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run_ner_loc.py
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from __future__ import absolute_import, division, print_function
import argparse
import csv
import json
import logging
import os
import random
import sys
import datetime
from torch.utils.data.sampler import Sampler
import numpy as np
np.set_printoptions(threshold=sys.maxsize)
import torch
import torch.nn.functional as F
from pytorch_transformers import (WEIGHTS_NAME, AdamW, BertConfig,
BertForTokenClassification, BertTokenizer,
WarmupLinearSchedule,BertModel,BertPreTrainedModel)
from torch.utils.data import (DataLoader, RandomSampler, SequentialSampler,
TensorDataset)
from torch.utils.data.distributed import DistributedSampler
from tqdm import tqdm, trange
from seqeval.metrics import classification_report,f1_score
from data_utils_loc import *
from model_loc import Ner
# set up log file
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__)
# set up seed
def seed_torch(seed):
random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.cuda.manual_seed_all(seed) # if you are using multi-GPU.
# torch.backends.cudnn.benchmark = False
# torch.backends.cudnn.enabled = False
# torch.backends.cudnn.deterministic = True
class WeightedCurriculumSampler(Sampler):
def __init__(self, dataset, weights, T=50, competence=0.5):
self.dataset = dataset
self.weights = weights
self.T = T
self.competence = competence
def set_T(self, T):
self.T = T
def set_competence(self, competence):
self.competence = competence
def update_competence(self, t):
square = self.init_competence ** 2
root = np.sqrt(t * (1 - square) / self.epoch + square)
self.competence = min(1, root)
def __iter__(self):
idx = int(self.competence * len(dataset))
weights = torch.as_tensor(self.weights[:idx], dtype = torch.double)
seed = int(torch.empty((), dtype=torch.int64).random_().item())
generator = torch.Generator()
generator.manual_seed(seed)
rand_tensor = torch.multinomial(weights, num_samples, False, generator=generator)
yield from iter(rand_tensor.tolist())
class CurriculumSampler(Sampler):
def __init__(self, dataset, difficulty_score=None, epoch = 50, competence=0.5, neutral=False):
self.dataset = dataset
self.init_competence = competence
self.competence = competence
self.epoch = epoch
self.difficulty_score = difficulty_score
self.neutral = neutral
def update_competence(self, t):
square = self.init_competence ** 2
root = np.sqrt(t * (1 - square) / self.epoch + square)
self.competence = min(1, root)
def set_difficulty_score(self, difficulty_score):
self.difficulty_score = difficulty_score
def set_competence(self, competence):
self.competence = competence
def __iter__(self):
i = 0
if self.difficulty_score is not None and len(self.difficulty_score) != 0 and self.neutral:
while i in range(len(self.difficulty_score)):
if self.difficulty_score[i] > self.competence:
break
i += 1
else:
i = int(self.competence * len(self.dataset))
print('Number of training samples:', i)
seed = int(torch.empty((), dtype=torch.int64).random_().item())
generator = torch.Generator()
generator.manual_seed(seed)
yield from torch.randperm(i, generator=generator).tolist()
class DynamicDataset(TensorDataset):
def init(self, *tensors):
assert all(tensors[0].size(0) == tensor.size(0) for tensor in tensors)
self.tensors = tensors
def __getitem__(self, index):
return tuple(tensor[index] for tensor in self.tensors)
def __len__(self):
return self.tensors[0].size(0)
def permute(self, inds):
self.tensors = list(self.tensors)
for i in range(6):
self.tensors[i] = self.tensors[i][inds]
self.tensors = tuple(self.tensors)
def prepare_data(features):
all_input_ids = torch.tensor([f.input_ids for f in features], dtype=torch.long)
all_input_mask = torch.tensor([f.input_mask for f in features], dtype=torch.long)
all_segment_ids = torch.tensor([f.segment_ids for f in features], dtype=torch.long)
all_label_ids = torch.tensor([f.label_id for f in features], dtype=torch.long)
all_valid_ids = torch.tensor([f.valid_ids for f in features], dtype=torch.long)
all_lmask_ids = torch.tensor([f.label_mask for f in features], dtype=torch.long)
data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids, all_valid_ids,
all_lmask_ids)
