SinaTools 0.1.40__py2.py3-none-any.whl → 1.0.1__py2.py3-none-any.whl

sinatools/arabert/arabert/run_squad.py

@@ -1,1440 +0,0 @@
-# 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.
-"""Run BERT on SQuAD 1.1 and SQuAD 2.0."""
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-
-import collections
-import json
-import math
-import os
-import random
-import modeling
-import optimization
-import tokenization
-import six
-import tensorflow as tf
-
-flags = tf.flags
-
-FLAGS = flags.FLAGS
-
-## Required parameters
-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(
-    "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(
-    "train_file", None, "SQuAD json for training. E.g., train-v1.1.json"
-)
-
-flags.DEFINE_string(
-    "predict_file",
-    None,
-    "SQuAD json for predictions. E.g., dev-v1.1.json or test-v1.1.json",
-)
-
-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",
-    384,
-    "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_integer(
-    "doc_stride",
-    128,
-    "When splitting up a long document into chunks, how much stride to "
-    "take between chunks.",
-)
-
-flags.DEFINE_integer(
-    "max_query_length",
-    64,
-    "The maximum number of tokens for the question. Questions longer than "
-    "this will be truncated to this length.",
-)
-
-flags.DEFINE_bool("do_train", False, "Whether to run training.")
-
-flags.DEFINE_bool("do_predict", False, "Whether to run eval on the dev set.")
-
-flags.DEFINE_integer("train_batch_size", 32, "Total batch size for training.")
-
-flags.DEFINE_integer("predict_batch_size", 8, "Total batch size for predictions.")
-
-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_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.",
-)
-
-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.",
-)
-
-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_bool(
-    "version_2_with_negative",
-    False,
-    "If true, the SQuAD examples contain some that do not have an answer.",
-)
-
-flags.DEFINE_float(
-    "null_score_diff_threshold",
-    0.0,
-    "If null_score - best_non_null is greater than the threshold predict null.",
-)
-
-
-class SquadExample(object):
-    """A single training/test example for simple sequence classification.
-
-    For examples without an answer, the start and end position are -1.
-    """
-
-    def __init__(
-        self,
-        qas_id,
-        question_text,
-        doc_tokens,
-        orig_answer_text=None,
-        start_position=None,
-        end_position=None,
-        is_impossible=False,
-    ):
-        self.qas_id = qas_id
-        self.question_text = question_text
-        self.doc_tokens = doc_tokens
-        self.orig_answer_text = orig_answer_text
-        self.start_position = start_position
-        self.end_position = end_position
-        self.is_impossible = is_impossible
-
-    def __str__(self):
-        return self.__repr__()
-
-    def __repr__(self):
-        s = ""
-        s += "qas_id: %s" % (tokenization.printable_text(self.qas_id))
-        s += ", question_text: %s" % (tokenization.printable_text(self.question_text))
-        s += ", doc_tokens: [%s]" % (" ".join(self.doc_tokens))
-        if self.start_position:
-            s += ", start_position: %d" % (self.start_position)
-        if self.start_position:
-            s += ", end_position: %d" % (self.end_position)
-        if self.start_position:
-            s += ", is_impossible: %r" % (self.is_impossible)
-        return s
-
-
-class InputFeatures(object):
-    """A single set of features of data."""
-
-    def __init__(
-        self,
-        unique_id,
-        example_index,
-        doc_span_index,
-        tokens,
-        token_to_orig_map,
-        token_is_max_context,
-        input_ids,
-        input_mask,
-        segment_ids,
-        start_position=None,
-        end_position=None,
-        is_impossible=None,
-    ):
-        self.unique_id = unique_id
-        self.example_index = example_index
-        self.doc_span_index = doc_span_index
-        self.tokens = tokens
-        self.token_to_orig_map = token_to_orig_map
-        self.token_is_max_context = token_is_max_context
-        self.input_ids = input_ids
-        self.input_mask = input_mask
-        self.segment_ids = segment_ids
-        self.start_position = start_position
-        self.end_position = end_position
-        self.is_impossible = is_impossible
-
-
-def read_squad_examples(input_file, is_training):
-    """Read a SQuAD json file into a list of SquadExample."""
-    with tf.gfile.Open(input_file, "r") as reader:
-        input_data = json.load(reader)["data"]
-
-    def is_whitespace(c):
-        if c == " " or c == "\t" or c == "\r" or c == "\n" or ord(c) == 0x202F:
-            return True
-        return False
-
-    examples = []
-    for entry in input_data:
-        for paragraph in entry["paragraphs"]:
-            paragraph_text = paragraph["context"]
-            doc_tokens = []
-            char_to_word_offset = []
-            prev_is_whitespace = True
-            for c in paragraph_text:
-                if is_whitespace(c):
-                    prev_is_whitespace = True
-                else:
-                    if prev_is_whitespace:
-                        doc_tokens.append(c)
-                    else:
-                        doc_tokens[-1] += c
-                    prev_is_whitespace = False
-                char_to_word_offset.append(len(doc_tokens) - 1)
-
-            for qa in paragraph["qas"]:
-                qas_id = qa["id"]
-                question_text = qa["question"]
-                start_position = None
-                end_position = None
-                orig_answer_text = None
-                is_impossible = False
-                if is_training:
-
-                    if FLAGS.version_2_with_negative:
-                        is_impossible = qa["is_impossible"]
-                    if (len(qa["answers"]) != 1) and (not is_impossible):
-                        raise ValueError(
-                            "For training, each question should have exactly 1 answer."
