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Diffstat (limited to 'scripts/api_squad.py')
| -rw-r--r-- | scripts/api_squad.py | 1045 |
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diff --git a/scripts/api_squad.py b/scripts/api_squad.py new file mode 100644 index 0000000..239bbd6 --- /dev/null +++ b/scripts/api_squad.py @@ -0,0 +1,1045 @@ +# coding=utf-8 +# squad interface +# Required parameters： +# FLAGS_output_dir ：the output path of the model training during training process, the output of the trained model, etc.; the output path of the model prediction during predicting process +# FLAGS_init_checkpoint_squad ： model initialization path, use bert pre-trained model for training; use the output path during training for prediction +# FLAGS_predict_file ： the file to be predicted, csv file +# FLAGS_train_file : file to be trained, csv file +# FLAGS_do_predict : whether to predict or not +# FLAGS_do_train ： whether to train or not +# FLAGS_train_batch_size ： the batch_size for training, default : 16 +# FLAGS_predict_batch_size : the batch_size when predicting, default: 8 +# FLAGS_learning_rate ： the learning_rate at training time, default: 5e-5 +# FLAGS_num_train_epochs ： epochs at training time, default: 3 +# FLAGS_max_answer_length ： the maximum length of the answer, default: 100 characters +# FLAGS_max_query_length ： the maximum length of the question, default: 64 +# FLAGS_version_2_with_negative ： whether there is no answer to the question, default false, must be set to False when reasoning + +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 +import pandas as pd +from global_setting import FLAGS_bert_config_file, FLAGS_vocab_file, FLAGS_init_checkpoint_squad + + + + +FLAGS_max_seq_length = 512 +FLAGS_do_lower_case = True +FLAGS_doc_stride = 128 + + +FLAGS_save_checkpoints_steps = 1000 +FLAGS_iterations_per_loop = 1000 +FLAGS_n_best_size = 20 +FLAGS_tpu_zone = None +FLAGS_tpu_name = None +FLAGS_num_tpu_cores = 8 +FLAGS_verbose_logging = False +FLAGS_master = None +FLAGS_use_tpu = False +FLAGS_warmup_proportion = 0.1 +FLAGS_gcp_project = None +FLAGS_null_score_diff_threshold = 0.0 + +def make_json(input_file,questions): + print(input_file) + data_train = pd.read_excel(input_file) + print(444) + data_train.fillna(0,inplace=True) + data_train.index = [i for i in range(len(data_train))] + question = questions + res = {} + res['data'] = [] + data_inside = {} + for i in data_train.index: + data_inside['title'] = 'Not available' + data_inside['paragraphs'] = [] + paragraphs_inside = {} + paragraphs_inside['context'] = data_train.loc[i,'text'] + paragraphs_inside['qas'] = [] + for ques in question: + qas_inside = {} + qas_inside['answers'] = [] + if data_train.loc[i,ques]: + answer_inside = {} + answer_inside['text'] = str(data_train.loc[i,ques]) + answer_inside['answer_start'] = paragraphs_inside['context'].find(answer_inside['text']) + qas_inside['is_impossible'] = 0 + + else: + qas_inside['is_impossible'] = 1 + answer_inside = {} + qas_inside['id'] = str(i) + ques + qas_inside['question'] = ques + qas_inside['answers'].append(answer_inside.copy()) + paragraphs_inside['qas'].append(qas_inside.copy()) + data_inside['paragraphs'].append(paragraphs_inside.copy()) + + res['data'].append(data_inside.copy()) + print('make json done') + return json.dumps(res) + + + + +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,questions,FLAGS_version_2_with_negative): + """Read a SQuAD json file into a list of SquadExample.""" + data = make_json(input_file,questions) + input_data = json.loads(data)["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])) + + 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)) + + # 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 + + all_predictions[example.qas_id] = nbest_json[0]["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") + + +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_squad) + + # 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)) |