Merge pull request #1275 from stecklin/ner-fine-tuning

Implement fine-tuning BERT on CoNLL-2003 named entity recognition task

examples/README.md

@@ -8,8 +8,9 @@ similar API between the different models.
 | [Language Model fine-tuning](#language-model-fine-tuning) | Fine-tuning the library models for language modeling on a text dataset. Causal language modeling for GPT/GPT-2, masked language modeling for BERT/RoBERTa. |
 | [Language Generation](#language-generation) | Conditional text generation using the auto-regressive models of the library: GPT, GPT-2, Transformer-XL and XLNet.                                         |
 | [GLUE](#glue) | Examples running BERT/XLM/XLNet/RoBERTa on the 9 GLUE tasks. Examples feature distributed training as well as half-precision.                              |
-| [SQuAD](#squad) | Using BERT for question answering, examples with distributed training.                                                                                  |
+| [SQuAD](#squad) | Using BERT/XLM/XLNet/RoBERTa for question answering, examples with distributed training.                                                                                  |
 | [Multiple Choice](#multiple-choice) | Examples running BERT/XLNet/RoBERTa on the SWAG/RACE/ARC tasks. 
+| [Named Entity Recognition](#named-entity-recognition) | Using BERT for Named Entity Recognition (NER) on the CoNLL 2003 dataset, examples with distributed training.                                                                                  |
 
 ## Language model fine-tuning
 
@@ -390,3 +391,103 @@ exact_match = 86.91
 This fine-tuneds model is available as a checkpoint under the reference
 `bert-large-uncased-whole-word-masking-finetuned-squad`.
 
+## Named Entity Recognition
+
+Based on the script [`run_ner.py`](https://github.com/huggingface/transformers/blob/master/examples/run_ner.py).
+This example fine-tune Bert Multilingual on GermEval 2014 (German NER).
+Details and results for the fine-tuning provided by @stefan-it.
+
+### Data (Download and pre-processing steps)
+
+Data can be obtained from the [GermEval 2014](https://sites.google.com/site/germeval2014ner/data) shared task page.
+
+Here are the commands for downloading and pre-processing train, dev and test datasets. The original data format has four (tab-separated) columns, in a pre-processing step only the two relevant columns (token and outer span NER annotation) are extracted:
+
+```bash
+curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-train.tsv?attredirects=0&d=1' \
+| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > train.txt.tmp
+curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-dev.tsv?attredirects=0&d=1' \
+| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > dev.txt.tmp
+curl -L 'https://sites.google.com/site/germeval2014ner/data/NER-de-test.tsv?attredirects=0&d=1' \
+| grep -v "^#" | cut -f 2,3 | tr '\t' ' ' > test.txt.tmp
+```
+
+The GermEval 2014 dataset contains some strange "control character" tokens like `'\x96', '\u200e', '\x95', '\xad' or '\x80'`. One problem with these tokens is, that `BertTokenizer` returns an empty token for them, resulting in misaligned `InputExample`s. I wrote a script that a) filters these tokens and b) splits longer sentences into smaller ones (once the max. subtoken length is reached).
+
+```bash
+wget "https://raw.githubusercontent.com/stefan-it/fine-tuned-berts-seq/master/scripts/preprocess.py"
+```
+Let's define some variables that we need for further pre-processing steps and training the model:
+
+```bash
+export MAX_LENGTH=128
+export BERT_MODEL=bert-base-multilingual-cased
+```
+
+Run the pre-processing script on training, dev and test datasets:
+
+```bash
+python3 preprocess.py train.txt.tmp $BERT_MODEL $MAX_LENGTH > train.txt
+python3 preprocess.py dev.txt.tmp $BERT_MODEL $MAX_LENGTH > dev.txt
+python3 preprocess.py test.txt.tmp $BERT_MODEL $MAX_LENGTH > test.txt
+```
+
+The GermEval 2014 dataset has much more labels than CoNLL-2002/2003 datasets, so an own set of labels must be used:
+
+```bash
+cat train.txt dev.txt test.txt | cut -d " " -f 2 | grep -v "^$"| sort | uniq > labels.txt
+```
+
+### Training
+
+Additional environment variables must be set:
+
+```bash
+export OUTPUT_DIR=germeval-model
+export BATCH_SIZE=32
+export NUM_EPOCHS=3
+export SAVE_STEPS=750
+export SEED=1
+```
+
+To start training, just run:
+
+```bash
+python3 run_ner.py --data_dir ./ \
+--model_type bert \
+--labels ./labels.txt \
+--model_name_or_path $BERT_MODEL \
+--output_dir $OUTPUT_DIR \
+--max_seq_length  $MAX_LENGTH \
+--num_train_epochs $NUM_EPOCHS \
+--per_gpu_train_batch_size $BATCH_SIZE \
+--save_steps $SAVE_STEPS \
+--seed $SEED \
+--do_train \
+--do_eval \
+--do_predict
+```
+
+If your GPU supports half-precision training, just add the `--fp16` flag. After training, the model will be both evaluated on development and test datasets.
