run_squad_helper.py

# Copyright 2019 The TensorFlow Authors. 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.
# ==============================================================================
"""Library for running BERT family models on SQuAD 1.1/2.0 in TF 2.x."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import collections
import json
import os
from absl import flags
from absl import logging
import tensorflow as tf
from official.modeling import performance
from official.nlp import optimization
from official.nlp.bert import bert_models
from official.nlp.bert import common_flags
from official.nlp.bert import input_pipeline
from official.nlp.bert import model_saving_utils
from official.nlp.bert import model_training_utils
from official.nlp.bert import squad_evaluate_v1_1
from official.nlp.bert import squad_evaluate_v2_0
from official.nlp.data import squad_lib_sp
from official.utils.misc import keras_utils


def define_common_squad_flags():
  """Defines common flags used by SQuAD tasks."""
  flags.DEFINE_enum(
      'mode', 'train_and_eval',
      ['train_and_eval', 'train_and_predict',
       'train', 'eval', 'predict', 'export_only'],
      'One of {"train_and_eval", "train_and_predict", '
      '"train", "eval", "predict", "export_only"}. '
      '`train_and_eval`: train & predict to json files & compute eval metrics. '
      '`train_and_predict`: train & predict to json files. '
      '`train`: only trains the model. '
      '`eval`: predict answers from squad json file & compute eval metrics. '
      '`predict`: predict answers from the squad json file. '
      '`export_only`: will take the latest checkpoint inside '
      'model_dir and export a `SavedModel`.')
  flags.DEFINE_string('train_data_path', '',
                      'Training data path with train tfrecords.')
  flags.DEFINE_string(
      'input_meta_data_path', None,
      'Path to file that contains meta data about input '
      'to be used for training and evaluation.')
  # Model training specific flags.
  flags.DEFINE_integer('train_batch_size', 32, 'Total batch size for training.')
  # Predict processing related.
  flags.DEFINE_string('predict_file', None,
                      'SQuAD prediction json file path. '
                      '`predict` mode supports multiple files: one can use '
                      'wildcard to specify multiple files and it can also be '
                      'multiple file patterns separated by comma. Note that '
                      '`eval` mode only supports a single predict file.')
  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_float(
      'null_score_diff_threshold', 0.0,
      'If null_score - best_non_null is greater than the threshold, '
      'predict null. This is only used for SQuAD v2.')
  flags.DEFINE_bool(
      'verbose_logging', False,
      'If true, all of the warnings related to data processing will be '
      'printed. A number of warnings are expected for a normal SQuAD '
      'evaluation.')
  flags.DEFINE_integer('predict_batch_size', 8,
                       'Total batch size for prediction.')
  flags.DEFINE_integer(
      'n_best_size', 20,
      'The total number of n-best predictions to generate in the '
      'nbest_predictions.json output file.')
  flags.DEFINE_integer(
      'max_answer_length', 30,
      'The maximum length of an answer that can be generated. This is needed '
      'because the start and end predictions are not conditioned on one '
      'another.')

  common_flags.define_common_bert_flags()


FLAGS = flags.FLAGS


def squad_loss_fn(start_positions,
                  end_positions,
                  start_logits,
                  end_logits):
  """Returns sparse categorical crossentropy for start/end logits."""
  start_loss = tf.keras.losses.sparse_categorical_crossentropy(
      start_positions, start_logits, from_logits=True)
  end_loss = tf.keras.losses.sparse_categorical_crossentropy(
      end_positions, end_logits, from_logits=True)

  total_loss = (tf.reduce_mean(start_loss) + tf.reduce_mean(end_loss)) / 2
  return total_loss


def get_loss_fn():
  """Gets a loss function for squad task."""

  def _loss_fn(labels, model_outputs):
    start_positions = labels['start_positions']
    end_positions = labels['end_positions']
    start_logits, end_logits = model_outputs
    return squad_loss_fn(
        start_positions,
        end_positions,
        start_logits,
        end_logits)

  return _loss_fn


RawResult = collections.namedtuple('RawResult',
                                   ['unique_id', 'start_logits', 'end_logits'])


def get_raw_results(predictions):
  """Converts multi-replica predictions to RawResult."""
  for unique_ids, start_logits, end_logits in zip(predictions['unique_ids'],
                                                  predictions['start_logits'],
                                                  predictions['end_logits']):
    for values in zip(unique_ids.numpy(), start_logits.numpy(),
                      end_logits.numpy()):
      yield RawResult(
          unique_id=values[0],
          start_logits=values[1].tolist(),
          end_logits=values[2].tolist())


def get_dataset_fn(input_file_pattern, max_seq_length, global_batch_size,
                   is_training):
  """Gets a closure to create a dataset.."""

