run_attention.py

# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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.
"""BERT finetuning runner."""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import collections
import csv
import os
import modeling
import optimization
import tokenization
import tensorflow as tf
import six

flags = tf.flags

FLAGS = flags.FLAGS

## Required parameters
flags.DEFINE_string(
    "data_dir", None,
    "The input data dir. Should contain the .tsv files (or other data files) "
    "for the task.")

flags.DEFINE_string(
    "bert_config_file", None,
    "The config json file corresponding to the pre-trained BERT model. "
    "This specifies the model architecture.")

flags.DEFINE_string("task_name", None, "The name of the task to train.")

flags.DEFINE_string("vocab_file", None,
                    "The vocabulary file that the BERT model was trained on.")

flags.DEFINE_string(
    "output_dir", None,
    "The output directory where the model checkpoints will be written.")

## Other parameters

flags.DEFINE_string(
    "init_checkpoint", None,
    "Initial checkpoint (usually from a pre-trained BERT model).")

flags.DEFINE_bool(
    "do_lower_case", True,
    "Whether to lower case the input text. Should be True for uncased "
    "models and False for cased models.")

flags.DEFINE_integer(
    "max_seq_length", 128,
    "The maximum total input sequence length after WordPiece tokenization. "
    "Sequences longer than this will be truncated, and sequences shorter "
    "than this will be padded.")

flags.DEFINE_bool("do_train", False, "Whether to run training.")

flags.DEFINE_bool("do_eval", False, "Whether to run eval on the dev set.")

flags.DEFINE_bool(
    "do_predict", False,
    "Whether to run the model in inference mode on the test set.")

flags.DEFINE_integer("train_batch_size", 32, "Total batch size for training.")

flags.DEFINE_integer("eval_batch_size", 8, "Total batch size for eval.")

flags.DEFINE_integer("predict_batch_size", 8, "Total batch size for predict.")

flags.DEFINE_float("learning_rate", 5e-5, "The initial learning rate for Adam.")

flags.DEFINE_float("num_train_epochs", 3.0,
                   "Total number of training epochs to perform.")

flags.DEFINE_float(
    "warmup_proportion", 0.1,
    "Proportion of training to perform linear learning rate warmup for. "
    "E.g., 0.1 = 10% of training.")

flags.DEFINE_integer("save_checkpoints_steps", 1000,
                     "How often to save the model checkpoint.")

flags.DEFINE_integer("iterations_per_loop", 1000,
                     "How many steps to make in each estimator call.")

flags.DEFINE_bool("use_tpu", False, "Whether to use TPU or GPU/CPU.")

tf.flags.DEFINE_string(
    "tpu_name", None,
    "The Cloud TPU to use for training. This should be either the name "
    "used when creating the Cloud TPU, or a grpc://ip.address.of.tpu:8470 "
    "url.")

tf.flags.DEFINE_string(
    "tpu_zone", None,
    "[Optional] GCE zone where the Cloud TPU is located in. If not "
    "specified, we will attempt to automatically detect the GCE project from "
    "metadata.")

tf.flags.DEFINE_string(
    "gcp_project", None,
    "[Optional] Project name for the Cloud TPU-enabled project. If not "
    "specified, we will attempt to automatically detect the GCE project from "
    "metadata.")

tf.flags.DEFINE_string("master", None, "[Optional] TensorFlow master URL.")

flags.DEFINE_integer(
    "num_tpu_cores", 8,
    "Only used if `use_tpu` is True. Total number of TPU cores to use.")


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

  def __init__(self, guid, text_a, text_b=None, label=None, masked_id=None, masked_expected=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
    self.masked_id = masked_id
    self.masked_expected = masked_expected


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

  def __init__(self, input_ids, input_mask, segment_ids, label_id, masked_id, masked_expected):
    self.input_ids = input_ids
    self.input_mask = input_mask
    self.segment_ids = segment_ids
    self.label_id = label_id
    self.masked_id = masked_id
    self.masked_expected = masked_expected


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_test_examples(self, data_dir):
    """Gets a collection of `InputExample`s for prediction."""
    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."""
    with tf.gfile.Open(input_file, "r") as f:
      reader = csv.reader(f, delimiter="\t", quotechar=quotechar)
      lines = []
      for line in reader:
        lines.append(line)
      return lines


class XnliProcessor(DataProcessor):
  """Processor for the XNLI data set."""