-                        )
-                    if not is_impossible:
-                        answer = qa["answers"][0]
-                        orig_answer_text = answer["text"]
-                        answer_offset = answer["answer_start"]
-                        answer_length = len(orig_answer_text)
-                        start_position = char_to_word_offset[answer_offset]
-                        end_position = char_to_word_offset[
-                            answer_offset + answer_length - 1
-                        ]
-                        # Only add answers where the text can be exactly recovered from the
-                        # document. If this CAN'T happen it's likely due to weird Unicode
-                        # stuff so we will just skip the example.
-                        #
-                        # Note that this means for training mode, every example is NOT
-                        # guaranteed to be preserved.
-                        actual_text = " ".join(
-                            doc_tokens[start_position : (end_position + 1)]
-                        )
-                        cleaned_answer_text = " ".join(
-                            tokenization.whitespace_tokenize(orig_answer_text)
-                        )
-                        if actual_text.find(cleaned_answer_text) == -1:
-                            tf.logging.warning(
-                                "Could not find answer: '%s' vs. '%s'",
-                                actual_text,
-                                cleaned_answer_text,
-                            )
-                            continue
-                    else:
-                        start_position = -1
-                        end_position = -1
-                        orig_answer_text = ""
-
-                example = SquadExample(
-                    qas_id=qas_id,
-                    question_text=question_text,
-                    doc_tokens=doc_tokens,
-                    orig_answer_text=orig_answer_text,
-                    start_position=start_position,
-                    end_position=end_position,
-                    is_impossible=is_impossible,
-                )
-                examples.append(example)
-
-    return examples
-
-
-def convert_examples_to_features(
-    examples,
-    tokenizer,
-    max_seq_length,
-    doc_stride,
-    max_query_length,
-    is_training,
-    output_fn,
-):
-    """Loads a data file into a list of `InputBatch`s."""
-
-    unique_id = 1000000000
-
-    for (example_index, example) in enumerate(examples):
-        query_tokens = tokenizer.tokenize(example.question_text)
-
-        if len(query_tokens) > max_query_length:
-            query_tokens = query_tokens[0:max_query_length]
-
-        tok_to_orig_index = []
-        orig_to_tok_index = []
-        all_doc_tokens = []
-        for (i, token) in enumerate(example.doc_tokens):
-            orig_to_tok_index.append(len(all_doc_tokens))
-            sub_tokens = tokenizer.tokenize(token)
-            for sub_token in sub_tokens:
-                tok_to_orig_index.append(i)
-                all_doc_tokens.append(sub_token)
-
-        tok_start_position = None
-        tok_end_position = None
-        if is_training and example.is_impossible:
-            tok_start_position = -1
-            tok_end_position = -1
-        if is_training and not example.is_impossible:
-            tok_start_position = orig_to_tok_index[example.start_position]
-            if example.end_position < len(example.doc_tokens) - 1:
-                tok_end_position = orig_to_tok_index[example.end_position + 1] - 1
-            else:
-                tok_end_position = len(all_doc_tokens) - 1
-            (tok_start_position, tok_end_position) = _improve_answer_span(
-                all_doc_tokens,
-                tok_start_position,
-                tok_end_position,
-                tokenizer,
-                example.orig_answer_text,
-            )
-
-        # The -3 accounts for [CLS], [SEP] and [SEP]
-        max_tokens_for_doc = max_seq_length - len(query_tokens) - 3
-
-        # We can have documents that are longer than the maximum sequence length.
-        # To deal with this we do a sliding window approach, where we take chunks
-        # of the up to our max length with a stride of `doc_stride`.
-        _DocSpan = collections.namedtuple(  # pylint: disable=invalid-name
-            "DocSpan", ["start", "length"]
-        )
-        doc_spans = []
-        start_offset = 0
-        while start_offset < len(all_doc_tokens):
-            length = len(all_doc_tokens) - start_offset
-            if length > max_tokens_for_doc:
-                length = max_tokens_for_doc
-            doc_spans.append(_DocSpan(start=start_offset, length=length))
-            if start_offset + length == len(all_doc_tokens):
-                break
-            start_offset += min(length, doc_stride)
-
-        for (doc_span_index, doc_span) in enumerate(doc_spans):
-            tokens = []
-            token_to_orig_map = {}
-            token_is_max_context = {}
-            segment_ids = []
-            tokens.append("[CLS]")
-            segment_ids.append(0)
-            for token in query_tokens:
-                tokens.append(token)
-                segment_ids.append(0)
-            tokens.append("[SEP]")
-            segment_ids.append(0)
-
-            for i in range(doc_span.length):
-                split_token_index = doc_span.start + i
-                token_to_orig_map[len(tokens)] = tok_to_orig_index[split_token_index]
-
-                is_max_context = _check_is_max_context(
-                    doc_spans, doc_span_index, split_token_index
-                )
-                token_is_max_context[len(tokens)] = is_max_context
-                tokens.append(all_doc_tokens[split_token_index])
-                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)
-
-            # 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
-
-            start_position = None
-            end_position = None
-            if is_training and not example.is_impossible:
-                # For training, if our document chunk does not contain an annotation
-                # we throw it out, since there is nothing to predict.