+
+### Evaluation
+
+Evaluation on development dataset outputs the following for our example:
+
+```bash
+10/04/2019 00:42:06 - INFO - __main__ -   ***** Eval results  *****
+10/04/2019 00:42:06 - INFO - __main__ -     f1 = 0.8623348017621146
+10/04/2019 00:42:06 - INFO - __main__ -     loss = 0.07183869666975543
+10/04/2019 00:42:06 - INFO - __main__ -     precision = 0.8467916366258111
+10/04/2019 00:42:06 - INFO - __main__ -     recall = 0.8784592370979806
+```
+
+On the test dataset the following results could be achieved:
+
+```bash
+10/04/2019 00:42:42 - INFO - __main__ -   ***** Eval results  *****
+10/04/2019 00:42:42 - INFO - __main__ -     f1 = 0.8614389652384803
+10/04/2019 00:42:42 - INFO - __main__ -     loss = 0.07064602487454782
+10/04/2019 00:42:42 - INFO - __main__ -     precision = 0.8604651162790697
+10/04/2019 00:42:42 - INFO - __main__ -     recall = 0.8624150210424085
+```

examples/requirements.txt

 tensorboardX
-scikit-learn
+scikit-learn
\ No newline at end of file
+seqeval
\ No newline at end of file

examples/run_ner.py

+# coding=utf-8
+# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
+# Copyright (c) 2018, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Fine-tuning the library models for named entity recognition on CoNLL-2003 (Bert). """
+
+from __future__ import absolute_import, division, print_function
+
+import argparse
+import glob
+import logging
+import os
+import random
+
+import numpy as np
+import torch
+from seqeval.metrics import precision_score, recall_score, f1_score
+from tensorboardX import SummaryWriter
+from torch.nn import CrossEntropyLoss
+from torch.utils.data import DataLoader, RandomSampler, SequentialSampler, TensorDataset
+from torch.utils.data.distributed import DistributedSampler
+from tqdm import tqdm, trange
+from utils_ner import convert_examples_to_features, get_labels, read_examples_from_file
+
+from transformers import AdamW, WarmupLinearSchedule
+from transformers import WEIGHTS_NAME, BertConfig, BertForTokenClassification, BertTokenizer
+
+logger = logging.getLogger(__name__)
+
+ALL_MODELS = sum(
+    (tuple(conf.pretrained_config_archive_map.keys()) for conf in (BertConfig, )),
+    ())
+
+MODEL_CLASSES = {
+    "bert": (BertConfig, BertForTokenClassification, BertTokenizer),
+}
+
+
+def set_seed(args):
+    random.seed(args.seed)
+    np.random.seed(args.seed)
+    torch.manual_seed(args.seed)
+    if args.n_gpu > 0:
+        torch.cuda.manual_seed_all(args.seed)
+
+
+def train(args, train_dataset, model, tokenizer, labels, pad_token_label_id):
+    """ Train the model """
+    if args.local_rank in [-1, 0]:
+        tb_writer = SummaryWriter()
+
+    args.train_batch_size = args.per_gpu_train_batch_size * max(1, args.n_gpu)
+    train_sampler = RandomSampler(train_dataset) if args.local_rank == -1 else DistributedSampler(train_dataset)
+    train_dataloader = DataLoader(train_dataset, sampler=train_sampler, batch_size=args.train_batch_size)
+
+    if args.max_steps > 0:
+        t_total = args.max_steps
+        args.num_train_epochs = args.max_steps // (len(train_dataloader) // args.gradient_accumulation_steps) + 1
+    else:
+        t_total = len(train_dataloader) // args.gradient_accumulation_steps * args.num_train_epochs
+
+    # Prepare optimizer and schedule (linear warmup and decay)
+    no_decay = ["bias", "LayerNorm.weight"]
+    optimizer_grouped_parameters = [
+        {"params": [p for n, p in model.named_parameters() if not any(nd in n for nd in no_decay)],
+         "weight_decay": args.weight_decay},
+        {"params": [p for n, p in model.named_parameters() if any(nd in n for nd in no_decay)], "weight_decay": 0.0}
+    ]
+    optimizer = AdamW(optimizer_grouped_parameters, lr=args.learning_rate, eps=args.adam_epsilon)
+    scheduler = WarmupLinearSchedule(optimizer, warmup_steps=args.warmup_steps, t_total=t_total)
+    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 args.n_gpu > 1:
+        model = torch.nn.DataParallel(model)
+
+    # Distributed training (should be after apex fp16 initialization)
+    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)
+
+    # Train!
