run_ner.py

from __future__ import absolute_import, division, print_function

import argparse
import csv
import json
import logging
import os
import random
import sys

import numpy as np
import torch
import torch.nn.functional as F
from pytorch_transformers import (WEIGHTS_NAME, AdamW, BertConfig,
                                  BertForTokenClassification, BertTokenizer,
                                  WarmupLinearSchedule)
from torch import nn
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

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 Ner(BertForTokenClassification):

    def forward(self, input_ids, token_type_ids=None, attention_mask=None, labels=None,valid_ids=None,attention_mask_label=None):
        sequence_output = self.bert(input_ids, token_type_ids, attention_mask,head_mask=None)[0]
        batch_size,max_len,feat_dim = sequence_output.shape
        valid_output = torch.zeros(batch_size,max_len,feat_dim,dtype=torch.float32,device='cuda')
        for i in range(batch_size):
            jj = -1
            for j in range(max_len):
                    if valid_ids[i][j].item() == 1:
                        jj += 1
                        valid_output[i][jj] = sequence_output[i][j]
        sequence_output = self.dropout(valid_output)
        logits = self.classifier(sequence_output)

        if labels is not None:
            loss_fct = nn.CrossEntropyLoss(ignore_index=0)
            # Only keep active parts of the loss
            #attention_mask_label = None
            if attention_mask_label is not None:
                active_loss = attention_mask_label.view(-1) == 1
                active_logits = logits.view(-1, self.num_labels)[active_loss]
                active_labels = labels.view(-1)[active_loss]
                loss = loss_fct(active_logits, active_labels)
            else:
                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
            return loss
        else:
            return logits


class InputExample(object):
    """A single training/test example for simple sequence classification."""

    def __init__(self, guid, text_a, text_b=None, label=None):
        """Constructs a InputExample.

        Args:
            guid: Unique id for the example.
            text_a: string. The untokenized text of the first sequence. For single
            sequence tasks, only this sequence must be specified.
            text_b: (Optional) string. The untokenized text of the second sequence.
            Only must be specified for sequence pair tasks.
            label: (Optional) string. The label of the example. This should be
            specified for train and dev examples, but not for test examples.
        """
        self.guid = guid
        self.text_a = text_a
        self.text_b = text_b
        self.label = label

class InputFeatures(object):
    """A single set of features of data."""

    def __init__(self, input_ids, input_mask, segment_ids, label_id, valid_ids=None, label_mask=None):
        self.input_ids = input_ids
        self.input_mask = input_mask
        self.segment_ids = segment_ids
        self.label_id = label_id
        self.valid_ids = valid_ids
        self.label_mask = label_mask

def readfile(filename):
    '''
    read file
    '''
    f = open(filename)
    data = []
    sentence = []
    label= []
    for line in f:
        if len(line)==0 or line.startswith('-DOCSTART') or line[0]=="\n":
            if len(sentence) > 0:
                data.append((sentence,label))
                sentence = []
                label = []
            continue
        splits = line.split(' ')
        sentence.append(splits[0])
        label.append(splits[-1][:-1])

    if len(sentence) >0:
        data.append((sentence,label))
        sentence = []
        label = []
    return data

class DataProcessor(object):
    """Base class for data converters for sequence classification data sets."""

    def get_train_examples(self, data_dir):
        """Gets a collection of `InputExample`s for the train set."""
        raise NotImplementedError()

    def get_dev_examples(self, data_dir):
        """Gets a collection of `InputExample`s for the dev set."""
        raise NotImplementedError()

    def get_labels(self):
        """Gets the list of labels for this data set."""
        raise NotImplementedError()

    @classmethod
    def _read_tsv(cls, input_file, quotechar=None):
        """Reads a tab separated value file."""
        return readfile(input_file)


class NerProcessor(DataProcessor):
    """Processor for the CoNLL-2003 data set."""

