
logits = model(train_features['input_ids'], **inputs)[0]
logits = tf.reshape(logits, (-1, len(labels) + 1))
active_loss = tf.reshape(train_features['input_mask'], (-1,))
active_logits = tf.boolean_mask(logits, active_loss)
train_labels = tf.reshape(train_labels, (-1,))
active_labels = tf.boolean_mask(train_labels, active_loss)
cross_entropy = loss_fct(active_labels, active_logits)
loss = tf.reduce_sum(cross_entropy) * (1.0 / train_batch_size)
grads = tape.gradient(loss, model.trainable_variables)
gradient_accumulator(grads)
return cross_entropy
per_example_losses = strategy.experimental_run_v2(step_fn, args=(train_features, train_labels))
mean_loss = strategy.reduce(tf.distribute.ReduceOp.MEAN, per_example_losses, axis=0)
return mean_loss
current_time = datetime.datetime.now()
train_iterator = master_bar(range(args['num_train_epochs']))
global_step = 0
logging_loss = 0.0
for epoch in train_iterator:
epoch_iterator = progress_bar(train_dataset, total=num_train_steps, parent=train_iterator, display=args['n_device'] > 1)
step = 1
with strategy.scope():
for train_features, train_labels in epoch_iterator:
loss = train_step(train_features, train_labels)
if step % args['gradient_accumulation_steps'] == 0:
strategy.experimental_run_v2(apply_gradients)
loss_metric(loss)
global_step += 1
if args['logging_steps'] > 0 and global_step % args['logging_steps'] == 0:
# Log metrics
if args['n_device'] == 1 and args['evaluate_during_training']: # Only evaluate when single GPU otherwise metrics may not average well
y_true, y_pred, eval_loss = evaluate(args, strategy, model, tokenizer, labels, pad_token_label_id, mode="dev")
report = metrics.classification_report(y_true, y_pred, digits=4)
logging.info("Eval at step " + str(global_step) + "\n" + report)
logging.info("eval_loss: " + str(eval_loss))
precision = metrics.precision_score(y_true, y_pred)
recall = metrics.recall_score(y_true, y_pred)
f1 = metrics.f1_score(y_true, y_pred)
with writer.as_default():
tf.summary.scalar("eval_loss", eval_loss, global_step)
tf.summary.scalar("precision", precision, global_step)
tf.summary.scalar("recall", recall, global_step)
tf.summary.scalar("f1", f1, global_step)
lr = optimizer.learning_rate
learning_rate = lr(step)
with writer.as_default():
tf.summary.scalar("lr", learning_rate, global_step)
tf.summary.scalar("loss", (loss_metric.result() - logging_loss) / args['logging_steps'], global_step)
logging_loss = loss_metric.result()
with writer.as_default():
tf.summary.scalar("loss", loss_metric.result(), step=step)
if args['save_steps'] > 0 and global_step % args['save_steps'] == 0:
# Save model checkpoint
output_dir = os.path.join(args['output_dir'], "checkpoint-{}".format(global_step))
if not os.path.exists(output_dir):
os.makedirs(output_dir)
model.save_pretrained(output_dir)
logging.info("Saving model checkpoint to %s", output_dir)
train_iterator.child.comment = f'loss : {loss_metric.result()}'
step += 1
train_iterator.write(f'loss epoch {epoch + 1}: {loss_metric.result()}')
loss_metric.reset_states()
logging.info(" Training took time = {}".format(datetime.datetime.now() - current_time))
def evaluate(args, strategy, model, tokenizer, labels, pad_token_label_id, mode):
eval_batch_size = args['per_device_eval_batch_size'] * args['n_device']
eval_dataset, size = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, eval_batch_size, mode=mode)
eval_dataset = strategy.experimental_distribute_dataset(eval_dataset)
preds = None
num_eval_steps = math.ceil(size / eval_batch_size)
master = master_bar(range(1))
eval_iterator = progress_bar(eval_dataset, total=num_eval_steps, parent=master, display=args['n_device'] > 1)