+    logger.info("***** Running training *****")
+    logger.info("  Num examples = %d", len(train_dataset))
+    logger.info("  Num Epochs = %d", args.num_train_epochs)
+    logger.info("  Instantaneous batch size per GPU = %d", args.per_gpu_train_batch_size)
+    logger.info("  Total train batch size (w. parallel, distributed & accumulation) = %d",
+                args.train_batch_size * args.gradient_accumulation_steps * (
+                    torch.distributed.get_world_size() if args.local_rank != -1 else 1))
+    logger.info("  Gradient Accumulation steps = %d", args.gradient_accumulation_steps)
+    logger.info("  Total optimization steps = %d", t_total)
+
+    global_step = 0
+    tr_loss, logging_loss = 0.0, 0.0
+    model.zero_grad()
+    train_iterator = trange(int(args.num_train_epochs), desc="Epoch", disable=args.local_rank not in [-1, 0])
+    set_seed(args)  # Added here for reproductibility (even between python 2 and 3)
+    for _ in train_iterator:
+        epoch_iterator = tqdm(train_dataloader, desc="Iteration", disable=args.local_rank not in [-1, 0])
+        for step, batch in enumerate(epoch_iterator):
+            model.train()
+            batch = tuple(t.to(args.device) for t in batch)
+            inputs = {"input_ids": batch[0],
+                      "attention_mask": batch[1],
+                      "token_type_ids": batch[2] if args.model_type in ["bert", "xlnet"] else None,
+                      # XLM and RoBERTa don"t use segment_ids
+                      "labels": batch[3]}
+            outputs = model(**inputs)
+            loss = outputs[0]  # model outputs are always tuple in pytorch-transformers (see doc)
+
+            if args.n_gpu > 1:
+                loss = loss.mean()  # mean() to average on multi-gpu parallel training
+            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()
+            if (step + 1) % args.gradient_accumulation_steps == 0:
+                scheduler.step()  # Update learning rate schedule
+                optimizer.step()
+                model.zero_grad()
+                global_step += 1
+
+                if args.local_rank in [-1, 0] and args.logging_steps > 0 and global_step % args.logging_steps == 0:
+                    # Log metrics
+                    if args.local_rank == -1 and args.evaluate_during_training:  # Only evaluate when single GPU otherwise metrics may not average well
+                        results, _ = evaluate(args, model, tokenizer, labels, pad_token_label_id)
+                        for key, value in results.items():
+                            tb_writer.add_scalar("eval_{}".format(key), value, global_step)
+                    tb_writer.add_scalar("lr", scheduler.get_lr()[0], global_step)
+                    tb_writer.add_scalar("loss", (tr_loss - logging_loss) / args.logging_steps, global_step)
+                    logging_loss = tr_loss
+
+                if args.local_rank in [-1, 0] and 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_to_save = model.module if hasattr(model, "module") else model  # Take care of distributed/parallel training
+                    model_to_save.save_pretrained(output_dir)
+                    torch.save(args, os.path.join(output_dir, "training_args.bin"))
+                    logger.info("Saving model checkpoint to %s", output_dir)
+
+            if args.max_steps > 0 and global_step > args.max_steps:
+                epoch_iterator.close()
+                break
+        if args.max_steps > 0 and global_step > args.max_steps:
+            train_iterator.close()
+            break
+
+    if args.local_rank in [-1, 0]:
+        tb_writer.close()
+
+    return global_step, tr_loss / global_step
+
+
+def evaluate(args, model, tokenizer, labels, pad_token_label_id, mode, prefix=""):
+    eval_dataset = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode=mode)
+
+    args.eval_batch_size = args.per_gpu_eval_batch_size * max(1, args.n_gpu)
+    # Note that DistributedSampler samples randomly
+    eval_sampler = SequentialSampler(eval_dataset) if args.local_rank == -1 else DistributedSampler(eval_dataset)
+    eval_dataloader = DataLoader(eval_dataset, sampler=eval_sampler, batch_size=args.eval_batch_size)
+
+    # Eval!