  def __init__(self):
    self.language = "zh"

  def get_train_examples(self, data_dir):
    """See base class."""
    lines = self._read_tsv(
        os.path.join(data_dir, "multinli",
                     "multinli.train.%s.tsv" % self.language))
    examples = []
    for (i, line) in enumerate(lines):
      if i == 0:
        continue
      guid = "train-%d" % (i)
      text_a = tokenization.convert_to_unicode(line[0])
      text_b = tokenization.convert_to_unicode(line[1])
      label = tokenization.convert_to_unicode(line[2])
      if label == tokenization.convert_to_unicode("contradictory"):
        label = tokenization.convert_to_unicode("contradiction")
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
    return examples

  def get_dev_examples(self, data_dir):
    """See base class."""
    lines = self._read_tsv(os.path.join(data_dir, "xnli.dev.tsv"))
    examples = []
    for (i, line) in enumerate(lines):
      if i == 0:
        continue
      guid = "dev-%d" % (i)
      language = tokenization.convert_to_unicode(line[0])
      if language != tokenization.convert_to_unicode(self.language):
        continue
      text_a = tokenization.convert_to_unicode(line[6])
      text_b = tokenization.convert_to_unicode(line[7])
      label = tokenization.convert_to_unicode(line[1])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
    return examples

  def get_labels(self):
    """See base class."""
    return ["contradiction", "entailment", "neutral"]


class MnliProcessor(DataProcessor):
  """Processor for the MultiNLI data set (GLUE version)."""

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

  def get_dev_examples(self, data_dir):
    """See base class."""
    return self._create_examples(
        self._read_tsv(os.path.join(data_dir, "dev_matched.tsv")),
        "dev_matched")

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

  def get_labels(self):
    """See base class."""
    return ["contradiction", "entailment", "neutral"]

  def _create_examples(self, lines, set_type):
    """Creates examples for the training and dev sets."""
    examples = []
    for (i, line) in enumerate(lines):
      if i == 0:
        continue
      guid = "%s-%s" % (set_type, tokenization.convert_to_unicode(line[0]))
      text_a = tokenization.convert_to_unicode(line[8])
      text_b = tokenization.convert_to_unicode(line[9])
      if set_type == "test":
        label = "contradiction"
      else:
        label = tokenization.convert_to_unicode(line[-1])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
    return examples


class MrpcProcessor(DataProcessor):
  """Processor for the MRPC data set (GLUE version)."""

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

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

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

  def get_labels(self):
    """See base class."""
    return ["0", "1"]

  def _create_examples(self, lines, set_type):
    """Creates examples for the training and dev sets."""
    examples = []
    for (i, line) in enumerate(lines):
      if i == 0:
        continue
      guid = "%s-%s" % (set_type, i)
      text_a = tokenization.convert_to_unicode(line[3])
      text_b = tokenization.convert_to_unicode(line[4])
      if set_type == "test":
        label = "0"
      else:
        label = tokenization.convert_to_unicode(line[0])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
    return examples


class NextSentenceProcessor(DataProcessor):
  """Processor for the MRPC data set (GLUE version)."""

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

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

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

  def get_labels(self):
    """See base class."""
    return ["0", "1"]

  def _create_examples(self, lines, set_type):
    """Creates examples for the training and dev sets."""
    examples = []
    for (i, line) in enumerate(lines):
      if i == 0:
        continue
      guid = "%s-%s" % (set_type, i)
      text_a = tokenization.convert_to_unicode(line[1])
      #print(line[1])
      text_b = tokenization.convert_to_unicode(line[2])
      if set_type == "test":
        label = "0"
      else:
        label = tokenization.convert_to_unicode(line[0])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=text_b, label=label))
    return examples

class LexsubProcessor(DataProcessor):
  """Processor for the MRPC data set (GLUE version)."""

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

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

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

  def get_labels(self):
    """See base class."""
    return ["0", "1"]

  def _create_examples(self, lines, set_type):
    """Creates examples for the training and dev sets."""
    examples = []
    for (i, line) in enumerate(lines):
      #if i == 0:
        #continue
      guid = "%s-%s" % (set_type, i)
      text_a = tokenization.convert_to_unicode(line[1])
      #print(line[1])
      
      masked_id = int(line[2])
      masked_expected = int(line[3])

      if set_type == "test":
        label = "0"
      else:
        label = tokenization.convert_to_unicode(line[0])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=None, label=label,
            masked_id=masked_id, masked_expected=masked_expected))
    return examples


class ColaProcessor(DataProcessor):
  """Processor for the CoLA data set (GLUE version)."""

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

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

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

  def get_labels(self):
    """See base class."""
    return ["0", "1"]

  def _create_examples(self, lines, set_type):
    """Creates examples for the training and dev sets."""
    examples = []
    for (i, line) in enumerate(lines):
      # Only the test set has a header
      if set_type == "test" and i == 0:
        continue
      guid = "%s-%s" % (set_type, i)
      if set_type == "test":
        text_a = tokenization.convert_to_unicode(line[1])
        label = "0"
      else:
        text_a = tokenization.convert_to_unicode(line[3])
        label = tokenization.convert_to_unicode(line[1])
      examples.append(
          InputExample(guid=guid, text_a=text_a, text_b=None, label=label))
    return examples


def convert_single_example(ex_index, example, label_list, max_seq_length,
                           tokenizer):
  """Converts a single `InputExample` into a single `InputFeatures`."""
  label_map = {}
  for (i, label) in enumerate(label_list):
    label_map[label] = i

  masked_word = example.text_a.split(' ')[example.masked_id]
  #print(masked_word)
  #print(example.text_a)
  #print("masked_id ",example.masked_id)
  #print("masked_word: ",masked_word)