loss_fct = tf.keras.losses.SparseCategoricalCrossentropy(reduction=tf.keras.losses.Reduction.NONE)
loss = 0.0
logging.info("***** Running evaluation *****")
logging.info(" Num examples = %d", size)
logging.info(" Batch size = %d", eval_batch_size)
for eval_features, eval_labels in eval_iterator:
inputs = {'attention_mask': eval_features['input_mask'], 'training': False}
if args['model_type'] != "distilbert":
inputs["token_type_ids"] = eval_features['segment_ids'] if args['model_type'] in ["bert", "xlnet"] else None
with strategy.scope():
logits = model(eval_features['input_ids'], **inputs)[0]
tmp_logits = tf.reshape(logits, (-1, len(labels) + 1))
active_loss = tf.reshape(eval_features['input_mask'], (-1,))
active_logits = tf.boolean_mask(tmp_logits, active_loss)
tmp_eval_labels = tf.reshape(eval_labels, (-1,))
active_labels = tf.boolean_mask(tmp_eval_labels, active_loss)
cross_entropy = loss_fct(active_labels, active_logits)
loss += tf.reduce_sum(cross_entropy) * (1.0 / eval_batch_size)
if preds is None:
preds = logits.numpy()
label_ids = eval_labels.numpy()
else:
preds = np.append(preds, logits.numpy(), axis=0)
label_ids = np.append(label_ids, eval_labels.numpy(), axis=0)
preds = np.argmax(preds, axis=2)
y_pred = [[] for _ in range(label_ids.shape[0])]
y_true = [[] for _ in range(label_ids.shape[0])]
loss = loss / num_eval_steps
for i in range(label_ids.shape[0]):
for j in range(label_ids.shape[1]):
if label_ids[i, j] != pad_token_label_id:
y_pred[i].append(labels[preds[i, j] - 1])
y_true[i].append(labels[label_ids[i, j] - 1])
return y_true, y_pred, loss.numpy()
def load_cache(cached_file, max_seq_length):
name_to_features = {
"input_ids": tf.io.FixedLenFeature([max_seq_length], tf.int64),
"input_mask": tf.io.FixedLenFeature([max_seq_length], tf.int64),
"segment_ids": tf.io.FixedLenFeature([max_seq_length], tf.int64),
"label_ids": tf.io.FixedLenFeature([max_seq_length], tf.int64),
}
def _decode_record(record):
example = tf.io.parse_single_example(record, name_to_features)
features = {}
features['input_ids'] = example['input_ids']
features['input_mask'] = example['input_mask']
features['segment_ids'] = example['segment_ids']
return features, example['label_ids']
d = tf.data.TFRecordDataset(cached_file)
d = d.map(_decode_record, num_parallel_calls=4)
count = d.reduce(0, lambda x, _: x + 1)
return d, count.numpy()
def save_cache(features, cached_features_file):
writer = tf.io.TFRecordWriter(cached_features_file)
for (ex_index, feature) in enumerate(features):
if ex_index % 5000 == 0:
logging.info("Writing example %d of %d" % (ex_index, len(features)))
def create_int_feature(values):
f = tf.train.Feature(int64_list=tf.train.Int64List(value=list(values)))
return f
record_feature = collections.OrderedDict()
record_feature["input_ids"] = create_int_feature(feature.input_ids)
record_feature["input_mask"] = create_int_feature(feature.input_mask)
record_feature["segment_ids"] = create_int_feature(feature.segment_ids)
record_feature["label_ids"] = create_int_feature(feature.label_ids)
tf_example = tf.train.Example(features=tf.train.Features(feature=record_feature))
writer.write(tf_example.SerializeToString())
writer.close()
def load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, batch_size, mode):
drop_remainder = True if args['tpu'] or mode == 'train' else False
# Load data features from cache or dataset file
cached_features_file = os.path.join(args['data_dir'], "cached_{}_{}_{}.tf_record".format(mode,
list(filter(None, args['model_name_or_path'].split("/"))).pop(),
str(args['max_seq_length'])))
if os.path.exists(cached_features_file) and not args['overwrite_cache']:
logging.info("Loading features from cached file %s", cached_features_file)