+    logger.info("***** Running evaluation %s *****", prefix)
+    logger.info("  Num examples = %d", len(eval_dataset))
+    logger.info("  Batch size = %d", args.eval_batch_size)
+    eval_loss = 0.0
+    nb_eval_steps = 0
+    preds = None
+    out_label_ids = None
+    model.eval()
+    for batch in tqdm(eval_dataloader, desc="Evaluating"):
+        batch = tuple(t.to(args.device) for t in batch)
+
+        with torch.no_grad():
+            inputs = {"input_ids": batch[0],
+                      "attention_mask": batch[1],
+                      "token_type_ids": batch[2] if args.model_type in ["bert", "xlnet"] else None,
+                      # XLM and RoBERTa don"t use segment_ids
+                      "labels": batch[3]}
+            outputs = model(**inputs)
+            tmp_eval_loss, logits = outputs[:2]
+
+            eval_loss += tmp_eval_loss.item()
+        nb_eval_steps += 1
+        if preds is None:
+            preds = logits.detach().cpu().numpy()
+            out_label_ids = inputs["labels"].detach().cpu().numpy()
+        else:
+            preds = np.append(preds, logits.detach().cpu().numpy(), axis=0)
+            out_label_ids = np.append(out_label_ids, inputs["labels"].detach().cpu().numpy(), axis=0)
+
+    eval_loss = eval_loss / nb_eval_steps
+    preds = np.argmax(preds, axis=2)
+
+    label_map = {i: label for i, label in enumerate(labels)}
+
+    out_label_list = [[] for _ in range(out_label_ids.shape[0])]
+    preds_list = [[] for _ in range(out_label_ids.shape[0])]
+
+    for i in range(out_label_ids.shape[0]):
+        for j in range(out_label_ids.shape[1]):
+            if out_label_ids[i, j] != pad_token_label_id:
+                out_label_list[i].append(label_map[out_label_ids[i][j]])
+                preds_list[i].append(label_map[preds[i][j]])
+
+    results = {
+        "loss": eval_loss,
+        "precision": precision_score(out_label_list, preds_list),
+        "recall": recall_score(out_label_list, preds_list),
+        "f1": f1_score(out_label_list, preds_list)
+    }
+
+    logger.info("***** Eval results %s *****", prefix)
+    for key in sorted(results.keys()):
+        logger.info("  %s = %s", key, str(results[key]))
+
+    return results, preds_list
+
+
+def load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode):
+    if args.local_rank not in [-1, 0] and not evaluate:
+        torch.distributed.barrier()  # Make sure only the first process in distributed training process the dataset, and the others will use the cache
+
+    # Load data features from cache or dataset file
+    cached_features_file = os.path.join(args.data_dir, "cached_{}_{}_{}".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:
+        logger.info("Loading features from cached file %s", cached_features_file)
+        features = torch.load(cached_features_file)
+    else:
+        logger.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
+                                                )
+        if args.local_rank in [-1, 0]:
+            logger.info("Saving features into cached file %s", cached_features_file)
+            torch.save(features, cached_features_file)
+
+    if args.local_rank == 0 and not evaluate:
+        torch.distributed.barrier()  # Make sure only the first process in distributed training process the dataset, and the others will use the cache
+
+    # Convert to Tensors and build dataset
+    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_ids for f in features], dtype=torch.long)
+
+    dataset = TensorDataset(all_input_ids, all_input_mask, all_segment_ids, all_label_ids)
+    return dataset
+
+
+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 training files for the CoNLL-2003 NER task.")