  #assert(masked_word == 'MASK')

  #tokens_a = tokenizer.tokenize(example.text_a)
  tokens_a = example.text_a.split(' ')
  tokens_b = None
  if example.text_b:
    tokens_b = tokenizer.tokenize(example.text_b)

  if tokens_b:
    # Modifies `tokens_a` and `tokens_b` in place so that the total
    # length is less than the specified length.
    # Account for [CLS], [SEP], [SEP] with "- 3"
    _truncate_seq_pair(tokens_a, tokens_b, max_seq_length - 3)
  else:
    # Account for [CLS] and [SEP] with "- 2"
    if len(tokens_a) > max_seq_length - 2:
      tokens_a = tokens_a[0:(max_seq_length - 2)]

  # 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 = []
  segment_ids = []
  tokens.append("[CLS]")
  segment_ids.append(0)

  found_mask_word = False

  #print(masked_word)
  for (i,token) in enumerate(tokens_a):
    #print(token)
    if token == "MASK" or token == masked_word:
      masked_id = i + 1
      found_mask_word = True
      if token == 'MASK':
        token = "[MASK]"
    tokens.append(token)
    segment_ids.append(0)
  #if not found_mask_word:
    #print('target word : %s has been tokenized...' %(masked_word))
  tokens.append("[SEP]")
  segment_ids.append(0)

  if tokens_b:
    for token in tokens_b:
      tokens.append(token)
      segment_ids.append(1)
    tokens.append("[SEP]")
    segment_ids.append(1)

  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] * len(input_ids)
  #print(masked_id)

  # Zero-pad up to the sequence length.
  while len(input_ids) < max_seq_length:
    input_ids.append(0)
    input_mask.append(0)
    segment_ids.append(0)

  assert len(input_ids) == max_seq_length
  assert len(input_mask) == max_seq_length
  assert len(segment_ids) == max_seq_length

  label_id = label_map[example.label]
  if ex_index < 5:
    tf.logging.info("*** Example ***")
    tf.logging.info("guid: %s" % (example.guid))
    tf.logging.info("tokens: %s" % " ".join(
        [tokenization.printable_text(x) for x in tokens]))
    tf.logging.info("input_ids: %s" % " ".join([str(x) for x in input_ids]))
    tf.logging.info("input_mask: %s" % " ".join([str(x) for x in input_mask]))
    tf.logging.info("segment_ids: %s" % " ".join([str(x) for x in segment_ids]))
    tf.logging.info("label: %s (id = %d)" % (example.label, label_id))

  feature = InputFeatures(
      input_ids=input_ids,
      input_mask=input_mask,
      segment_ids=segment_ids,
      label_id=label_id,
      masked_id=masked_id,
      masked_expected=example.masked_expected)

  return feature


def file_based_convert_examples_to_features(
    examples, label_list, max_seq_length, tokenizer, output_file):
  """Convert a set of `InputExample`s to a TFRecord file."""

  writer = tf.python_io.TFRecordWriter(output_file)

  for (ex_index, example) in enumerate(examples):
    if ex_index % 10000 == 0:
      tf.logging.info("Writing example %d of %d" % (ex_index, len(examples)))

    feature = convert_single_example(ex_index, example, label_list,
                                     max_seq_length, tokenizer)

    def create_int_feature(values):
      f = tf.train.Feature(int64_list=tf.train.Int64List(value=list(values)))
      return f

    features = collections.OrderedDict()
    features["input_ids"] = create_int_feature(feature.input_ids)
    features["input_mask"] = create_int_feature(feature.input_mask)
    features["segment_ids"] = create_int_feature(feature.segment_ids)
    features["label_ids"] = create_int_feature([feature.label_id])
    features["masked_id"] = create_int_feature([feature.masked_id])
    features["masked_expected"] = create_int_feature([feature.masked_expected])

    tf_example = tf.train.Example(features=tf.train.Features(feature=features))
    writer.write(tf_example.SerializeToString())


def file_based_input_fn_builder(input_file, seq_length, is_training,
                                drop_remainder):
  """Creates an `input_fn` closure to be passed to TPUEstimator."""

  name_to_features = {
      "input_ids": tf.FixedLenFeature([seq_length], tf.int64),
      "input_mask": tf.FixedLenFeature([seq_length], tf.int64),
      "segment_ids": tf.FixedLenFeature([seq_length], tf.int64),
      "label_ids": tf.FixedLenFeature([], tf.int64),
      "masked_id": tf.FixedLenFeature([], tf.int64),
      "masked_expected": tf.FixedLenFeature([], tf.int64),
  }

  def _decode_record(record, name_to_features):
    """Decodes a record to a TensorFlow example."""
    example = tf.parse_single_example(record, name_to_features)

