coref_model.py

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

import os
import operator
import random
import math
import json
import threading
import numpy as np
import tensorflow as tf
import tensorflow_hub as hub
import h5py

import util
import coref_ops
import conll
import metrics,codecs

class CorefModel(object):
  def __init__(self, config):
    self.config = config
    self.context_embeddings = util.EmbeddingDictionary(config["context_embeddings"])
    self.head_embeddings = util.EmbeddingDictionary(config["head_embeddings"], maybe_cache=self.context_embeddings)
    self.char_embedding_size = config["char_embedding_size"]
    self.char_dict = util.load_char_dict(config["char_vocab_path"])
    self.max_span_width = config["max_span_width"]
    self.genres = { g:i for i,g in enumerate(config["genres"]) }
    self.lm_file = h5py.File(self.config["lm_path"], "r")

    self.use_e2e_annealing = self.config['use_e2e_annealing']
    self.use_joint_coref = self.config["use_joint_coref"]

    self.lm_layers = self.config["lm_layers"]
    self.lm_size = self.config["lm_size"]
    self.eval_data = None # Load eval data lazily.

    input_props = []
    input_props.append((tf.string, [None, None])) # Tokens.
    input_props.append((tf.float32, [None, None, self.context_embeddings.size])) # Context embeddings.
    input_props.append((tf.float32, [None, None, self.head_embeddings.size])) # Head embeddings.
    input_props.append((tf.float32, [None, None, self.lm_size, self.lm_layers])) # LM embeddings.
    input_props.append((tf.int32, [None, None, None])) # Character indices.
    input_props.append((tf.int32, [None])) # Text lengths.
    input_props.append((tf.int32, [None])) # Speaker IDs.
    input_props.append((tf.int32, [])) # Genre.
    input_props.append((tf.bool, [])) # Is training.
    input_props.append((tf.int32, [None])) # Gold starts.
    input_props.append((tf.int32, [None])) # Gold ends.
    input_props.append((tf.int32, [None])) # Cluster ids.
    input_props.append((tf.int32, [None])) # Pred starts
    input_props.append((tf.int32, [None])) # Pred ends
    input_props.append((tf.bool,[])) #use_pred_mention

    self.queue_input_tensors = [tf.placeholder(dtype, shape) for dtype, shape in input_props]
    dtypes, shapes = zip(*input_props)
    queue = tf.PaddingFIFOQueue(capacity=10, dtypes=dtypes, shapes=shapes)
    self.enqueue_op = queue.enqueue(self.queue_input_tensors)
    self.input_tensors = queue.dequeue()

    self.predictions, self.loss = self.get_predictions_and_loss(*self.input_tensors)
    self.global_step = tf.Variable(0, name="global_step", trainable=False)
    self.reset_global_step = tf.assign(self.global_step, 0)
    learning_rate = tf.train.exponential_decay(self.config["learning_rate"], self.global_step,
                                               self.config["decay_frequency"], self.config["decay_rate"], staircase=True)
    trainable_params = tf.trainable_variables()
    gradients = tf.gradients(self.loss, trainable_params)
    gradients, _ = tf.clip_by_global_norm(gradients, self.config["max_gradient_norm"])
    optimizers = {
      "adam" : tf.train.AdamOptimizer,
      "sgd" : tf.train.GradientDescentOptimizer
    }
    optimizer = optimizers[self.config["optimizer"]](learning_rate)
    self.train_op = optimizer.apply_gradients(zip(gradients, trainable_params), global_step=self.global_step)

  def start_enqueue_thread(self, session):
    with open(self.config["train_path"]) as f:
      train_examples = [json.loads(jsonline) for jsonline in f.readlines()]
    def _enqueue_loop():
      max_step = self.config["max_step"]
      curr_step = 0
      while True:
        pred_ratio = 0.0 if not self.use_e2e_annealing else curr_step * 1.0 / max_step
        random.shuffle(train_examples)
        for example in train_examples:
          use_pred_mentions = True if not self.use_joint_coref else random.random() <= pred_ratio
          tensorized_example = self.tensorize_example(example, is_training=True,use_pred_mentions=use_pred_mentions)
          feed_dict = dict(zip(self.queue_input_tensors, tensorized_example))
          session.run(self.enqueue_op, feed_dict=feed_dict)
          curr_step+=1
    enqueue_thread = threading.Thread(target=_enqueue_loop)
    enqueue_thread.daemon = True
    enqueue_thread.start()