+    parser.add_argument("--model_type", default=None, type=str, required=True,
+                        help="Model type selected in the list: " + ", ".join(MODEL_CLASSES.keys()))
+    parser.add_argument("--model_name_or_path", default=None, type=str, required=True,
+                        help="Path to pre-trained model or shortcut name selected in the list: " + ", ".join(ALL_MODELS))
+    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("--labels", default="", type=str,
+                        help="Path to a file containing all labels. If not specified, CoNLL-2003 labels are used.")
+    parser.add_argument("--config_name", default="", type=str,
+                        help="Pretrained config name or path if not the same as model_name")
+    parser.add_argument("--tokenizer_name", default="", type=str,
+                        help="Pretrained tokenizer name or path if not the same as model_name")
+    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 tokenization. Sequences longer "
+                             "than this will be truncated, sequences shorter 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 on the dev set.")
+    parser.add_argument("--do_predict", action="store_true",
+                        help="Whether to run predictions on the test set.")
+    parser.add_argument("--evaluate_during_training", action="store_true",
+                        help="Whether to run evaluation during training at each logging step.")
+    parser.add_argument("--do_lower_case", action="store_true",
+                        help="Set this flag if you are using an uncased model.")
+
+    parser.add_argument("--per_gpu_train_batch_size", default=8, type=int,
+                        help="Batch size per GPU/CPU for training.")
+    parser.add_argument("--per_gpu_eval_batch_size", default=8, type=int,
+                        help="Batch size per GPU/CPU for evaluation.")
+    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("--learning_rate", default=5e-5, type=float,
+                        help="The initial learning rate for Adam.")
+    parser.add_argument("--weight_decay", default=0.0, type=float,
+                        help="Weight decay 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("--num_train_epochs", default=3.0, type=float,
+                        help="Total number of training epochs to perform.")
+    parser.add_argument("--max_steps", default=-1, type=int,
+                        help="If > 0: set total number of training steps to perform. Override num_train_epochs.")
+    parser.add_argument("--warmup_steps", default=0, type=int,
+                        help="Linear warmup over warmup_steps.")
+
+    parser.add_argument("--logging_steps", type=int, default=50,
+                        help="Log every X updates steps.")
+    parser.add_argument("--save_steps", type=int, default=50,
+                        help="Save checkpoint every X updates steps.")
+    parser.add_argument("--eval_all_checkpoints", action="store_true",
+                        help="Evaluate all checkpoints starting with the same prefix as model_name ending and ending with step number")
+    parser.add_argument("--no_cuda", action="store_true",
+                        help="Avoid using CUDA when available")
+    parser.add_argument("--overwrite_output_dir", action="store_true",
+                        help="Overwrite the content of the output directory")
+    parser.add_argument("--overwrite_cache", action="store_true",
+                        help="Overwrite the cached training and evaluation sets")
+    parser.add_argument("--seed", type=int, default=42,
+                        help="random seed for initialization")
+
+    parser.add_argument("--fp16", action="store_true",
+                        help="Whether to use 16-bit (mixed) precision (through NVIDIA apex) 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("--local_rank", type=int, default=-1,
+                        help="For distributed training: local_rank")
+    parser.add_argument("--server_ip", type=str, default="", help="For distant debugging.")
+    parser.add_argument("--server_port", type=str, default="", help="For distant debugging.")