    # tf.Example only supports tf.int64, but the TPU only supports tf.int32.
    # So cast all int64 to int32.
    for name in list(example.keys()):
      t = example[name]
      if t.dtype == tf.int64:
        t = tf.to_int32(t)
      example[name] = t

    return example

  def input_fn(params):
    """The actual input function."""
    batch_size = params["batch_size"]

    # For training, we want a lot of parallel reading and shuffling.
    # For eval, we want no shuffling and parallel reading doesn't matter.
    d = tf.data.TFRecordDataset(input_file)
    if is_training:
      d = d.repeat()
      d = d.shuffle(buffer_size=100)

    d = d.apply(
        tf.contrib.data.map_and_batch(
            lambda record: _decode_record(record, name_to_features),
            batch_size=batch_size,
            drop_remainder=drop_remainder))

    return d

  return input_fn


def _truncate_seq_pair(tokens_a, tokens_b, max_length):
  """Truncates a sequence pair in place to the maximum length."""

  # This is a simple heuristic which will always truncate the longer sequence
  # one token at a time. This makes more sense than truncating an equal percent
  # of tokens from each, since if one sequence is very short then each token
  # that's truncated likely contains more information than a longer sequence.
  while True:
    total_length = len(tokens_a) + len(tokens_b)
    if total_length <= max_length:
      break
    if len(tokens_a) > len(tokens_b):
      tokens_a.pop()
    else:
      tokens_b.pop()


def create_model(bert_config, is_training, input_ids, input_mask, segment_ids,
                 labels, num_labels, use_one_hot_embeddings, masked_id, masked_expected):
  """Creates a classification model."""
  model = modeling.BertModel(
      config=bert_config,
      is_training=is_training,
      input_ids=input_ids,
      input_mask=input_mask,
      token_type_ids=segment_ids,
      use_one_hot_embeddings=use_one_hot_embeddings,
      masked_id=masked_id)

  # In the demo, we are doing a simple classification task on the entire
  # segment.
  #
  # If you want to use the token-level output, use model.get_sequence_output()
  # instead.
  logits = get_masked_lm_output_logits(bert_config, model.get_sequence_output(),model.get_embedding_table(),
    masked_id)
  labels = masked_expected
  one_hot_labels = tf.one_hot(
      labels, depth=bert_config.vocab_size, dtype=tf.float32)
  all_probabilities = tf.cast(tf.nn.softmax(logits, axis=-1),tf.float32)
  proposal_values, proposal_indices = tf.nn.top_k(all_probabilities, k=200)

  probabilities = proposal_indices
  log_probs = tf.nn.log_softmax(logits, axis=-1)

  #one_hot_labels = tf.one_hot(labels, depth=num_labels, dtype=tf.float32)

  per_example_loss = -tf.reduce_sum(one_hot_labels * log_probs, axis=-1)
  loss = tf.reduce_mean(per_example_loss)
  attn_data_list = model.get_attn_data_list()
  attn_tensor = tf.stack([attn_data['attn_probs'] for attn_data in attn_data_list])
  seq_len = attn_tensor.shape[-1] 
  attention_list = []
  value_list = []
  for i in range(8):
    target_attention = attn_tensor[:,i,:,masked_id[i],:]
    target_attention = tf.reshape(target_attention,[-1,seq_len])
    target_attention = tf.reduce_mean(target_attention,axis=0)

    attention_values, attention_indices = tf.nn.top_k(target_attention, k=20)
    attention_list.append(attention_indices)
    value_list.append(attention_values)
  probabilities = {'attention_indices':tf.stack(attention_list), 'attention_values': tf.stack(value_list), 'indice_proposed':proposal_indices}
  return (loss, per_example_loss, logits, probabilities)


def get_masked_lm_output_logits(bert_config, input_tensor, output_weights, positions):
  """Get loss and log probs for the masked LM."""

  input_tensor = gather_indexes(input_tensor, positions)

  with tf.variable_scope("cls/predictions"):
    # We apply one more non-linear transformation before the output layer.
    # This matrix is not used after pre-training.
    with tf.variable_scope("transform"):
      input_tensor = tf.layers.dense(
          input_tensor,
          units=bert_config.hidden_size,
          activation=modeling.get_activation(bert_config.hidden_act),
          kernel_initializer=modeling.create_initializer(
              bert_config.initializer_range))
      input_tensor = modeling.layer_norm(input_tensor)

    # The output weights are the same as the input embeddings, but there is
    # an output-only bias for each token.
    output_bias = tf.get_variable(
        "output_bias",
        shape=[bert_config.vocab_size],
        initializer=tf.zeros_initializer())
    logits = tf.matmul(input_tensor, output_weights, transpose_b=True)
    logits = tf.nn.bias_add(logits, output_bias)


  return logits


def get_next_sentence_logits(bert_config, input_tensor):
  """Get loss and log probs for the next sentence prediction."""

