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

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"]