    def get_train_examples(self, data_dir):
        """See base class."""
        return self._create_examples(
            self._read_tsv(os.path.join(data_dir, "train.txt")), "train")

    def get_dev_examples(self, data_dir):
        """See base class."""
        return self._create_examples(
            self._read_tsv(os.path.join(data_dir, "valid.txt")), "dev")

    def get_test_examples(self, data_dir):
        """See base class."""
        return self._create_examples(
            self._read_tsv(os.path.join(data_dir, "test.txt")), "test")

    def get_labels(self):
        return ["O",
                "B-PER",
                "I-PER",
                "B-ORG",
                "I-ORG",
                "B-LOC",
                "I-LOC",
                "B-DAT",
                "I-DAT",
                "B-REF",
                "I-REF",
                "B-DOM",
                "I-DOM",
                "B-QUA",
                "I-QUA",
                "B-MISC",
                "I-MISC",
                "[CLS]",
                "[SEP]"]

    def _create_examples(self,lines,set_type):
        examples = []
        for i,(sentence,label) in enumerate(lines):
            guid = "%s-%s" % (set_type, i)
            text_a = ' '.join(sentence)
            text_b = None
            label = label
            examples.append(InputExample(guid=guid,text_a=text_a,text_b=text_b,label=label))
        return examples

def convert_examples_to_features(examples, label_list, max_seq_length, tokenizer):
    """Loads a data file into a list of `InputBatch`s."""

    label_map = {label : i for i, label in enumerate(label_list,1)}

    features = []
    for (ex_index,example) in enumerate(examples):
        textlist = example.text_a.split(' ')
        labellist = example.label
        tokens = []
        labels = []
        valid = []
        label_mask = []
        for i, word in enumerate(textlist):
            token = tokenizer.tokenize(word)
            tokens.extend(token)
            label_1 = labellist[i]
            for m in range(len(token)):
                if m == 0:
                    labels.append(label_1)
                    valid.append(1)
                    label_mask.append(1)
                else:
                    valid.append(0)
        if len(tokens) >= max_seq_length - 1:
            tokens = tokens[0:(max_seq_length - 2)]
            labels = labels[0:(max_seq_length - 2)]
            valid = valid[0:(max_seq_length - 2)]
            label_mask = label_mask[0:(max_seq_length - 2)]
        ntokens = []
        segment_ids = []
        label_ids = []
        ntokens.append("[CLS]")
        segment_ids.append(0)
        valid.insert(0,1)
        label_mask.insert(0,1)
        label_ids.append(label_map["[CLS]"])
        for i, token in enumerate(tokens):
            ntokens.append(token)
            segment_ids.append(0)
            if len(labels) > i:
                label_ids.append(label_map[labels[i]])
        ntokens.append("[SEP]")
        segment_ids.append(0)
        valid.append(1)
        label_mask.append(1)
        label_ids.append(label_map["[SEP]"])
        input_ids = tokenizer.convert_tokens_to_ids(ntokens)
        input_mask = [1] * len(input_ids)
        label_mask = [1] * len(label_ids)
        while len(input_ids) < max_seq_length:
            input_ids.append(0)
            input_mask.append(0)
            segment_ids.append(0)
            label_ids.append(0)
            valid.append(1)
            label_mask.append(0)
        while len(label_ids) < max_seq_length:
            label_ids.append(0)
            label_mask.append(0)
        assert len(input_ids) == max_seq_length
        assert len(input_mask) == max_seq_length
        assert len(segment_ids) == max_seq_length
        assert len(label_ids) == max_seq_length
        assert len(valid) == max_seq_length
        assert len(label_mask) == max_seq_length

        if ex_index < 5:
            logger.info("*** Example ***")
            logger.info("guid: %s" % (example.guid))
            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.label, label_ids))

        features.append(
                InputFeatures(input_ids=input_ids,
                              input_mask=input_mask,
                              segment_ids=segment_ids,
                              label_id=label_ids,
                              valid_ids=valid,
                              label_mask=label_mask))
    return features

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.")
    parser.add_argument("--output_dir",
                        default=None,
                        type=str,
                        required=True,
                        help="The output directory where the model predictions and checkpoints will be written.")