  # Simple binary classification. Note that 0 is "next sentence" and 1 is
  # "random sentence". This weight matrix is not used after pre-training.
  with tf.variable_scope("cls/seq_relationship"):
    output_weights = tf.get_variable(
        "output_weights",
        shape=[2, bert_config.hidden_size],
        initializer=modeling.create_initializer(bert_config.initializer_range))
    output_bias = tf.get_variable(
        "output_bias", shape=[2], initializer=tf.zeros_initializer())

    logits = tf.matmul(input_tensor, output_weights, transpose_b=True)
    logits = tf.nn.bias_add(logits, output_bias)

    return logits

def gather_indexes(sequence_tensor, positions):
  """Gathers the vectors at the specific positions over a minibatch."""
  sequence_shape = modeling.get_shape_list(sequence_tensor, expected_rank=3)
  batch_size = sequence_shape[0]
  seq_length = sequence_shape[1]
  width = sequence_shape[2]

  positions = tf.reshape(positions,[batch_size,-1])

  flat_offsets = tf.reshape(
      tf.range(0, batch_size, dtype=tf.int32) * seq_length, [-1, 1])
  flat_positions = tf.reshape(positions + flat_offsets, [-1])
  flat_sequence_tensor = tf.reshape(sequence_tensor,
                                    [batch_size * seq_length, width])
  output_tensor = tf.gather(flat_sequence_tensor, flat_positions)
  return output_tensor


def model_fn_builder(bert_config, num_labels, init_checkpoint, learning_rate,
                     num_train_steps, num_warmup_steps, use_tpu,
                     use_one_hot_embeddings):
  """Returns `model_fn` closure for TPUEstimator."""

  def model_fn(features, labels, mode, params):  # pylint: disable=unused-argument
    """The `model_fn` for TPUEstimator."""

    tf.logging.info("*** Features ***")
    for name in sorted(features.keys()):
      tf.logging.info("  name = %s, shape = %s" % (name, features[name].shape))

    input_ids = features["input_ids"]
    input_mask = features["input_mask"]
    segment_ids = features["segment_ids"]
    label_ids = features["label_ids"]
    masked_id = features["masked_id"]
    masked_expected = features["masked_expected"]

    is_training = (mode == tf.estimator.ModeKeys.TRAIN)

    (total_loss, per_example_loss, logits, probabilities) = create_model(
        bert_config, is_training, input_ids, input_mask, segment_ids, label_ids,
        num_labels, use_one_hot_embeddings, masked_id, masked_expected)

    tvars = tf.trainable_variables()
    initialized_variable_names = {}
    scaffold_fn = None
    if init_checkpoint:
      (assignment_map, initialized_variable_names
      ) = modeling.get_assignment_map_from_checkpoint(tvars, init_checkpoint)
      if use_tpu:

        def tpu_scaffold():
          tf.train.init_from_checkpoint(init_checkpoint, assignment_map)
          return tf.train.Scaffold()

        scaffold_fn = tpu_scaffold
      else:
        tf.train.init_from_checkpoint(init_checkpoint, assignment_map)

    tf.logging.info("**** Trainable Variables ****")
    for var in tvars:
      init_string = ""
      if var.name in initialized_variable_names:
        init_string = ", *INIT_FROM_CKPT*"
      tf.logging.info("  name = %s, shape = %s%s", var.name, var.shape,
                      init_string)

    output_spec = None
    if mode == tf.estimator.ModeKeys.TRAIN:

      train_op = optimization.create_optimizer(
          total_loss, learning_rate, num_train_steps, num_warmup_steps, use_tpu)

      output_spec = tf.contrib.tpu.TPUEstimatorSpec(
          mode=mode,
          loss=total_loss,
          train_op=train_op,
          scaffold_fn=scaffold_fn)
    elif mode == tf.estimator.ModeKeys.EVAL:

      def metric_fn(per_example_loss, label_ids, logits):
        predictions = tf.argmax(logits, axis=-1, output_type=tf.int32)
        accuracy = tf.metrics.accuracy(label_ids, predictions)
        loss = tf.metrics.mean(per_example_loss)
        return {
            "eval_accuracy": accuracy,
            "eval_loss": loss,
        }

      eval_metrics = (metric_fn, [per_example_loss, label_ids, logits])
      output_spec = tf.contrib.tpu.TPUEstimatorSpec(
          mode=mode,
          loss=total_loss,
          eval_metrics=eval_metrics,
          scaffold_fn=scaffold_fn)
    else:
      output_spec = tf.contrib.tpu.TPUEstimatorSpec(
          mode=mode, predictions=probabilities, scaffold_fn=scaffold_fn)
    return output_spec

  return model_fn


# This function is not used by this file but is still used by the Colab and
# people who depend on it.
def input_fn_builder(features, seq_length, is_training, drop_remainder):
  """Creates an `input_fn` closure to be passed to TPUEstimator."""