return data
def evaluate(eval_dataloader,model,label_map,args,tokenizer,device):
y_true = []
y_pred = []
for batch in tqdm(eval_dataloader,desc="Evaluating"):
batch = tuple(t.to(device) for t in batch)
input_ids, input_mask, segment_ids, label_ids, valid_ids, l_mask = batch
with torch.no_grad():
if args.use_crf:
logits = model(input_ids, segment_ids, input_mask, valid_ids=valid_ids,
attention_mask_label=l_mask)
else:
logits = model(input_ids, segment_ids, input_mask, valid_ids=valid_ids,
attention_mask_label=l_mask)
logits = torch.argmax(F.log_softmax(logits, dim=2), dim=2)
# print(logits)
logits = logits.detach().cpu().numpy()
label_ids = label_ids.to('cpu').numpy()
input_mask = input_mask.to('cpu').numpy()
# print(logits.shape, logits)
for i, label in enumerate(label_ids):
temp_1 = []
temp_2 = []
for j, m in enumerate(label):
if j == 0:
continue
elif label_ids[i][j] == len(label_map): # end of sentence
y_true.append(temp_1)
y_pred.append(temp_2)
break
else:
temp_1.append(label_map[label_ids[i][j]])
try:
if label_map[logits[i][j]] not in ["[CLS]", "[SEP]"]:
temp_2.append(label_map[logits[i][j]])
else:
temp_2.append('O')
except:
#the longest sentence lose some, predict as 'O', this is from the data process and cannot be avoided when valid/label masks both exist
temp_2.append('O')
return y_true,y_pred
def main():
parser = argparse.ArgumentParser()
## Required parameters
parser.add_argument("--data_dir",
default=None,
type=str,
required=True,
help="The input data dir. Should contain the .tsv files (or other data files) for the task.")
parser.add_argument("--bert_model", default=None, type=str, required=True,
help="Bert pre-trained model selected in the list: bert-base-uncased, "
"bert-large-uncased, bert-base-cased, bert-large-cased, bert-base-multilingual-uncased, "
"bert-base-multilingual-cased, bert-base-chinese.")
parser.add_argument("--task_name",
default=None,
type=str,
required=True,
help="The name of the task to train.")
## Other parameters
parser.add_argument("--cache_dir",
default="",
type=str,
help="Where do you want to store the pre-trained models downloaded from s3")
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("--do_train",
action='store_true',
help="Whether to run training.")
parser.add_argument("--do_eval",
action='store_true',
help="Whether to run eval or not.")
parser.add_argument("--eval_on",
default="dev",
help="Whether to run eval on the dev set or test set.")
parser.add_argument("--do_predict",
action='store_true',
help="Whether to predict on test set or not.")
parser.add_argument("--do_lower_case",
action='store_true',
help="Set this flag if you are using an uncased model.")
parser.add_argument("--use_rnn",
action='store_true',
help="Whether to use rnn.")
parser.add_argument("--use_crf",
action='store_true',
help="Whether to use crf.")
parser.add_argument("--train_batch_size",
default=32,
type=int,
help="Total batch size for training.")
parser.add_argument("--eval_batch_size",
default=32,
type=int,
help="Total batch size for eval.")
parser.add_argument("--learning_rate",
default=5e-5,
type=float,
help="The initial learning rate for Adam.")
parser.add_argument("--bert_lr",
default=5e-5,
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("--weight_decay", default=0.01, type=float,
help="Weight deay if we apply some.")
parser.add_argument("--adam_epsilon", default=1e-8, type=float,
help="Epsilon for Adam optimizer.")
parser.add_argument("--max_grad_norm", default=1.0, type=float,
help="Max gradient norm.")
parser.add_argument("--no_cuda",
action='store_true',
help="Whether not to use CUDA when available")
parser.add_argument("--local_rank",
type=int,
default=-1,
help="local_rank for distributed training on gpus")
parser.add_argument('--seed',
type=int,
default=42,
help="random seed for initialization")
parser.add_argument('--gradient_accumulation_steps',
type=int,
default=1,
help="Number of updates steps to accumulate before performing a backward/update pass.")
parser.add_argument('--fp16',
action='store_true',
help="Whether to use 16-bit float precision instead of 32-bit")
parser.add_argument('--fp16_opt_level', type=str, default='O1',
help="For fp16: Apex AMP optimization level selected in ['O0', 'O1', 'O2', and 'O3']."