  def _dataset_fn(ctx=None):
    """Returns tf.data.Dataset for distributed BERT pretraining."""
    batch_size = ctx.get_per_replica_batch_size(
        global_batch_size) if ctx else global_batch_size
    dataset = input_pipeline.create_squad_dataset(
        input_file_pattern,
        max_seq_length,
        batch_size,
        is_training=is_training,
        input_pipeline_context=ctx)
    return dataset

  return _dataset_fn


def get_squad_model_to_predict(strategy, bert_config, checkpoint_path,
                               input_meta_data):
  """Gets a squad model to make predictions."""
  with strategy.scope():
    # Prediction always uses float32, even if training uses mixed precision.
    tf.keras.mixed_precision.experimental.set_policy('float32')
    squad_model, _ = bert_models.squad_model(
        bert_config,
        input_meta_data['max_seq_length'],
        hub_module_url=FLAGS.hub_module_url)

  if checkpoint_path is None:
    checkpoint_path = tf.train.latest_checkpoint(FLAGS.model_dir)
  logging.info('Restoring checkpoints from %s', checkpoint_path)
  checkpoint = tf.train.Checkpoint(model=squad_model)
  checkpoint.restore(checkpoint_path).expect_partial()
  return squad_model


def predict_squad_customized(strategy,
                             input_meta_data,
                             predict_tfrecord_path,
                             num_steps,
                             squad_model):
  """Make predictions using a Bert-based squad model."""
  predict_dataset_fn = get_dataset_fn(
      predict_tfrecord_path,
      input_meta_data['max_seq_length'],
      FLAGS.predict_batch_size,
      is_training=False)
  predict_iterator = iter(
      strategy.experimental_distribute_datasets_from_function(
          predict_dataset_fn))

  @tf.function
  def predict_step(iterator):
    """Predicts on distributed devices."""

    def _replicated_step(inputs):
      """Replicated prediction calculation."""
      x, _ = inputs
      unique_ids = x.pop('unique_ids')
      start_logits, end_logits = squad_model(x, training=False)
      return dict(
          unique_ids=unique_ids,
          start_logits=start_logits,
          end_logits=end_logits)

    outputs = strategy.run(_replicated_step, args=(next(iterator),))
    return tf.nest.map_structure(strategy.experimental_local_results, outputs)

  all_results = []
  for _ in range(num_steps):
    predictions = predict_step(predict_iterator)
    for result in get_raw_results(predictions):
      all_results.append(result)
    if len(all_results) % 100 == 0:
      logging.info('Made predictions for %d records.', len(all_results))
  return all_results


def train_squad(strategy,
                input_meta_data,
                bert_config,
                custom_callbacks=None,
                run_eagerly=False,
                init_checkpoint=None,
                sub_model_export_name=None):
  """Run bert squad training."""
  if strategy:
    logging.info('Training using customized training loop with distribution'
                 ' strategy.')
  # Enables XLA in Session Config. Should not be set for TPU.
  keras_utils.set_session_config(FLAGS.enable_xla)
  performance.set_mixed_precision_policy(common_flags.dtype())

  epochs = FLAGS.num_train_epochs
  num_train_examples = input_meta_data['train_data_size']
  max_seq_length = input_meta_data['max_seq_length']
  steps_per_epoch = int(num_train_examples / FLAGS.train_batch_size)
  warmup_steps = int(epochs * num_train_examples * 0.1 / FLAGS.train_batch_size)
  train_input_fn = get_dataset_fn(
      FLAGS.train_data_path,
      max_seq_length,
      FLAGS.train_batch_size,
      is_training=True)

  def _get_squad_model():
    """Get Squad model and optimizer."""
    squad_model, core_model = bert_models.squad_model(
        bert_config,
        max_seq_length,
        hub_module_url=FLAGS.hub_module_url,
        hub_module_trainable=FLAGS.hub_module_trainable)
    optimizer = optimization.create_optimizer(FLAGS.learning_rate,
                                              steps_per_epoch * epochs,
                                              warmup_steps,
                                              FLAGS.end_lr,
                                              FLAGS.optimizer_type)

    squad_model.optimizer = performance.configure_optimizer(
        optimizer,
        use_float16=common_flags.use_float16(),
        use_graph_rewrite=common_flags.use_graph_rewrite())
    return squad_model, core_model