  def restore(self, session):
    # Don't try to restore unused variables from the TF-Hub ELMo module.
    vars_to_restore = [v for v in tf.global_variables() if "module/" not in v.name]
    saver = tf.train.Saver(vars_to_restore)
    checkpoint_path = os.path.join(self.config["log_dir"], "model.max.ckpt")
    print("Restoring from {}".format(checkpoint_path))
    session.run(tf.global_variables_initializer())
    saver.restore(session, checkpoint_path)

  def load_lm_embeddings(self, doc_key):
    if self.lm_file is None:
      return np.zeros([0, 0, self.lm_size, self.lm_layers])
    file_key = doc_key.replace("/", ":")
    if not file_key in self.lm_file and file_key[:-2] in self.lm_file:
      file_key = file_key[:-2]
    group = self.lm_file[file_key]
    num_sentences = len(list(group.keys()))
    sentences = [group[str(i)][...] for i in range(num_sentences)]
    lm_emb = np.zeros([num_sentences, max(s.shape[0] for s in sentences), self.lm_size, self.lm_layers])
    for i, s in enumerate(sentences):
      lm_emb[i, :s.shape[0], :, :] = s
    return lm_emb

  def tensorize_mentions(self, mentions):
    if len(mentions) > 0:
      starts, ends = zip(*mentions)
    else:
      starts, ends = [], []
    return np.array(starts), np.array(ends)


  def tensorize_example(self, example, is_training,use_pred_mentions):
    clusters = example["clusters"]

    gold_mentions = sorted(tuple(m) for m in util.flatten(clusters))
    gold_mention_map = {m:i for i,m in enumerate(gold_mentions)}
    cluster_ids = np.zeros(len(gold_mentions))
    for cluster_id, cluster in enumerate(clusters):
      for mention in cluster:
        cluster_ids[gold_mention_map[tuple(mention)]] = cluster_id + 1

    sentences = example["sentences"]
    num_words = sum(len(s) for s in sentences)
    speakers = util.flatten(example["speakers"])

    assert num_words == len(speakers)

    max_sentence_length = max(len(s) for s in sentences)
    max_word_length = max(max(max(len(w) for w in s) for s in sentences), max(self.config["filter_widths"]))
    text_len = np.array([len(s) for s in sentences])
    tokens = [[""] * max_sentence_length for _ in sentences]
    context_word_emb = np.zeros([len(sentences), max_sentence_length, self.context_embeddings.size])
    head_word_emb = np.zeros([len(sentences), max_sentence_length, self.head_embeddings.size])
    char_index = np.zeros([len(sentences), max_sentence_length, max_word_length])
    for i, sentence in enumerate(sentences):
      for j, word in enumerate(sentence):
        tokens[i][j] = word
        context_word_emb[i, j] = self.context_embeddings[word]
        head_word_emb[i, j] = self.head_embeddings[word]
        char_index[i, j, :len(word)] = [self.char_dict[c] for c in word]
    tokens = np.array(tokens)

    speaker_dict = { s:i for i,s in enumerate(set(speakers)) }
    speaker_ids = np.array([speaker_dict[s] for s in speakers])

    doc_key = example["doc_key"]
    genre = self.genres[doc_key[:2]]

    gold_starts, gold_ends = self.tensorize_mentions(gold_mentions)
    if "pred_mentions" in example:
      pred_starts, pred_ends = zip(*example["pred_mentions"])
      pred_starts, pred_ends= np.array(pred_starts),np.array(pred_ends)
    else:
      pred_starts,pred_ends = np.array([]),np.array([])
    lm_emb = self.load_lm_embeddings(doc_key)

    example_tensors = (tokens, context_word_emb, head_word_emb, lm_emb, char_index, text_len, speaker_ids, genre, is_training, gold_starts, gold_ends, cluster_ids,pred_starts,pred_ends,use_pred_mentions)