    ## 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_lower_case",
                        action='store_true',
                        help="Set this flag if you are using an uncased model.")
    parser.add_argument("--train_batch_size",
                        default=20,
                        type=int,
                        help="Total batch size for training.")
    parser.add_argument("--eval_batch_size",
                        default=10,
                        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("--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.")
    args = parser.parse_args()

    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()

    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

    random.seed(args.seed)
    np.random.seed(args.seed)
    torch.manual_seed(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 os.path.exists(args.output_dir) and os.listdir(args.output_dir) and args.do_train:
        raise ValueError("Output directory ({}) already exists and is not empty.".format(args.output_dir))
    if not os.path.exists(args.output_dir):
        os.makedirs(args.output_dir)

    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()
    num_labels = len(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.from_pretrained(args.bert_model,
              from_tf = False,
              config = config)

    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)], 'weight_decay': args.weight_decay},
        {'params': [p for n, p in param_optimizer if any(nd in n for nd in no_decay)], '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
    label_map = {i : label for i, label in enumerate(label_list,1)}
    if args.do_train:
        train_features = convert_examples_to_features(
            train_examples, label_list, args.max_seq_length, tokenizer)
        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)
        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_valid_ids = torch.tensor([f.valid_ids for f in train_features], dtype=torch.long)
        all_lmask_ids = torch.tensor([f.label_mask for f in train_features], dtype=torch.long)
        train_data = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids,all_valid_ids,all_lmask_ids)
        if 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)

        model.train()
        for _ in trange(int(args.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, 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 (step + 1) % args.gradient_accumulation_steps == 0:
                    optimizer.step()
                    scheduler.step()  # Update learning rate schedule
                    model.zero_grad()
                    global_step += 1

        # 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
        model_to_save.save_pretrained(args.output_dir)
        tokenizer.save_pretrained(args.output_dir)
        label_map = {i : label for i, label in enumerate(label_list,1)}
        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(args.output_dir,"model_config.json"),"w"))
        # Load a trained model and config that you have fine-tuned
    else:
        # Load a trained model and vocabulary that you have fine-tuned
        model = Ner.from_pretrained(args.output_dir)
        tokenizer = BertTokenizer.from_pretrained(args.output_dir, do_lower_case=args.do_lower_case)

    model.to(device)

    if args.do_eval and (args.local_rank == -1 or torch.distributed.get_rank() == 0):
        if args.eval_on == "dev":
            eval_examples = processor.get_dev_examples(args.data_dir)
        elif args.eval_on == "test":
            eval_examples = processor.get_test_examples(args.data_dir)
        else:
            raise ValueError("eval on dev or test set only")
        eval_features = convert_examples_to_features(eval_examples, label_list, args.max_seq_length, tokenizer)
        logger.info("***** Running evaluation *****")
        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_valid_ids = torch.tensor([f.valid_ids for f in eval_features], dtype=torch.long)
        all_lmask_ids = 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_valid_ids,all_lmask_ids)
        # Run prediction for full data
        eval_sampler = SequentialSampler(eval_data)
        eval_dataloader = DataLoader(eval_data, sampler=eval_sampler, batch_size=args.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,valid_ids,l_mask in tqdm(eval_dataloader, desc="Evaluating"):
            input_ids = input_ids.to(device)
            input_mask = input_mask.to(device)
            segment_ids = segment_ids.to(device)
            valid_ids = valid_ids.to(device)
            label_ids = label_ids.to(device)
            l_mask = l_mask.to(device)

            with torch.no_grad():
                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)
            logits = logits.detach().cpu().numpy()
            label_ids = label_ids.to('cpu').numpy()
            input_mask = input_mask.to('cpu').numpy()

            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):
                        if logits[i][j]:
                            y_true.append(temp_1)
                            y_pred.append(temp_2)
                        break
                    else:
                        if logits[i][j]:
                            temp_1.append(label_map[label_ids[i][j]])
                            temp_2.append(label_map[logits[i][j]])

        #report = classification_report(y_true, y_pred,digits=4)
        #logger.info("\n%s", report)
        #output_eval_file = os.path.join(args.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)


if __name__ == "__main__":
    main()