  # If explicit_allreduce = True, apply_gradients() no longer implicitly
  # allreduce gradients, users manually allreduce gradient and pass the
  # allreduced grads_and_vars to apply_gradients(). clip_by_global_norm will be
  # applied to allreduced gradients.
  def clip_by_global_norm_callback(grads_and_vars):
    grads, variables = zip(*grads_and_vars)
    (clipped_grads, _) = tf.clip_by_global_norm(grads, clip_norm=1.0)
    return zip(clipped_grads, variables)

  model_training_utils.run_customized_training_loop(
      strategy=strategy,
      model_fn=_get_squad_model,
      loss_fn=get_loss_fn(),
      model_dir=FLAGS.model_dir,
      steps_per_epoch=steps_per_epoch,
      steps_per_loop=FLAGS.steps_per_loop,
      epochs=epochs,
      train_input_fn=train_input_fn,
      init_checkpoint=init_checkpoint or FLAGS.init_checkpoint,
      sub_model_export_name=sub_model_export_name,
      run_eagerly=run_eagerly,
      custom_callbacks=custom_callbacks,
      explicit_allreduce=False,
      post_allreduce_callbacks=[clip_by_global_norm_callback])


def prediction_output_squad(strategy, input_meta_data, tokenizer, squad_lib,
                            predict_file, squad_model):
  """Makes predictions for a squad dataset."""
  doc_stride = input_meta_data['doc_stride']
  max_query_length = input_meta_data['max_query_length']
  # Whether data should be in Ver 2.0 format.
  version_2_with_negative = input_meta_data.get('version_2_with_negative',
                                                False)
  eval_examples = squad_lib.read_squad_examples(
      input_file=predict_file,
      is_training=False,
      version_2_with_negative=version_2_with_negative)

  eval_writer = squad_lib.FeatureWriter(
      filename=os.path.join(FLAGS.model_dir, 'eval.tf_record'),
      is_training=False)
  eval_features = []

  def _append_feature(feature, is_padding):
    if not is_padding:
      eval_features.append(feature)
    eval_writer.process_feature(feature)

  # TPU requires a fixed batch size for all batches, therefore the number
  # of examples must be a multiple of the batch size, or else examples
  # will get dropped. So we pad with fake examples which are ignored
  # later on.
  kwargs = dict(
      examples=eval_examples,
      tokenizer=tokenizer,
      max_seq_length=input_meta_data['max_seq_length'],
      doc_stride=doc_stride,
      max_query_length=max_query_length,
      is_training=False,
      output_fn=_append_feature,
      batch_size=FLAGS.predict_batch_size)

  # squad_lib_sp requires one more argument 'do_lower_case'.
  if squad_lib == squad_lib_sp:
    kwargs['do_lower_case'] = FLAGS.do_lower_case
  dataset_size = squad_lib.convert_examples_to_features(**kwargs)
  eval_writer.close()

  logging.info('***** Running predictions *****')
  logging.info('  Num orig examples = %d', len(eval_examples))
  logging.info('  Num split examples = %d', len(eval_features))
  logging.info('  Batch size = %d', FLAGS.predict_batch_size)

  num_steps = int(dataset_size / FLAGS.predict_batch_size)
  all_results = predict_squad_customized(
      strategy, input_meta_data, eval_writer.filename, num_steps, squad_model)

  all_predictions, all_nbest_json, scores_diff_json = (
      squad_lib.postprocess_output(
          eval_examples,
          eval_features,
          all_results,
          FLAGS.n_best_size,
          FLAGS.max_answer_length,
          FLAGS.do_lower_case,
          version_2_with_negative=version_2_with_negative,
          null_score_diff_threshold=FLAGS.null_score_diff_threshold,
          verbose=FLAGS.verbose_logging))

  return all_predictions, all_nbest_json, scores_diff_json


def dump_to_files(all_predictions, all_nbest_json, scores_diff_json,
                  squad_lib, version_2_with_negative, file_prefix=''):
  """Save output to json files."""
  output_prediction_file = os.path.join(FLAGS.model_dir,
                                        '%spredictions.json' % file_prefix)
  output_nbest_file = os.path.join(FLAGS.model_dir,
                                   '%snbest_predictions.json' % file_prefix)
  output_null_log_odds_file = os.path.join(FLAGS.model_dir, file_prefix,
                                           '%snull_odds.json' % file_prefix)
  logging.info('Writing predictions to: %s', (output_prediction_file))
  logging.info('Writing nbest to: %s', (output_nbest_file))