-                doc_start = doc_span.start
-                doc_end = doc_span.start + doc_span.length - 1
-                out_of_span = False
-                if not (
-                    tok_start_position >= doc_start and tok_end_position <= doc_end
-                ):
-                    out_of_span = True
-                if out_of_span:
-                    start_position = 0
-                    end_position = 0
-                else:
-                    doc_offset = len(query_tokens) + 2
-                    start_position = tok_start_position - doc_start + doc_offset
-                    end_position = tok_end_position - doc_start + doc_offset
-
-            if is_training and example.is_impossible:
-                start_position = 0
-                end_position = 0
-
-            if example_index < 20:
-                tf.logging.info("*** Example ***")
-                tf.logging.info("unique_id: %s" % (unique_id))
-                tf.logging.info("example_index: %s" % (example_index))
-                tf.logging.info("doc_span_index: %s" % (doc_span_index))
-                tf.logging.info(
-                    "tokens: %s"
-                    % " ".join([tokenization.printable_text(x) for x in tokens])
-                )
-                tf.logging.info(
-                    "token_to_orig_map: %s"
-                    % " ".join(
-                        [
-                            "%d:%d" % (x, y)
-                            for (x, y) in six.iteritems(token_to_orig_map)
-                        ]
-                    )
-                )
-                tf.logging.info(
-                    "token_is_max_context: %s"
-                    % " ".join(
-                        [
-                            "%d:%s" % (x, y)
-                            for (x, y) in six.iteritems(token_is_max_context)
-                        ]
-                    )
-                )
-                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])
-                )
-                if is_training and example.is_impossible:
-                    tf.logging.info("impossible example")
-                if is_training and not example.is_impossible:
-                    answer_text = " ".join(tokens[start_position : (end_position + 1)])
-                    tf.logging.info("start_position: %d" % (start_position))
-                    tf.logging.info("end_position: %d" % (end_position))
-                    tf.logging.info(
-                        "answer: %s" % (tokenization.printable_text(answer_text))
-                    )
-
-            feature = InputFeatures(
-                unique_id=unique_id,
-                example_index=example_index,
-                doc_span_index=doc_span_index,
-                tokens=tokens,
-                token_to_orig_map=token_to_orig_map,
-                token_is_max_context=token_is_max_context,
-                input_ids=input_ids,
-                input_mask=input_mask,
-                segment_ids=segment_ids,
-                start_position=start_position,
-                end_position=end_position,
-                is_impossible=example.is_impossible,
-            )
-
-            # Run callback
-            output_fn(feature)
-
-            unique_id += 1
-
-
-def _improve_answer_span(
-    doc_tokens, input_start, input_end, tokenizer, orig_answer_text
-):
-    """Returns tokenized answer spans that better match the annotated answer."""
-
-    # The SQuAD annotations are character based. We first project them to
-    # whitespace-tokenized words. But then after WordPiece tokenization, we can
-    # often find a "better match". For example:
-    #
-    #   Question: What year was John Smith born?
-    #   Context: The leader was John Smith (1895-1943).
-    #   Answer: 1895
-    #
-    # The original whitespace-tokenized answer will be "(1895-1943).". However
-    # after tokenization, our tokens will be "( 1895 - 1943 ) .". So we can match
-    # the exact answer, 1895.
-    #
-    # However, this is not always possible. Consider the following:
-    #
-    #   Question: What country is the top exporter of electornics?
-    #   Context: The Japanese electronics industry is the lagest in the world.
-    #   Answer: Japan
-    #
-    # In this case, the annotator chose "Japan" as a character sub-span of
-    # the word "Japanese". Since our WordPiece tokenizer does not split
-    # "Japanese", we just use "Japanese" as the annotation. This is fairly rare
-    # in SQuAD, but does happen.
-    tok_answer_text = " ".join(tokenizer.tokenize(orig_answer_text))
-
-    for new_start in range(input_start, input_end + 1):
-        for new_end in range(input_end, new_start - 1, -1):
-            text_span = " ".join(doc_tokens[new_start : (new_end + 1)])
-            if text_span == tok_answer_text:
-                return (new_start, new_end)
-
-    return (input_start, input_end)
-
-
-def _check_is_max_context(doc_spans, cur_span_index, position):
-    """Check if this is the 'max context' doc span for the token."""