  all_input_ids = []
  all_input_mask = []
  all_segment_ids = []
  all_label_ids = []
  all_masked_id = []
  all_masked_expected = []

  for feature in features:
    all_input_ids.append(feature.input_ids)
    all_input_mask.append(feature.input_mask)
    all_segment_ids.append(feature.segment_ids)
    all_label_ids.append(feature.label_id)
    all_masked_id.append(feature.masked_id)
    all_masked_expected.append(feature.masked_expected)


  def input_fn(params):
    """The actual input function."""
    batch_size = params["batch_size"]

    num_examples = len(features)

    # This is for demo purposes and does NOT scale to large data sets. We do
    # not use Dataset.from_generator() because that uses tf.py_func which is
    # not TPU compatible. The right way to load data is with TFRecordReader.
    d = tf.data.Dataset.from_tensor_slices({
        "input_ids":
            tf.constant(
                all_input_ids, shape=[num_examples, seq_length],
                dtype=tf.int32),
        "input_mask":
            tf.constant(
                all_input_mask,
                shape=[num_examples, seq_length],
                dtype=tf.int32),
        "segment_ids":
            tf.constant(
                all_segment_ids,
                shape=[num_examples, seq_length],
                dtype=tf.int32),
        "label_ids":
            tf.constant(all_label_ids, shape=[num_examples], dtype=tf.int32),
        "masked_id":
            tf.constant(all_masked_id, shape=[num_examples], dtype=tf.int32),
        "masked_expected":
            tf.constant(all_masked_expected, shape=[num_examples], dtype=tf.int32),
    })

    if is_training:
      d = d.repeat()
      d = d.shuffle(buffer_size=100)

    d = d.batch(batch_size=batch_size, drop_remainder=drop_remainder)
    return d

  return input_fn


# This function is not used by this file but is still used by the Colab and
# people who depend on it.
def convert_examples_to_features(examples, label_list, max_seq_length,
                                 tokenizer):
  """Convert a set of `InputExample`s to a list of `InputFeatures`."""

  features = []
  for (ex_index, example) in enumerate(examples):
    if ex_index % 10000 == 0:
      tf.logging.info("Writing example %d of %d" % (ex_index, len(examples)))

    feature = convert_single_example(ex_index, example, label_list,
                                     max_seq_length, tokenizer)

    features.append(feature)
  return features



def convert_to_unicode(text):
  """Converts `text` to Unicode (if it's not already), assuming utf-8 input."""
  if six.PY3:
    if isinstance(text, str):
      return text
    elif isinstance(text, bytes):
      return text.decode("utf-8", "ignore")
    else:
      raise ValueError("Unsupported string type: %s" % (type(text)))
  elif six.PY2:
    if isinstance(text, str):
      return text.decode("utf-8", "ignore")
    elif isinstance(text, unicode):
      return text
    else:
      raise ValueError("Unsupported string type: %s" % (type(text)))
  else:
    raise ValueError("Not running on Python2 or Python 3?")


def load_vocab(vocab_file):
  """Loads a vocabulary file into a dictionary."""
  vocab = collections.OrderedDict()
  index = 0
  with tf.gfile.GFile(vocab_file, "r") as reader:
    while True:
      token = convert_to_unicode(reader.readline())
      if not token:
        break
      token = token.strip()
      vocab[token] = index
      index += 1
  return vocab

def get_index(list_candidates, candidate):

    if candidate in list_candidates:
        return list_candidates.index(candidate)
    else:
        return 200
    
def line2candidate(result_file, input_file, vocab, methode = 'add'):
    results = open(result_file,'r',encoding='utf-8').readlines()
    print(len(results))
    #print(results[-1])
    inputs = open(input_file,'r').readlines()
    print(len(inputs))
    output_index = 0
    #inv_vocab = {index : word for (word, index) in vocab.items()}
    with tf.gfile.GFile("candidates", "w") as writer:    
        for input_line in inputs:
            all_candidates = []
            candidate_1 = results[output_index].split(' ')
            all_candidates.extend(candidate_1)
            output_index += 1
            candidate_2 = results[output_index].split(' ')
            all_candidates.extend(candidate_2)
            output_index += 1
            candidate_3 = results[output_index].split(' ')
            all_candidates.extend(candidate_3)
            output_index += 1
            candidates = set(all_candidates)
            candidate_scores = []
            for candidate in candidates:
                if candidate in vocab.keys() and (vocab[candidate] > 29613 or vocab[candidate] < 1996):
                    continue
                if candidate == '...':
                    continue
                score_1 = get_index(candidate_1, candidate)
                score_2 = get_index(candidate_2, candidate)
                score_3 = get_index(candidate_3, candidate)
                candidate_scores.append([candidate, score_1 + score_2 * 0.2 + score_3 * 0.8 ])
            candidate_scores.sort(key=itemgetter(1))
            candidates_proposed = candidate_scores[:50]
            for item,score in candidates_proposed:
                writer.write(item + ' ')
            writer.write('\n')
    return