"See details at https://nvidia.github.io/apex/amp.html")
parser.add_argument('--loss_scale',
type=float, default=0,
help="Loss scaling to improve fp16 numeric stability. Only used when fp16 set to True.\n"
"0 (default value): dynamic loss scaling.\n"
"Positive power of 2: static loss scaling value.\n")
parser.add_argument('--server_ip', type=str, default='', help="Can be used for distant debugging.")
parser.add_argument('--server_port', type=str, default='', help="Can be used for distant debugging.")
parser.add_argument('--curriculum', type=str, default='', help="Determine difficulty score for curriculum learning")
parser.add_argument('--neutral', action='store_true', default=False, help='Whether set the unlabeled samples as neutral ones or not')
parser.add_argument('--initial_competence', type = float, default = 0.5, help='set the initial competence value for curriculum learning')
parser.add_argument('--ordered', action='store_true', default=False)
parser.add_argument('--length_lambda', type=float, default=0, help="weight for sentence length")
parser.add_argument('--complexity_lambda', type=float, default=0, help='weight for complexity')
parser.add_argument('--average_lambda', type=float, default=0, help='weight for average entity length')
parser.add_argument('--oov_lambda', type=float, default=0, help='weight for oov')
parser.add_argument('--cumulative_lambda', type=float, default=0, help='weight for cumulative complexity')
parser.add_argument('--maximum_lambda', type=float, default=0, help='weight for maximum entity length')
parser.add_argument('--ratio_lambda', type=float, default=0, help='weight for entity proportion')
parser.add_argument('--number_lambda', type=float, default=0, help='weight for entity number')
parser.add_argument('--anti', action='store_true', default=False, help='set to use anti-curriculum')
args = parser.parse_args()
output_dir = '_'.join(['./saver/',args.data_dir.split('/')[-1], args.bert_model, str(args.max_seq_length), str(args.learning_rate), str(args.bert_lr), str(args.warmup_proportion),str(args.train_batch_size),str(int(args.num_train_epochs)), str(args.seed) ])
if args.server_ip and args.server_port:
# Distant debugging - see https://code.visualstudio.com/docs/python/debugging#_attach-to-a-local-script
import ptvsd
print("Waiting for debugger attach")
ptvsd.enable_attach(address=(args.server_ip, args.server_port), redirect_output=True)
ptvsd.wait_for_attach()
if os.path.exists(output_dir) and os.listdir(output_dir) and args.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)
fh = logging.FileHandler(output_dir+'/logging.log', mode="w", encoding="utf-8")
logger.addHandler(fh)
processors = {"ner":NerProcessor}
if args.local_rank == -1 or args.no_cuda:
device = torch.device("cuda" if torch.cuda.is_available() and not args.no_cuda else "cpu")
n_gpu = torch.cuda.device_count()
else:
torch.cuda.set_device(args.local_rank)
device = torch.device("cuda", args.local_rank)
n_gpu = 1
# Initializes the distributed backend which will take care of sychronizing nodes/GPUs
torch.distributed.init_process_group(backend='nccl')
logger.info("device: {} n_gpu: {}, distributed training: {}, 16-bits training: {}".format(
device, n_gpu, bool(args.local_rank != -1), args.fp16))
if args.gradient_accumulation_steps < 1:
raise ValueError("Invalid gradient_accumulation_steps parameter: {}, should be >= 1".format(
args.gradient_accumulation_steps))
args.train_batch_size = args.train_batch_size // args.gradient_accumulation_steps
seed_torch(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.")
task_name = args.task_name.lower()
if task_name not in processors:
raise ValueError("Task not found: %s" % (task_name))
processor = processors[task_name]()
label_list = processor.get_labels(args.data_dir)
num_labels = len(label_list) + 1 # why plus 1? because of the pad id 0
label_map = {i : label for i, label in enumerate(label_list,1)} # start from 1, 0 is keeped
tag2ix = {label: i for i, label in enumerate(label_list, 1)}
tokenizer = BertTokenizer.from_pretrained(args.bert_model, do_lower_case=args.do_lower_case)
train_examples = None
num_train_optimization_steps = 0
if args.do_train:
train_examples = processor.get_train_examples(args.data_dir)
num_train_optimization_steps = int(
len(train_examples) / args.train_batch_size / args.gradient_accumulation_steps) * args.num_train_epochs
if args.local_rank != -1:
num_train_optimization_steps = num_train_optimization_steps // torch.distributed.get_world_size()