-
-    # Because of the sliding window approach taken to scoring documents, a single
-    # token can appear in multiple documents. E.g.
-    #  Doc: the man went to the store and bought a gallon of milk
-    #  Span A: the man went to the
-    #  Span B: to the store and bought
-    #  Span C: and bought a gallon of
-    #  ...
-    #
-    # Now the word 'bought' will have two scores from spans B and C. We only
-    # want to consider the score with "maximum context", which we define as
-    # the *minimum* of its left and right context (the *sum* of left and
-    # right context will always be the same, of course).
-    #
-    # In the example the maximum context for 'bought' would be span C since
-    # it has 1 left context and 3 right context, while span B has 4 left context
-    # and 0 right context.
-    best_score = None
-    best_span_index = None
-    for (span_index, doc_span) in enumerate(doc_spans):
-        end = doc_span.start + doc_span.length - 1
-        if position < doc_span.start:
-            continue
-        if position > end:
-            continue
-        num_left_context = position - doc_span.start
-        num_right_context = end - position
-        score = min(num_left_context, num_right_context) + 0.01 * doc_span.length
-        if best_score is None or score > best_score:
-            best_score = score
-            best_span_index = span_index
-
-    return cur_span_index == best_span_index
-
-
-def create_model(
-    bert_config, is_training, input_ids, input_mask, segment_ids, use_one_hot_embeddings
-):
-    """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,
-    )
-
-    final_hidden = model.get_sequence_output()
-
-    final_hidden_shape = modeling.get_shape_list(final_hidden, expected_rank=3)
-    batch_size = final_hidden_shape[0]
-    seq_length = final_hidden_shape[1]
-    hidden_size = final_hidden_shape[2]
-
-    output_weights = tf.get_variable(
-        "cls/squad/output_weights",
-        [2, hidden_size],
-        initializer=tf.truncated_normal_initializer(stddev=0.02),
-    )
-
-    output_bias = tf.get_variable(
-        "cls/squad/output_bias", [2], initializer=tf.zeros_initializer()
-    )
-
-    final_hidden_matrix = tf.reshape(
-        final_hidden, [batch_size * seq_length, hidden_size]
-    )
-    logits = tf.matmul(final_hidden_matrix, output_weights, transpose_b=True)
-    logits = tf.nn.bias_add(logits, output_bias)
-
-    logits = tf.reshape(logits, [batch_size, seq_length, 2])
-    logits = tf.transpose(logits, [2, 0, 1])
-
-    unstacked_logits = tf.unstack(logits, axis=0)
-
-    (start_logits, end_logits) = (unstacked_logits[0], unstacked_logits[1])
-
-    return (start_logits, end_logits)
-
-
-def model_fn_builder(
-    bert_config,
-    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))
-
-        unique_ids = features["unique_ids"]
-        input_ids = features["input_ids"]
-        input_mask = features["input_mask"]
-        segment_ids = features["segment_ids"]
-
-        is_training = mode == tf.estimator.ModeKeys.TRAIN
-
-        (start_logits, end_logits) = create_model(
-            bert_config=bert_config,
-            is_training=is_training,
-            input_ids=input_ids,
-            input_mask=input_mask,
-            segment_ids=segment_ids,
-            use_one_hot_embeddings=use_one_hot_embeddings,
-        )
-
-        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:
-            seq_length = modeling.get_shape_list(input_ids)[1]
-
-            def compute_loss(logits, positions):
-                one_hot_positions = tf.one_hot(
-                    positions, depth=seq_length, dtype=tf.float32
-                )
-                log_probs = tf.nn.log_softmax(logits, axis=-1)
-                loss = -tf.reduce_mean(
-                    tf.reduce_sum(one_hot_positions * log_probs, axis=-1)
-                )
-                return loss
-
-            start_positions = features["start_positions"]
-            end_positions = features["end_positions"]
-
-            start_loss = compute_loss(start_logits, start_positions)
-            end_loss = compute_loss(end_logits, end_positions)
-
-            total_loss = (start_loss + end_loss) / 2.0
-
-            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.PREDICT:
-            predictions = {
-                "unique_ids": unique_ids,
-                "start_logits": start_logits,
-                "end_logits": end_logits,
-            }
-            output_spec = tf.contrib.tpu.TPUEstimatorSpec(
-                mode=mode, predictions=predictions, scaffold_fn=scaffold_fn
-            )
-        else:
-            raise ValueError("Only TRAIN and PREDICT modes are supported: %s" % (mode))
-
-        return output_spec
-
-    return model_fn
-
-
-def input_fn_builder(input_file, seq_length, is_training, drop_remainder):
-    """Creates an `input_fn` closure to be passed to TPUEstimator."""