def attention2context(num_lines, attention_file='./lexsub_output/attention.tsv',context_file='context', max_context_len=12):

    attention_scores = open(attention_file,'r').readlines()
    with tf.gfile.GFile(context_file, "w") as writer:
        for i in range(num_lines):
            target_index = i*3
            attention_line = attention_scores[target_index]
            pairs = attention_line.split('\t')
            #print(pairs)
            context = []
            score_total = 0
            for j in range(12):
                next_pair = pairs[j+1]
                if float(next_pair.split(' ')[1]) <= 0.01:
                    break
                #context.append(next_pair)
                score_total += float(next_pair.split(' ')[1])

            factor = 1/score_total
            
            for j in range(12):
                next_pair = pairs[j+1]
                if float(next_pair.split(' ')[1]) <= 0.01:
                    break
                context.append(next_pair.split(' ')[0] + ' ' + str(float(next_pair.split(' ')[1]) * factor))
                
            line = '\t'.join(context)+'\n'
            writer.write(line)

def main(_):
  tf.logging.set_verbosity(tf.logging.INFO)

  vocab = load_vocab("../uncased_L-24_H-1024_A-16/vocab.txt")

  processors = {
      "cola": ColaProcessor,
      "mnli": MnliProcessor,
      "mrpc": MrpcProcessor,
      "xnli": XnliProcessor,
      "next": NextSentenceProcessor,
      "lexsub": LexsubProcessor,
  }

  if not FLAGS.do_train and not FLAGS.do_eval and not FLAGS.do_predict:
    raise ValueError(
        "At least one of `do_train`, `do_eval` or `do_predict' must be True.")

  bert_config = modeling.BertConfig.from_json_file(FLAGS.bert_config_file)

  if FLAGS.max_seq_length > bert_config.max_position_embeddings:
    raise ValueError(
        "Cannot use sequence length %d because the BERT model "
        "was only trained up to sequence length %d" %
        (FLAGS.max_seq_length, bert_config.max_position_embeddings))

  tf.gfile.MakeDirs(FLAGS.output_dir)

  task_name = FLAGS.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()

  tokenizer = tokenization.FullTokenizer(
      vocab_file=FLAGS.vocab_file, do_lower_case=FLAGS.do_lower_case)

  tpu_cluster_resolver = None
  if FLAGS.use_tpu and FLAGS.tpu_name:
    tpu_cluster_resolver = tf.contrib.cluster_resolver.TPUClusterResolver(
        FLAGS.tpu_name, zone=FLAGS.tpu_zone, project=FLAGS.gcp_project)

  is_per_host = tf.contrib.tpu.InputPipelineConfig.PER_HOST_V2
  run_config = tf.contrib.tpu.RunConfig(
      cluster=tpu_cluster_resolver,
      master=FLAGS.master,
      model_dir=FLAGS.output_dir,
      save_checkpoints_steps=FLAGS.save_checkpoints_steps,
      tpu_config=tf.contrib.tpu.TPUConfig(
          iterations_per_loop=FLAGS.iterations_per_loop,
          num_shards=FLAGS.num_tpu_cores,
          per_host_input_for_training=is_per_host))

  train_examples = None
  num_train_steps = None
  num_warmup_steps = None
  if FLAGS.do_train:
    train_examples = processor.get_train_examples(FLAGS.data_dir)
    num_train_steps = int(
        len(train_examples) / FLAGS.train_batch_size * FLAGS.num_train_epochs)
    num_warmup_steps = int(num_train_steps * FLAGS.warmup_proportion)

  model_fn = model_fn_builder(
      bert_config=bert_config,
      num_labels=len(label_list),
      init_checkpoint=FLAGS.init_checkpoint,
      learning_rate=FLAGS.learning_rate,
      num_train_steps=num_train_steps,
      num_warmup_steps=num_warmup_steps,
      use_tpu=FLAGS.use_tpu,
      use_one_hot_embeddings=FLAGS.use_tpu)