if args.local_rank not in [-1, 0]:
torch.distributed.barrier() # Make sure only the first process in distributed training will download model & vocab
# Prepare model
config = BertConfig.from_pretrained(args.bert_model, num_labels=num_labels, finetuning_task=args.task_name)
model = Ner(args.bert_model,from_tf = False, config = config,tag_to_ix=tag2ix, device=device, use_rnn=args.use_rnn, use_crf=args.use_crf)
if args.local_rank == 0:
torch.distributed.barrier() # Make sure only the first process in distributed training will download model & vocab
model.to(device)
param_optimizer = list(model.named_parameters())
no_decay = ['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)) and ('bert' in n )) ],'lr': args.bert_lr, 'weight_decay': args.weight_decay},
{'params': [p for n, p in param_optimizer if ((not any(nd in n for nd in no_decay)) and ( not 'bert' in n )) ],'lr': args.learning_rate, 'weight_decay': args.weight_decay},
{'params': [p for n, p in param_optimizer if ((any(nd in n for nd in no_decay)) and ('bert' in n))],'lr': args.bert_lr, 'weight_decay': 0.0},
{'params': [p for n, p in param_optimizer if ((any(nd in n for nd in no_decay)) and (not 'bert' in n))] ,'lr': args.learning_rate, 'weight_decay': 0.0}
]
warmup_steps = int(args.warmup_proportion * num_train_optimization_steps)
optimizer = AdamW(optimizer_grouped_parameters, lr=args.learning_rate, eps=args.adam_epsilon)
scheduler = WarmupLinearSchedule(optimizer, warmup_steps=warmup_steps, t_total=num_train_optimization_steps)
if args.fp16:
try:
from apex import amp
except ImportError:
raise ImportError("Please install apex from https://www.github.com/nvidia/apex to use fp16 training.")
model, optimizer = amp.initialize(model, optimizer, opt_level=args.fp16_opt_level)
# multi-gpu training (should be after apex fp16 initialization)
if n_gpu > 1:
model = torch.nn.DataParallel(model)
if args.local_rank != -1:
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[args.local_rank],
output_device=args.local_rank,
find_unused_parameters=True)
global_step = 0
nb_tr_steps = 0
tr_loss = 0
if args.do_train:
print(args.curriculum, args.neutral)
weights = np.array([args.complexity_lambda, args.maximum_lambda])
train_features, difficulty_score = convert_examples_to_features(
train_examples, label_list, args.max_seq_length, tokenizer, True, args.curriculum, neutral=args.neutral, ordered=args.ordered, word_emb_dir='glove/glove.twitter.27B.100d.txt', weights=weights, anti=args.anti)
logger.info("***** Running 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)
train_data = prepare_data(train_features)
if len(difficulty_score) != 0:
difficulty_score = difficulty_score / np.max(difficulty_score)
print(difficulty_score)
print(len(difficulty_score))
if args.neutral and len(difficulty_score) != 0:
init_comp = np.quantile(difficulty_score, args.initial_competence)
else:
init_comp = args.initial_competence
if args.curriculum != '':
train_sampler = CurriculumSampler(train_data,difficulty_score = difficulty_score, epoch = 25, competence=init_comp, neutral=args.neutral)
elif args.local_rank == -1:
train_sampler = RandomSampler(train_data)
else:
train_sampler = DistributedSampler(train_data)
train_dataloader = DataLoader(train_data, sampler=train_sampler, batch_size=args.train_batch_size)
# Dev data
if args.do_eval:
logger.info("***** evaluation data process*****")
eval_examples = processor.get_dev_examples(args.data_dir)
logger.info(" Num eval examples = %d", len(eval_examples))
eval_features = convert_examples_to_features(eval_examples, label_list, args.max_seq_length, tokenizer)
eval_data = prepare_data(eval_features)
eval_sampler = SequentialSampler(eval_data)
eval_dataloader = DataLoader(eval_data, sampler=eval_sampler, batch_size=args.eval_batch_size)
test_examples = processor.get_test_examples(args.data_dir)
test_features = convert_examples_to_features(test_examples, label_list, args.max_seq_length, tokenizer)
logger.info(" Num test examples = %d", len(test_examples))
test_data = prepare_data(test_features)
test_sampler = SequentialSampler(test_data)
test_dataloader = DataLoader(test_data, sampler=test_sampler, batch_size=args.eval_batch_size)
max_eval_f1 = -1
for epoch in range(int(args.num_train_epochs)):
model.train()
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, valid_ids, l_mask = batch
loss = model(input_ids, segment_ids, input_mask, label_ids, valid_ids, l_mask)
if n_gpu > 1:
loss = loss.mean() # mean() to average on multi-gpu.