-
-    name_to_features = {
-        "unique_ids": tf.FixedLenFeature([], tf.int64),
-        "input_ids": tf.FixedLenFeature([seq_length], tf.int64),
-        "input_mask": tf.FixedLenFeature([seq_length], tf.int64),
-        "segment_ids": tf.FixedLenFeature([seq_length], tf.int64),
-    }
-
-    if is_training:
-        name_to_features["start_positions"] = tf.FixedLenFeature([], tf.int64)
-        name_to_features["end_positions"] = 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
-
-
-RawResult = collections.namedtuple(
-    "RawResult", ["unique_id", "start_logits", "end_logits"]
-)
-
-
-def write_predictions(
-    all_examples,
-    all_features,
-    all_results,
-    n_best_size,
-    max_answer_length,
-    do_lower_case,
-    output_prediction_file,
-    output_nbest_file,
-    output_null_log_odds_file,
-):
-    """Write final predictions to the json file and log-odds of null if needed."""
-    tf.logging.info("Writing predictions to: %s" % (output_prediction_file))
-    tf.logging.info("Writing nbest to: %s" % (output_nbest_file))
-
-    example_index_to_features = collections.defaultdict(list)
-    for feature in all_features:
-        example_index_to_features[feature.example_index].append(feature)
-
-    unique_id_to_result = {}
-    for result in all_results:
-        unique_id_to_result[result.unique_id] = result
-
-    _PrelimPrediction = collections.namedtuple(  # pylint: disable=invalid-name
-        "PrelimPrediction",
-        ["feature_index", "start_index", "end_index", "start_logit", "end_logit"],
-    )
-
-    all_predictions = collections.OrderedDict()
-    all_nbest_json = collections.OrderedDict()
-    scores_diff_json = collections.OrderedDict()
-
-    for (example_index, example) in enumerate(all_examples):
-        features = example_index_to_features[example_index]
-
-        prelim_predictions = []
-        # keep track of the minimum score of null start+end of position 0
-        score_null = 1000000  # large and positive
-        min_null_feature_index = 0  # the paragraph slice with min mull score
-        null_start_logit = 0  # the start logit at the slice with min null score
-        null_end_logit = 0  # the end logit at the slice with min null score
-        for (feature_index, feature) in enumerate(features):
-            result = unique_id_to_result[feature.unique_id]
-            start_indexes = _get_best_indexes(result.start_logits, n_best_size)
-            end_indexes = _get_best_indexes(result.end_logits, n_best_size)
-            # if we could have irrelevant answers, get the min score of irrelevant
-            if FLAGS.version_2_with_negative:
-                feature_null_score = result.start_logits[0] + result.end_logits[0]
-                if feature_null_score < score_null:
-                    score_null = feature_null_score
-                    min_null_feature_index = feature_index
-                    null_start_logit = result.start_logits[0]
-                    null_end_logit = result.end_logits[0]
-            for start_index in start_indexes:
-                for end_index in end_indexes:
-                    # We could hypothetically create invalid predictions, e.g., predict
-                    # that the start of the span is in the question. We throw out all
-                    # invalid predictions.
-                    if start_index >= len(feature.tokens):
-                        continue
-                    if end_index >= len(feature.tokens):
-                        continue
-                    if start_index not in feature.token_to_orig_map:
-                        continue
-                    if end_index not in feature.token_to_orig_map:
-                        continue
-                    if not feature.token_is_max_context.get(start_index, False):
-                        continue
-                    if end_index < start_index:
-                        continue
-                    length = end_index - start_index + 1
-                    if length > max_answer_length:
-                        continue
-                    prelim_predictions.append(
-                        _PrelimPrediction(
-                            feature_index=feature_index,
-                            start_index=start_index,
-                            end_index=end_index,
-                            start_logit=result.start_logits[start_index],
-                            end_logit=result.end_logits[end_index],
-                        )
-                    )
-
-        if FLAGS.version_2_with_negative:
-            prelim_predictions.append(
-                _PrelimPrediction(
-                    feature_index=min_null_feature_index,
-                    start_index=0,
-                    end_index=0,
-                    start_logit=null_start_logit,
-                    end_logit=null_end_logit,
-                )
-            )
-        prelim_predictions = sorted(
-            prelim_predictions,
-            key=lambda x: (x.start_logit + x.end_logit),
-            reverse=True,
-        )
-
-        _NbestPrediction = collections.namedtuple(  # pylint: disable=invalid-name
-            "NbestPrediction", ["text", "start_logit", "end_logit"]
-        )
-
-        seen_predictions = {}
-        nbest = []
-        for pred in prelim_predictions:
-            if len(nbest) >= n_best_size:
-                break
-            feature = features[pred.feature_index]
-            if pred.start_index > 0:  # this is a non-null prediction
-                tok_tokens = feature.tokens[pred.start_index : (pred.end_index + 1)]
-                orig_doc_start = feature.token_to_orig_map[pred.start_index]
-                orig_doc_end = feature.token_to_orig_map[pred.end_index]
-                orig_tokens = example.doc_tokens[orig_doc_start : (orig_doc_end + 1)]
-                tok_text = " ".join(tok_tokens)
-
-                # De-tokenize WordPieces that have been split off.