  squad_lib.write_to_json_files(all_predictions, output_prediction_file)
  squad_lib.write_to_json_files(all_nbest_json, output_nbest_file)
  if version_2_with_negative:
    squad_lib.write_to_json_files(scores_diff_json, output_null_log_odds_file)


def _get_matched_files(input_path):
  """Returns all files that matches the input_path."""
  input_patterns = input_path.strip().split(',')
  all_matched_files = []
  for input_pattern in input_patterns:
    input_pattern = input_pattern.strip()
    if not input_pattern:
      continue
    matched_files = tf.io.gfile.glob(input_pattern)
    if not matched_files:
      raise ValueError('%s does not match any files.' % input_pattern)
    else:
      all_matched_files.extend(matched_files)
  return sorted(all_matched_files)


def predict_squad(strategy,
                  input_meta_data,
                  tokenizer,
                  bert_config,
                  squad_lib,
                  init_checkpoint=None):
  """Get prediction results and evaluate them to hard drive."""
  if init_checkpoint is None:
    init_checkpoint = tf.train.latest_checkpoint(FLAGS.model_dir)

  all_predict_files = _get_matched_files(FLAGS.predict_file)
  squad_model = get_squad_model_to_predict(strategy, bert_config,
                                           init_checkpoint, input_meta_data)
  for idx, predict_file in enumerate(all_predict_files):
    all_predictions, all_nbest_json, scores_diff_json = prediction_output_squad(
        strategy, input_meta_data, tokenizer, squad_lib, predict_file,
        squad_model)
    if len(all_predict_files) == 1:
      file_prefix = ''
    else:
      # if predict_file is /path/xquad.ar.json, the `file_prefix` may be
      # "xquad.ar-0-"
      file_prefix = '%s-' % os.path.splitext(
          os.path.basename(all_predict_files[idx]))[0]
    dump_to_files(all_predictions, all_nbest_json, scores_diff_json, squad_lib,
                  input_meta_data.get('version_2_with_negative', False),
                  file_prefix)


def eval_squad(strategy,
               input_meta_data,
               tokenizer,
               bert_config,
               squad_lib,
               init_checkpoint=None):
  """Get prediction results and evaluate them against ground truth."""
  if init_checkpoint is None:
    init_checkpoint = tf.train.latest_checkpoint(FLAGS.model_dir)

  all_predict_files = _get_matched_files(FLAGS.predict_file)
  if len(all_predict_files) != 1:
    raise ValueError('`eval_squad` only supports one predict file, '
                     'but got %s' % all_predict_files)

  squad_model = get_squad_model_to_predict(strategy, bert_config,
                                           init_checkpoint, input_meta_data)
  all_predictions, all_nbest_json, scores_diff_json = prediction_output_squad(
      strategy, input_meta_data, tokenizer, squad_lib, all_predict_files[0],
      squad_model)
  dump_to_files(all_predictions, all_nbest_json, scores_diff_json, squad_lib,
                input_meta_data.get('version_2_with_negative', False))

  with tf.io.gfile.GFile(FLAGS.predict_file, 'r') as reader:
    dataset_json = json.load(reader)
    pred_dataset = dataset_json['data']
  if input_meta_data.get('version_2_with_negative', False):
    eval_metrics = squad_evaluate_v2_0.evaluate(pred_dataset,
                                                all_predictions,
                                                scores_diff_json)
  else:
    eval_metrics = squad_evaluate_v1_1.evaluate(pred_dataset, all_predictions)
  return eval_metrics


def export_squad(model_export_path, input_meta_data, bert_config):
  """Exports a trained model as a `SavedModel` for inference.

  Args:
    model_export_path: a string specifying the path to the SavedModel directory.
    input_meta_data: dictionary containing meta data about input and model.
    bert_config: Bert configuration file to define core bert layers.

  Raises:
    Export path is not specified, got an empty string or None.
  """
  if not model_export_path:
    raise ValueError('Export path is not specified: %s' % model_export_path)
  # Export uses float32 for now, even if training uses mixed precision.
  tf.keras.mixed_precision.experimental.set_policy('float32')
  squad_model, _ = bert_models.squad_model(bert_config,
                                           input_meta_data['max_seq_length'])
  model_saving_utils.export_bert_model(
      model_export_path, model=squad_model, checkpoint_dir=FLAGS.model_dir)