if args.gradient_accumulation_steps > 1:
loss = loss / args.gradient_accumulation_steps
if args.fp16:
with amp.scale_loss(loss, optimizer) as scaled_loss:
scaled_loss.backward()
torch.nn.utils.clip_grad_norm_(amp.master_params(optimizer), args.max_grad_norm)
else:
loss.backward()
torch.nn.utils.clip_grad_norm_(model.parameters(), args.max_grad_norm)
tr_loss += loss.item()
nb_tr_examples += input_ids.size(0)
nb_tr_steps += 1
if nb_tr_steps %20 ==0:
logger.info('loss[%d,%d]: %f' %(epoch+1,nb_tr_steps,tr_loss/nb_tr_steps))
if (step + 1) % args.gradient_accumulation_steps == 0:
optimizer.step()
scheduler.step() # Update learning rate schedule
model.zero_grad()
global_step += 1
# Evaluation after each epoch
if args.do_eval and (args.local_rank == -1 or torch.distributed.get_rank() == 0):
model.eval()
logger.info("***** Running evaluation *****")
logger.info(" Num examples = %d", len(eval_examples))
logger.info(" Batch size = %d", args.eval_batch_size)
eval_loss, eval_accuracy = 0, 0
nb_eval_steps, nb_eval_examples = 0, 0
y_true, y_pred = evaluate(eval_dataloader,model,label_map,args,tokenizer, device)
report = classification_report(y_true, y_pred, digits=6)
logger.info("***** Eval results *****")
logger.info("\n%s", report)
eval_f1 = f1_score(y_true,y_pred)
print(datetime.datetime.now(), eval_f1)
if eval_f1 > max_eval_f1:
max_eval_f1 = eval_f1
output_eval_file = os.path.join(output_dir, "eval_results.txt")
write2report(output_eval_file, report)
write2file(eval_examples,y_true, y_pred, os.path.join(output_dir, "eval_results.conll"))
# Save a trained model and the associated configuration
save_dir = output_dir + '/best_model/'
if not os.path.exists(save_dir):
os.makedirs(save_dir)
logger.info("Save best model to: %s", save_dir)
torch.save(model.state_dict(), os.path.join(save_dir, 'best_model.pt'))
model_config = {"bert_model": args.bert_model, "do_lower": args.do_lower_case,
"max_seq_length": args.max_seq_length, "num_labels": len(label_list) + 1,
"label_map": label_map}
json.dump(model_config, open(os.path.join(save_dir, "model_config.json"), "w"))
test_y_true, test_y_pred = evaluate(test_dataloader,model,label_map,args,tokenizer, device)
test_report = classification_report(test_y_true, test_y_pred, digits=6)
logger.info("***** Test results *****")
logger.info("\n%s", test_report)
logger.info("best f1 till now: %f", max_eval_f1)
if args.curriculum != '':
train_dataloader.sampler.update_competence(epoch)
if args.do_predict:
# Load a trained model and vocabulary that you have fine-tuned
config = BertConfig.from_pretrained(args.bert_model, num_labels=num_labels, finetuning_task=args.task_name)
tokenizer = BertTokenizer.from_pretrained(args.bert_model, do_lower_case=args.do_lower_case)
model = Ner(args.bert_model, from_tf=False, config=config, tag_to_ix=tag2ix, device=device, use_rnn=args.use_rnn, use_crf=args.use_crf)
model.to(device)
if n_gpu > 1:
model = torch.nn.DataParallel(model)
if args.local_rank != -1:
model = torch.nn.parallel.DistributedDataParallel(model, device_ids=[args.local_rank],
output_device=args.local_rank,
find_unused_parameters=True)
save_dir = output_dir + '/best_model/'
model.load_state_dict(torch.load(os.path.join(save_dir,'best_model.pt')))
test_examples = processor.get_test_examples(args.data_dir)
test_features = convert_examples_to_features(test_examples, label_list, args.max_seq_length, tokenizer)
logger.info("***** Running prediction *****")
logger.info(" Num examples = %d", len(test_examples))
logger.info(" Batch size = %d", args.eval_batch_size)
test_data = prepare_data(test_features)
test_sampler = SequentialSampler(test_data)
test_dataloader = DataLoader(test_data, sampler=test_sampler, batch_size=args.eval_batch_size)
model.eval()
y_true, y_pred = evaluate(test_dataloader,model,label_map,args,tokenizer, device)
report = classification_report(y_true, y_pred, digits=6)
logger.info("***** Test results *****")
logger.info("\n%s", report)
output_test_file = os.path.join(output_dir, "test_results.txt")
write2report(output_test_file, report)
write2file(test_examples, y_true, y_pred, os.path.join(output_dir, "test_results.conll"))
if __name__ == "__main__":
main()