dataset, size = load_cache(cached_features_file, args['max_seq_length'])
else:
logging.info("Creating features from dataset file at %s", args['data_dir'])
examples = read_examples_from_file(args['data_dir'], mode)
features = convert_examples_to_features(examples, labels, args['max_seq_length'], tokenizer,
cls_token_at_end=bool(args['model_type'] in ["xlnet"]),
# xlnet has a cls token at the end
cls_token=tokenizer.cls_token,
cls_token_segment_id=2 if args['model_type'] in ["xlnet"] else 0,
sep_token=tokenizer.sep_token,
sep_token_extra=bool(args['model_type'] in ["roberta"]),
# roberta uses an extra separator b/w pairs of sentences, cf. github.com/pytorch/fairseq/commit/1684e166e3da03f5b600dbb7855cb98ddfcd0805
pad_on_left=bool(args['model_type'] in ["xlnet"]),
# pad on the left for xlnet
pad_token=tokenizer.convert_tokens_to_ids([tokenizer.pad_token])[0],
pad_token_segment_id=4 if args['model_type'] in ["xlnet"] else 0,
pad_token_label_id=pad_token_label_id
)
logging.info("Saving features into cached file %s", cached_features_file)
save_cache(features, cached_features_file)
dataset, size = load_cache(cached_features_file, args['max_seq_length'])
if mode == 'train':
dataset = dataset.repeat()
dataset = dataset.shuffle(buffer_size=8192, seed=args['seed'])
dataset = dataset.batch(batch_size, drop_remainder)
dataset = dataset.prefetch(buffer_size=batch_size)
return dataset, size
def main(_):
logging.set_verbosity(logging.INFO)
args = flags.FLAGS.flag_values_dict()
if os.path.exists(args['output_dir']) and os.listdir(
args['output_dir']) and args['do_train'] and not args['overwrite_output_dir']:
raise ValueError(
"Output directory ({}) already exists and is not empty. Use --overwrite_output_dir to overcome.".format(
args['output_dir']))
if args['fp16']:
tf.config.optimizer.set_experimental_options({"auto_mixed_precision": True})
if args['tpu']:
resolver = tf.distribute.cluster_resolver.TPUClusterResolver(tpu=args['tpu'])
tf.config.experimental_connect_to_cluster(resolver)
tf.tpu.experimental.initialize_tpu_system(resolver)
strategy = tf.distribute.experimental.TPUStrategy(resolver)
args['n_device'] = args['num_tpu_cores']
elif len(args['gpus'].split(',')) > 1:
args['n_device'] = len([f"/gpu:{gpu}" for gpu in args['gpus'].split(',')])
strategy = tf.distribute.MirroredStrategy(devices=[f"/gpu:{gpu}" for gpu in args['gpus'].split(',')])
elif args['no_cuda']:
args['n_device'] = 1
strategy = tf.distribute.OneDeviceStrategy(device="/cpu:0")
else:
args['n_device'] = len(args['gpus'].split(','))
strategy = tf.distribute.OneDeviceStrategy(device="/gpu:" + args['gpus'].split(',')[0])
logging.warning("n_device: %s, distributed training: %s, 16-bits training: %s",
args['n_device'], bool(args['n_device'] > 1), args['fp16'])
labels = get_labels(args['labels'])
num_labels = len(labels) + 1
pad_token_label_id = 0
config_class, model_class, tokenizer_class = MODEL_CLASSES[args['model_type']]
config = config_class.from_pretrained(args['config_name'] if args['config_name'] else args['model_name_or_path'],
num_labels=num_labels,
cache_dir=args['cache_dir'] if args['cache_dir'] else None)
logging.info("Training/evaluation parameters %s", args)
# Training
if args['do_train']:
tokenizer = tokenizer_class.from_pretrained(args['tokenizer_name'] if args['tokenizer_name'] else args['model_name_or_path'],
do_lower_case=args['do_lower_case'],
cache_dir=args['cache_dir'] if args['cache_dir'] else None)
with strategy.scope():
model = model_class.from_pretrained(args['model_name_or_path'],
from_pt=bool(".bin" in args['model_name_or_path']),
config=config,
cache_dir=args['cache_dir'] if args['cache_dir'] else None)
model.layers[-1].activation = tf.keras.activations.softmax