+    args = parser.parse_args()
+
+    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))
+
+    # Setup distant debugging if needed
+    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()
+
+    # Setup CUDA, GPU & distributed training
+    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")
+        args.n_gpu = torch.cuda.device_count()
+    else:  # Initializes the distributed backend which will take care of sychronizing nodes/GPUs
+        torch.cuda.set_device(args.local_rank)
+        device = torch.device("cuda", args.local_rank)
+        torch.distributed.init_process_group(backend="nccl")
+        args.n_gpu = 1
+    args.device = device
+
+    # Setup logging
+    logging.basicConfig(format="%(asctime)s - %(levelname)s - %(name)s -   %(message)s",
+                        datefmt="%m/%d/%Y %H:%M:%S",
+                        level=logging.INFO if args.local_rank in [-1, 0] else logging.WARN)
+    logger.warning("Process rank: %s, device: %s, n_gpu: %s, distributed training: %s, 16-bits training: %s",
+                   args.local_rank, device, args.n_gpu, bool(args.local_rank != -1), args.fp16)
+
+    # Set seed
+    set_seed(args)
+
+    # Prepare CONLL-2003 task
+    labels = get_labels(args.labels)
+    num_labels = len(labels)
+    # Use cross entropy ignore index as padding label id so that only real label ids contribute to the loss later
+    pad_token_label_id = CrossEntropyLoss().ignore_index
+
+    # Load pretrained model and tokenizer
+    if args.local_rank not in [-1, 0]:
+        torch.distributed.barrier()  # Make sure only the first process in distributed training will download model & vocab
+
+    args.model_type = args.model_type.lower()
+    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)
+    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)
+    model = model_class.from_pretrained(args.model_name_or_path, from_tf=bool(".ckpt" in args.model_name_or_path),
+                                        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(args.device)
+
+    logger.info("Training/evaluation parameters %s", args)
+
+    # Training
+    if args.do_train:
+        train_dataset = load_and_cache_examples(args, tokenizer, labels, pad_token_label_id, mode="train")
+        global_step, tr_loss = train(args, train_dataset, model, tokenizer, labels, pad_token_label_id)
+        logger.info(" global_step = %s, average loss = %s", global_step, tr_loss)
+
+    # Saving best-practices: if you use defaults names for the model, you can reload it using from_pretrained()
+    if args.do_train and (args.local_rank == -1 or torch.distributed.get_rank() == 0):
+        # Create output directory if needed
+        if not os.path.exists(args.output_dir) and args.local_rank in [-1, 0]:
+            os.makedirs(args.output_dir)
+
+        logger.info("Saving model checkpoint to %s", args.output_dir)
+        # Save a trained model, configuration and tokenizer using `save_pretrained()`.
+        # They can then be reloaded using `from_pretrained()`
+        model_to_save = model.module if hasattr(model, "module") else model  # Take care of distributed/parallel training
+        model_to_save.save_pretrained(args.output_dir)
+        tokenizer.save_pretrained(args.output_dir)
+
+        # Good practice: save your training arguments together with the trained model
+        torch.save(args, os.path.join(args.output_dir, "training_args.bin"))
+
+    # Evaluation
+    results = {}
+    if args.do_eval and args.local_rank in [-1, 0]:
+        tokenizer = tokenizer_class.from_pretrained(args.output_dir, do_lower_case=args.do_lower_case)
+        checkpoints = [args.output_dir]
+        if args.eval_all_checkpoints:
+            checkpoints = list(os.path.dirname(c) for c in sorted(glob.glob(args.output_dir + "/**/" + WEIGHTS_NAME, recursive=True)))
+            logging.getLogger("pytorch_transformers.modeling_utils").setLevel(logging.WARN)  # Reduce logging
+        logger.info("Evaluate the following checkpoints: %s", checkpoints)
+        for checkpoint in checkpoints:
+            global_step = checkpoint.split("-")[-1] if len(checkpoints) > 1 else ""
+            model = model_class.from_pretrained(checkpoint)
+            model.to(args.device)
+            result, _ = evaluate(args, model, tokenizer, labels, pad_token_label_id, mode="dev", prefix=global_step)
+            if global_step:
+                result = {"{}_{}".format(global_step, k): v for k, v in result.items()}
+            results.update(result)
+        output_eval_file = os.path.join(args.output_dir, "eval_results.txt")
+        with open(output_eval_file, "w") as writer:
+            for key in sorted(results.keys()):
+                writer.write("{} = {}\n".format(key, str(results[key])))
+
+    if args.do_predict and args.local_rank in [-1, 0]:
+        tokenizer = tokenizer_class.from_pretrained(args.output_dir, do_lower_case=args.do_lower_case)
+        model = model_class.from_pretrained(args.output_dir)
+        model.to(args.device)
+        result, predictions = evaluate(args, model, tokenizer, labels, pad_token_label_id, mode="test")
+        # Save results
+        output_test_results_file = os.path.join(args.output_dir, "test_results.txt")