  # If TPU is not available, this will fall back to normal Estimator on CPU
  # or GPU.
  estimator = tf.contrib.tpu.TPUEstimator(
      use_tpu=FLAGS.use_tpu,
      model_fn=model_fn,
      config=run_config,
      train_batch_size=FLAGS.train_batch_size,
      eval_batch_size=FLAGS.eval_batch_size,
      predict_batch_size=FLAGS.predict_batch_size)

  if FLAGS.do_train:
    train_file = os.path.join(FLAGS.output_dir, "train.tf_record")
    file_based_convert_examples_to_features(
        train_examples, label_list, FLAGS.max_seq_length, tokenizer, train_file)
    tf.logging.info("***** Running training *****")
    tf.logging.info("  Num examples = %d", len(train_examples))
    tf.logging.info("  Batch size = %d", FLAGS.train_batch_size)
    tf.logging.info("  Num steps = %d", num_train_steps)
    train_input_fn = file_based_input_fn_builder(
        input_file=train_file,
        seq_length=FLAGS.max_seq_length,
        is_training=True,
        drop_remainder=True)
    estimator.train(input_fn=train_input_fn, max_steps=num_train_steps)

  if FLAGS.do_eval:
    eval_examples = processor.get_dev_examples(FLAGS.data_dir)
    eval_file = os.path.join(FLAGS.output_dir, "eval.tf_record")
    file_based_convert_examples_to_features(
        eval_examples, label_list, FLAGS.max_seq_length, tokenizer, eval_file)

    tf.logging.info("***** Running evaluation *****")
    tf.logging.info("  Num examples = %d", len(eval_examples))
    tf.logging.info("  Batch size = %d", FLAGS.eval_batch_size)

    # This tells the estimator to run through the entire set.
    eval_steps = None
    # However, if running eval on the TPU, you will need to specify the
    # number of steps.
    if FLAGS.use_tpu:
      # Eval will be slightly WRONG on the TPU because it will truncate
      # the last batch.
      eval_steps = int(len(eval_examples) / FLAGS.eval_batch_size)

    eval_drop_remainder = True if FLAGS.use_tpu else False
    eval_input_fn = file_based_input_fn_builder(
        input_file=eval_file,
        seq_length=FLAGS.max_seq_length,
        is_training=False,
        drop_remainder=eval_drop_remainder)

    result = estimator.evaluate(input_fn=eval_input_fn, steps=eval_steps)

    output_eval_file = os.path.join(FLAGS.output_dir, "eval_results.txt")
    with tf.gfile.GFile(output_eval_file, "w") as writer:
      tf.logging.info("***** Eval results *****")
      for key in sorted(result.keys()):
        tf.logging.info("  %s = %s", key, str(result[key]))
        writer.write("%s = %s\n" % (key, str(result[key])))

  if FLAGS.do_predict:
    predict_examples = processor.get_test_examples(FLAGS.data_dir)
    predict_file = os.path.join(FLAGS.output_dir, "predict.tf_record")
    file_based_convert_examples_to_features(predict_examples, label_list,
                                            FLAGS.max_seq_length, tokenizer,
                                            predict_file)

    tf.logging.info("***** Running prediction*****")
    tf.logging.info("  Num examples = %d", len(predict_examples))
    tf.logging.info("  Batch size = %d", FLAGS.predict_batch_size)

    if FLAGS.use_tpu:
      # Warning: According to tpu_estimator.py Prediction on TPU is an
      # experimental feature and hence not supported here
      raise ValueError("Prediction in TPU not supported")

    predict_drop_remainder = True if FLAGS.use_tpu else False
    predict_input_fn = file_based_input_fn_builder(
        input_file=predict_file,
        seq_length=FLAGS.max_seq_length,
        is_training=False,
        drop_remainder=predict_drop_remainder)

    result = estimator.predict(input_fn=predict_input_fn)
    print(result)

    output_predict_file = os.path.join(FLAGS.output_dir, "attention.tsv")
    output_proposal_file = os.path.join(FLAGS.output_dir, "proposed_substitute_candidates.tsv")
    inv_vocab = {index : word for (word, index) in vocab.items()}

    with tf.gfile.GFile(output_predict_file, "w") as writer:
        with tf.gfile.GFile(output_proposal_file, "w") as writer_p:
          tf.logging.info("***** Predict results *****")
          for prediction in result:
            for candidate_id in prediction['indice_proposed']:
              output_line = inv_vocab[candidate_id] + ' '
              writer_p.write(output_line)
            writer_p.write('\n')
            for indice,value in zip(prediction['attention_indices'], prediction['attention_values']):
              output_line = str(indice) + ' ' + str(value) + '\t'
              writer.write(output_line)
            writer.write('\n')
            
    num_lines = len(open("lst_all.preprocessed",'r').readlines())
    line2candidate("./lexsub_output/proposed_substitute_candidates.tsv",'lst_all.preprocessed',vocab)
    attention2context(num_lines)


if __name__ == "__main__":
  flags.mark_flag_as_required("data_dir")
  flags.mark_flag_as_required("task_name")
  flags.mark_flag_as_required("vocab_file")
  flags.mark_flag_as_required("bert_config_file")
  flags.mark_flag_as_required("output_dir")
  tf.app.run()