-                tok_text = tok_text.replace(" ##", "")
-                tok_text = tok_text.replace("##", "")
-
-                # Clean whitespace
-                tok_text = tok_text.strip()
-                tok_text = " ".join(tok_text.split())
-                orig_text = " ".join(orig_tokens)
-
-                final_text = get_final_text(tok_text, orig_text, do_lower_case)
-                if final_text in seen_predictions:
-                    continue
-
-                seen_predictions[final_text] = True
-            else:
-                final_text = ""
-                seen_predictions[final_text] = True
-
-            nbest.append(
-                _NbestPrediction(
-                    text=final_text,
-                    start_logit=pred.start_logit,
-                    end_logit=pred.end_logit,
-                )
-            )
-
-        # if we didn't inlude the empty option in the n-best, inlcude it
-        if FLAGS.version_2_with_negative:
-            if "" not in seen_predictions:
-                nbest.append(
-                    _NbestPrediction(
-                        text="", start_logit=null_start_logit, end_logit=null_end_logit
-                    )
-                )
-        # In very rare edge cases we could have no valid predictions. So we
-        # just create a nonce prediction in this case to avoid failure.
-        if not nbest:
-            nbest.append(_NbestPrediction(text="empty", start_logit=0.0, end_logit=0.0))
-
-        assert len(nbest) >= 1
-
-        total_scores = []
-        best_non_null_entry = None
-        for entry in nbest:
-            total_scores.append(entry.start_logit + entry.end_logit)
-            if not best_non_null_entry:
-                if entry.text:
-                    best_non_null_entry = entry
-
-        probs = _compute_softmax(total_scores)
-
-        nbest_json = []
-        for (i, entry) in enumerate(nbest):
-            output = collections.OrderedDict()
-            output["text"] = entry.text
-            output["probability"] = probs[i]
-            output["start_logit"] = entry.start_logit
-            output["end_logit"] = entry.end_logit
-            nbest_json.append(output)
-
-        assert len(nbest_json) >= 1
-
-        if not FLAGS.version_2_with_negative:
-            all_predictions[example.qas_id] = nbest_json[0]["text"]
-        else:
-            # predict "" iff the null score - the score of best non-null > threshold
-            score_diff = (
-                score_null
-                - best_non_null_entry.start_logit
-                - (best_non_null_entry.end_logit)
-            )
-            scores_diff_json[example.qas_id] = score_diff
-            if score_diff > FLAGS.null_score_diff_threshold:
-                all_predictions[example.qas_id] = ""
-            else:
-                all_predictions[example.qas_id] = best_non_null_entry.text
-
-        all_nbest_json[example.qas_id] = nbest_json
-
-    with tf.gfile.GFile(output_prediction_file, "w") as writer:
-        writer.write(json.dumps(all_predictions, indent=4) + "\n")
-
-    with tf.gfile.GFile(output_nbest_file, "w") as writer:
-        writer.write(json.dumps(all_nbest_json, indent=4) + "\n")
-
-    if FLAGS.version_2_with_negative:
-        with tf.gfile.GFile(output_null_log_odds_file, "w") as writer:
-            writer.write(json.dumps(scores_diff_json, indent=4) + "\n")
-
-
-def get_final_text(pred_text, orig_text, do_lower_case):
-    """Project the tokenized prediction back to the original text."""
-
-    # When we created the data, we kept track of the alignment between original
-    # (whitespace tokenized) tokens and our WordPiece tokenized tokens. So
-    # now `orig_text` contains the span of our original text corresponding to the
-    # span that we predicted.
-    #
-    # However, `orig_text` may contain extra characters that we don't want in
-    # our prediction.
-    #
-    # For example, let's say:
-    #   pred_text = steve smith
-    #   orig_text = Steve Smith's
-    #
-    # We don't want to return `orig_text` because it contains the extra "'s".
-    #
-    # We don't want to return `pred_text` because it's already been normalized
-    # (the SQuAD eval script also does punctuation stripping/lower casing but
-    # our tokenizer does additional normalization like stripping accent
-    # characters).
-    #
-    # What we really want to return is "Steve Smith".
-    #
-    # Therefore, we have to apply a semi-complicated alignment heruistic between
-    # `pred_text` and `orig_text` to get a character-to-charcter alignment. This
-    # can fail in certain cases in which case we just return `orig_text`.
-
-    def _strip_spaces(text):
-        ns_chars = []
-        ns_to_s_map = collections.OrderedDict()
-        for (i, c) in enumerate(text):
-            if c == " ":
-                continue
-            ns_to_s_map[len(ns_chars)] = i
-            ns_chars.append(c)
-        ns_text = "".join(ns_chars)
-        return (ns_text, ns_to_s_map)
-
-    # We first tokenize `orig_text`, strip whitespace from the result
-    # and `pred_text`, and check if they are the same length. If they are
-    # NOT the same length, the heuristic has failed. If they are the same
-    # length, we assume the characters are one-to-one aligned.