+        with open(output_test_results_file, "w") as writer:
+            for key in sorted(result.keys()):
+                writer.write("{} = {}\n".format(key, str(result[key])))
+        # Save predictions
+        output_test_predictions_file = os.path.join(args.output_dir, "test_predictions.txt")
+        with open(output_test_predictions_file, "w") as writer:
+            with open(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 predictions[example_id]:
+                            example_id += 1
+                    elif predictions[example_id]:
+                        output_line = line.split()[0] + " " + predictions[example_id].pop(0) + "\n"
+                        writer.write(output_line)
+                    else:
+                        logger.warning("Maximum sequence length exceeded: No prediction for '%s'.", line.split()[0])
+
+    return results
+
+
+if __name__ == "__main__":
+    main()

examples/utils_ner.py

+# coding=utf-8
+# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
+# Copyright (c) 2018, NVIDIA CORPORATION.  All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Named entity recognition fine-tuning: utilities to work with CoNLL-2003 task. """
+
+from __future__ import absolute_import, division, print_function
+
+import logging
+import os
+from io import open
+
+logger = logging.getLogger(__name__)
+
+
+class InputExample(object):
+    """A single training/test example for token classification."""
+
+    def __init__(self, guid, words, labels):
+        """Constructs a InputExample.
+
+        Args:
+            guid: Unique id for the example.
+            words: list. The words of the sequence.
+            labels: (Optional) list. The labels for each word of the sequence. This should be
+            specified for train and dev examples, but not for test examples.
+        """
+        self.guid = guid
+        self.words = words
+        self.labels = labels
+
+
+class InputFeatures(object):
+    """A single set of features of data."""
+
+    def __init__(self, input_ids, input_mask, segment_ids, label_ids):
+        self.input_ids = input_ids
+        self.input_mask = input_mask
+        self.segment_ids = segment_ids
+        self.label_ids = label_ids
+
+
+def read_examples_from_file(data_dir, mode):
+    file_path = os.path.join(data_dir, "{}.txt".format(mode))
+    guid_index = 1
+    examples = []
+    with open(file_path, encoding="utf-8") as f:
+        words = []
+        labels = []
+        for line in f:
+            if line.startswith("-DOCSTART-") or line == "" or line == "\n":
+                if words:
+                    examples.append(InputExample(guid="{}-{}".format(mode, guid_index),
+                                                 words=words,
+                                                 labels=labels))
+                    guid_index += 1
+                    words = []
+                    labels = []
+            else:
+                splits = line.split(" ")
+                words.append(splits[0])
+                if len(splits) > 1:
+                    labels.append(splits[-1].replace("\n", ""))
+                else:
+                    # Examples could have no label for mode = "test"
+                    labels.append("O")
+        if words:
+            examples.append(InputExample(guid="%s-%d".format(mode, guid_index),
+                                         words=words,
+                                         labels=labels))
+    return examples
+
+
+def convert_examples_to_features(examples,
+                                 label_list,
+                                 max_seq_length,
+                                 tokenizer,
+                                 cls_token_at_end=False,
+                                 cls_token="[CLS]",
+                                 cls_token_segment_id=1,
+                                 sep_token="[SEP]",
+                                 sep_token_extra=False,
+                                 pad_on_left=False,
+                                 pad_token=0,
+                                 pad_token_segment_id=0,
+                                 pad_token_label_id=-1,
+                                 sequence_a_segment_id=0,
+                                 mask_padding_with_zero=True):
+    """ Loads a data file into a list of `InputBatch`s
+        `cls_token_at_end` define the location of the CLS token:
+            - False (Default, BERT/XLM pattern): [CLS] + A + [SEP] + B + [SEP]
+            - True (XLNet/GPT pattern): A + [SEP] + B + [SEP] + [CLS]
+        `cls_token_segment_id` define the segment id associated to the CLS token (0 for BERT, 2 for XLNet)
+    """
+
+    label_map = {label: i for i, label in enumerate(label_list)}
+
+    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 = []
+        label_ids = []
+        for word, label in zip(example.words, example.labels):
+            word_tokens = tokenizer.tokenize(word)
+            tokens.extend(word_tokens)
+            # Use the real label id for the first token of the word, and padding ids for the remaining tokens
+            label_ids.extend([label_map[label]] + [pad_token_label_id] * (len(word_tokens) - 1))
+
+        # Account for [CLS] and [SEP] with "- 2" and with "- 3" for RoBERTa.