train_batch_size = args['per_device_train_batch_size'] * args['n_device']
train_dataset, num_train_examples = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, train_batch_size, mode="train")
train_dataset = strategy.experimental_distribute_dataset(train_dataset)
train(args, strategy, train_dataset, tokenizer, model, num_train_examples, labels, train_batch_size, pad_token_label_id)
if not os.path.exists(args['output_dir']):
os.makedirs(args['output_dir'])
logging.info("Saving model to %s", args['output_dir'])
model.save_pretrained(args['output_dir'])
tokenizer.save_pretrained(args['output_dir'])
# Evaluation
if args['do_eval']:
tokenizer = tokenizer_class.from_pretrained(args['output_dir'], do_lower_case=args['do_lower_case'])
checkpoints = []
results = []
if args['eval_all_checkpoints']:
checkpoints = list(os.path.dirname(c) for c in sorted(glob.glob(args['output_dir'] + "/**/" + TF2_WEIGHTS_NAME, recursive=True), key=lambda f: int(''.join(filter(str.isdigit, f)) or -1)))
logging.info("Evaluate the following checkpoints: %s", checkpoints)
if len(checkpoints) == 0:
checkpoints.append(args['output_dir'])
for checkpoint in checkpoints:
global_step = checkpoint.split("-")[-1] if re.match(".*checkpoint-[0-9]", checkpoint) else "final"
with strategy.scope():
model = model_class.from_pretrained(checkpoint)
y_true, y_pred, eval_loss = evaluate(args, strategy, model, tokenizer, labels, pad_token_label_id, mode="dev")
report = metrics.classification_report(y_true, y_pred, digits=4)
if global_step:
results.append({global_step + "_report": report, global_step + "_loss": eval_loss})
output_eval_file = os.path.join(args['output_dir'], "eval_results.txt")
with tf.io.gfile.GFile(output_eval_file, "w") as writer:
for res in results:
for key, val in res.items():
if "loss" in key:
logging.info(key + " = " + str(val))
writer.write(key + " = " + str(val))
writer.write("\n")
else:
logging.info(key)
logging.info("\n" + report)
writer.write(key + "\n")
writer.write(report)
writer.write("\n")
if args['do_predict']:
tokenizer = tokenizer_class.from_pretrained(args['output_dir'], do_lower_case=args['do_lower_case'])
model = model_class.from_pretrained(args['output_dir'])
eval_batch_size = args['per_device_eval_batch_size'] * args['n_device']
predict_dataset, _ = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, eval_batch_size, mode="test")
y_true, y_pred, pred_loss = evaluate(args, strategy, model, tokenizer, labels, pad_token_label_id, mode="test")
output_test_results_file = os.path.join(args['output_dir'], "test_results.txt")
output_test_predictions_file = os.path.join(args['output_dir'], "test_predictions.txt")
report = metrics.classification_report(y_true, y_pred, digits=4)
with tf.io.gfile.GFile(output_test_results_file, "w") as writer:
report = metrics.classification_report(y_true, y_pred, digits=4)
logging.info("\n" + report)
writer.write(report)
writer.write("\n\nloss = " + str(pred_loss))
with tf.io.gfile.GFile(output_test_predictions_file, "w") as writer:
with tf.io.gfile.GFile(os.path.join(args['data_dir'], "test.txt"), "r") as f:
example_id = 0
for line in f:
if line.startswith("-DOCSTART-") or line == "" or line == "\n":
writer.write(line)
if not y_pred[example_id]:
example_id += 1
elif y_pred[example_id]:
output_line = line.split()[0] + " " + y_pred[example_id].pop(0) + "\n"
writer.write(output_line)
else:
logging.warning("Maximum sequence length exceeded: No prediction for '%s'.", line.split()[0])
if __name__ == "__main__":
flags.mark_flag_as_required("data_dir")
flags.mark_flag_as_required("output_dir")
flags.mark_flag_as_required("model_name_or_path")
flags.mark_flag_as_required("model_type")
app.run(main)