-    tokenizer = tokenization.BasicTokenizer(do_lower_case=do_lower_case)
-
-    tok_text = " ".join(tokenizer.tokenize(orig_text))
-
-    start_position = tok_text.find(pred_text)
-    if start_position == -1:
-        if FLAGS.verbose_logging:
-            tf.logging.info(
-                "Unable to find text: '%s' in '%s'" % (pred_text, orig_text)
-            )
-        return orig_text
-    end_position = start_position + len(pred_text) - 1
-
-    (orig_ns_text, orig_ns_to_s_map) = _strip_spaces(orig_text)
-    (tok_ns_text, tok_ns_to_s_map) = _strip_spaces(tok_text)
-
-    if len(orig_ns_text) != len(tok_ns_text):
-        if FLAGS.verbose_logging:
-            tf.logging.info(
-                "Length not equal after stripping spaces: '%s' vs '%s'",
-                orig_ns_text,
-                tok_ns_text,
-            )
-        return orig_text
-
-    # We then project the characters in `pred_text` back to `orig_text` using
-    # the character-to-character alignment.
-    tok_s_to_ns_map = {}
-    for (i, tok_index) in six.iteritems(tok_ns_to_s_map):
-        tok_s_to_ns_map[tok_index] = i
-
-    orig_start_position = None
-    if start_position in tok_s_to_ns_map:
-        ns_start_position = tok_s_to_ns_map[start_position]
-        if ns_start_position in orig_ns_to_s_map:
-            orig_start_position = orig_ns_to_s_map[ns_start_position]
-
-    if orig_start_position is None:
-        if FLAGS.verbose_logging:
-            tf.logging.info("Couldn't map start position")
-        return orig_text
-
-    orig_end_position = None
-    if end_position in tok_s_to_ns_map:
-        ns_end_position = tok_s_to_ns_map[end_position]
-        if ns_end_position in orig_ns_to_s_map:
-            orig_end_position = orig_ns_to_s_map[ns_end_position]
-
-    if orig_end_position is None:
-        if FLAGS.verbose_logging:
-            tf.logging.info("Couldn't map end position")
-        return orig_text
-
-    output_text = orig_text[orig_start_position : (orig_end_position + 1)]
-    return output_text
-
-
-def _get_best_indexes(logits, n_best_size):
-    """Get the n-best logits from a list."""
-    index_and_score = sorted(enumerate(logits), key=lambda x: x[1], reverse=True)
-
-    best_indexes = []
-    for i in range(len(index_and_score)):
-        if i >= n_best_size:
-            break
-        best_indexes.append(index_and_score[i][0])
-    return best_indexes
-
-
-def _compute_softmax(scores):
-    """Compute softmax probability over raw logits."""
-    if not scores:
-        return []
-
-    max_score = None
-    for score in scores:
-        if max_score is None or score > max_score:
-            max_score = score
-
-    exp_scores = []
-    total_sum = 0.0
-    for score in scores:
-        x = math.exp(score - max_score)
-        exp_scores.append(x)
-        total_sum += x
-
-    probs = []
-    for score in exp_scores:
-        probs.append(score / total_sum)
-    return probs
-
-
-class FeatureWriter(object):
-    """Writes InputFeature to TF example file."""
-
-    def __init__(self, filename, is_training):
-        self.filename = filename
-        self.is_training = is_training
-        self.num_features = 0
-        self._writer = tf.python_io.TFRecordWriter(filename)
-
-    def process_feature(self, feature):
-        """Write a InputFeature to the TFRecordWriter as a tf.train.Example."""
-        self.num_features += 1
-
-        def create_int_feature(values):
-            feature = tf.train.Feature(
-                int64_list=tf.train.Int64List(value=list(values))
-            )
-            return feature
-
-        features = collections.OrderedDict()
-        features["unique_ids"] = create_int_feature([feature.unique_id])
-        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)
-
-        if self.is_training:
-            features["start_positions"] = create_int_feature([feature.start_position])
-            features["end_positions"] = create_int_feature([feature.end_position])
-            impossible = 0
-            if feature.is_impossible:
-                impossible = 1
-            features["is_impossible"] = create_int_feature([impossible])
-
-        tf_example = tf.train.Example(features=tf.train.Features(feature=features))
-        self._writer.write(tf_example.SerializeToString())
-
-    def close(self):
-        self._writer.close()
-
-
-def validate_flags_or_throw(bert_config):
-    """Validate the input FLAGS or throw an exception."""
-    tokenization.validate_case_matches_checkpoint(
-        FLAGS.do_lower_case, FLAGS.init_checkpoint
-    )
-
-    if not FLAGS.do_train and not FLAGS.do_predict:
-        raise ValueError("At least one of `do_train` or `do_predict` must be True.")
-
-    if FLAGS.do_train:
-        if not FLAGS.train_file:
-            raise ValueError(
-                "If `do_train` is True, then `train_file` must be specified."