+        special_tokens_count = 3 if sep_token_extra else 2
+        if len(tokens) > max_seq_length - special_tokens_count:
+            tokens = tokens[:(max_seq_length - special_tokens_count)]
+            label_ids = label_ids[:(max_seq_length - special_tokens_count)]
+
+        # The convention in BERT is:
+        # (a) For sequence pairs:
+        #  tokens:   [CLS] is this jack ##son ##ville ? [SEP] no it is not . [SEP]
+        #  type_ids:   0   0  0    0    0     0       0   0   1  1  1  1   1   1
+        # (b) For single sequences:
+        #  tokens:   [CLS] the dog is hairy . [SEP]
+        #  type_ids:   0   0   0   0  0     0   0
+        #
+        # Where "type_ids" are used to indicate whether this is the first
+        # sequence or the second sequence. The embedding vectors for `type=0` and
+        # `type=1` were learned during pre-training and are added to the wordpiece
+        # embedding vector (and position vector). This is not *strictly* necessary
+        # since the [SEP] token unambiguously separates the sequences, but it makes
+        # it easier for the model to learn the concept of sequences.
+        #
+        # For classification tasks, the first vector (corresponding to [CLS]) is
+        # used as as the "sentence vector". Note that this only makes sense because
+        # the entire model is fine-tuned.
+        tokens += [sep_token]
+        label_ids += [pad_token_label_id]
+        if sep_token_extra:
+            # roberta uses an extra separator b/w pairs of sentences
+            tokens += [sep_token]
+            label_ids += [pad_token_label_id]
+        segment_ids = [sequence_a_segment_id] * len(tokens)
+
+        if cls_token_at_end:
+            tokens += [cls_token]
+            label_ids += [pad_token_label_id]
+            segment_ids += [cls_token_segment_id]
+        else:
+            tokens = [cls_token] + tokens
+            label_ids = [pad_token_label_id] + label_ids
+            segment_ids = [cls_token_segment_id] + segment_ids
+
+        input_ids = tokenizer.convert_tokens_to_ids(tokens)
+
+        # The mask has 1 for real tokens and 0 for padding tokens. Only real
+        # tokens are attended to.
+        input_mask = [1 if mask_padding_with_zero else 0] * len(input_ids)
+
+        # Zero-pad up to the sequence length.
+        padding_length = max_seq_length - len(input_ids)
+        if pad_on_left:
+            input_ids = ([pad_token] * padding_length) + input_ids
+            input_mask = ([0 if mask_padding_with_zero else 1] * padding_length) + input_mask
+            segment_ids = ([pad_token_segment_id] * padding_length) + segment_ids
+            label_ids = ([pad_token_label_id] * padding_length) + label_ids
+        else:
+            input_ids += ([pad_token] * padding_length)
+            input_mask += ([0 if mask_padding_with_zero else 1] * padding_length)
+            segment_ids += ([pad_token_segment_id] * padding_length)
+            label_ids += ([pad_token_label_id] * padding_length)
+
+        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
+
+        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_ids: %s", " ".join([str(x) for x in label_ids]))
+
+        features.append(
+                InputFeatures(input_ids=input_ids,
+                              input_mask=input_mask,
+                              segment_ids=segment_ids,
+                              label_ids=label_ids))
+    return features
+
+
+def get_labels(path):
+    if path:
+        with open(path, "r") as f:
+            labels = f.read().splitlines()
+        if "O" not in labels:
+            labels = ["O"] + labels
+        return labels
+    else:
+        return ["O", "B-MISC", "I-MISC",  "B-PER", "I-PER", "B-ORG", "I-ORG", "B-LOC", "I-LOC"]