-            )
-    if FLAGS.do_predict:
-        if not FLAGS.predict_file:
-            raise ValueError(
-                "If `do_predict` is True, then `predict_file` must be specified."
-            )
-
-    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)
-        )
-
-    if FLAGS.max_seq_length <= FLAGS.max_query_length + 3:
-        raise ValueError(
-            "The max_seq_length (%d) must be greater than max_query_length "
-            "(%d) + 3" % (FLAGS.max_seq_length, FLAGS.max_query_length)
-        )
-
-
-def main(_):
-    tf.logging.set_verbosity(tf.logging.INFO)
-    logger = tf.get_logger()
-    logger.propagate = False
-
-    bert_config = modeling.BertConfig.from_json_file(FLAGS.bert_config_file)
-
-    validate_flags_or_throw(bert_config)
-
-    tf.gfile.MakeDirs(FLAGS.output_dir)
-
-    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 = read_squad_examples(
-            input_file=FLAGS.train_file, is_training=True
-        )
-        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)
-
-        # Pre-shuffle the input to avoid having to make a very large shuffle
-        # buffer in in the `input_fn`.
-        rng = random.Random(12345)
-        rng.shuffle(train_examples)
-
-    model_fn = model_fn_builder(
-        bert_config=bert_config,
-        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,
-        predict_batch_size=FLAGS.predict_batch_size,
-    )
-
-    if FLAGS.do_train:
-        # We write to a temporary file to avoid storing very large constant tensors
-        # in memory.
-        train_writer = FeatureWriter(
-            filename=os.path.join(FLAGS.output_dir, "train.tf_record"), is_training=True
-        )
-        convert_examples_to_features(
-            examples=train_examples,
-            tokenizer=tokenizer,
-            max_seq_length=FLAGS.max_seq_length,
-            doc_stride=FLAGS.doc_stride,
-            max_query_length=FLAGS.max_query_length,
-            is_training=True,
-            output_fn=train_writer.process_feature,
-        )
-        train_writer.close()
-
-        tf.logging.info("***** Running training *****")
-        tf.logging.info("  Num orig examples = %d", len(train_examples))
-        tf.logging.info("  Num split examples = %d", train_writer.num_features)
-        tf.logging.info("  Batch size = %d", FLAGS.train_batch_size)
-        tf.logging.info("  Num steps = %d", num_train_steps)
-        del train_examples
-
-        train_input_fn = input_fn_builder(
-            input_file=train_writer.filename,
-            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_predict:
-        eval_examples = read_squad_examples(
-            input_file=FLAGS.predict_file, is_training=False
-        )
-
-        eval_writer = FeatureWriter(
-            filename=os.path.join(FLAGS.output_dir, "eval.tf_record"), is_training=False
-        )
-        eval_features = []
-
-        def append_feature(feature):
-            eval_features.append(feature)
-            eval_writer.process_feature(feature)
-
-        convert_examples_to_features(
-            examples=eval_examples,
-            tokenizer=tokenizer,
-            max_seq_length=FLAGS.max_seq_length,
-            doc_stride=FLAGS.doc_stride,
-            max_query_length=FLAGS.max_query_length,
-            is_training=False,
-            output_fn=append_feature,
-        )
-        eval_writer.close()
-
-        tf.logging.info("***** Running predictions *****")
-        tf.logging.info("  Num orig examples = %d", len(eval_examples))
-        tf.logging.info("  Num split examples = %d", len(eval_features))
-        tf.logging.info("  Batch size = %d", FLAGS.predict_batch_size)
-
-        all_results = []
-
-        predict_input_fn = input_fn_builder(
-            input_file=eval_writer.filename,
-            seq_length=FLAGS.max_seq_length,
-            is_training=False,
-            drop_remainder=False,
-        )
-
-        # If running eval on the TPU, you will need to specify the number of
-        # steps.
-        all_results = []
-        for result in estimator.predict(predict_input_fn, yield_single_examples=True):
-            if len(all_results) % 1000 == 0:
-                tf.logging.info("Processing example: %d" % (len(all_results)))
-            unique_id = int(result["unique_ids"])
-            start_logits = [float(x) for x in result["start_logits"].flat]
-            end_logits = [float(x) for x in result["end_logits"].flat]
-            all_results.append(
-                RawResult(
-                    unique_id=unique_id,
-                    start_logits=start_logits,
-                    end_logits=end_logits,
-                )
-            )
-
-        output_prediction_file = os.path.join(FLAGS.output_dir, "predictions.json")
-        output_nbest_file = os.path.join(FLAGS.output_dir, "nbest_predictions.json")
-        output_null_log_odds_file = os.path.join(FLAGS.output_dir, "null_odds.json")
-
-        write_predictions(
-            eval_examples,
-            eval_features,
-            all_results,
-            FLAGS.n_best_size,
-            FLAGS.max_answer_length,
-            FLAGS.do_lower_case,
-            output_prediction_file,
-            output_nbest_file,
-            output_null_log_odds_file,
-        )
-
-
-if __name__ == "__main__":
-    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()