    if is_training and len(sentences) > self.config["max_training_sentences"]:
      return self.truncate_example(*example_tensors)
    else:
      return example_tensors

  def truncate_example(self, tokens, context_word_emb, head_word_emb, lm_emb, char_index, text_len, speaker_ids, genre, is_training, gold_starts, gold_ends, cluster_ids,pred_starts,pred_ends,use_pred_mentions):
    max_training_sentences = self.config["max_training_sentences"]
    num_sentences = context_word_emb.shape[0]
    assert num_sentences > max_training_sentences

    sentence_offset = random.randint(0, num_sentences - max_training_sentences)
    word_offset = text_len[:sentence_offset].sum()
    num_words = text_len[sentence_offset:sentence_offset + max_training_sentences].sum()
    tokens = tokens[sentence_offset:sentence_offset + max_training_sentences, :]
    context_word_emb = context_word_emb[sentence_offset:sentence_offset + max_training_sentences, :, :]
    head_word_emb = head_word_emb[sentence_offset:sentence_offset + max_training_sentences, :, :]
    lm_emb = lm_emb[sentence_offset:sentence_offset + max_training_sentences, :, :, :]
    char_index = char_index[sentence_offset:sentence_offset + max_training_sentences, :, :]
    text_len = text_len[sentence_offset:sentence_offset + max_training_sentences]

    speaker_ids = speaker_ids[word_offset: word_offset + num_words]
    gold_spans = np.logical_and(gold_ends >= word_offset, gold_starts < word_offset + num_words)
    gold_starts = gold_starts[gold_spans] - word_offset
    gold_ends = gold_ends[gold_spans] - word_offset
    cluster_ids = cluster_ids[gold_spans]
    pred_spans = np.logical_and(pred_ends >= word_offset, pred_starts < word_offset + num_words)
    pred_starts = pred_starts[pred_spans] - word_offset
    pred_ends = pred_ends[pred_spans] - word_offset

    return tokens, context_word_emb, head_word_emb, lm_emb, char_index, text_len, speaker_ids, genre, is_training, gold_starts, gold_ends, cluster_ids, pred_starts,pred_ends,use_pred_mentions


  def get_pred_mention_scores(self, candidate_starts,candidate_ends, pred_mention_starts, pred_mention_ends, pred_mention_scores):
    same_start = tf.equal(tf.expand_dims(pred_mention_starts, 1),
                          tf.expand_dims(candidate_starts, 0))  # [num_labeled, num_candidates]
    same_end = tf.equal(tf.expand_dims(pred_mention_ends, 1),
                        tf.expand_dims(candidate_ends, 0))  # [num_labeled, num_candidates]
    same_span = tf.logical_and(same_start, same_end)  # [num_labeled, num_candidates]
    candidate_scores = tf.matmul(tf.expand_dims(pred_mention_scores, 0), tf.to_float(same_span))  # [1, num_candidates]
    candidate_scores = tf.squeeze(candidate_scores, 0)  # [num_candidates]
    return candidate_scores

  def get_candidate_labels(self, candidate_starts, candidate_ends, labeled_starts, labeled_ends, labels):
    same_start = tf.equal(tf.expand_dims(labeled_starts, 1), tf.expand_dims(candidate_starts, 0)) # [num_labeled, num_candidates]
    same_end = tf.equal(tf.expand_dims(labeled_ends, 1), tf.expand_dims(candidate_ends, 0)) # [num_labeled, num_candidates]
    same_span = tf.logical_and(same_start, same_end) # [num_labeled, num_candidates]
    candidate_labels = tf.matmul(tf.expand_dims(labels, 0), tf.to_int32(same_span)) # [1, num_candidates]
    candidate_labels = tf.squeeze(candidate_labels, 0) # [num_candidates]
    return candidate_labels

  def get_dropout(self, dropout_rate, is_training):
    return 1 - (tf.to_float(is_training) * dropout_rate)

  def coarse_to_fine_pruning(self, top_span_emb, top_span_mention_scores, c):
    k = util.shape(top_span_emb, 0)
    top_span_range = tf.range(k)  # [k]
    antecedent_offsets = tf.expand_dims(top_span_range, 1) - tf.expand_dims(top_span_range, 0)  # [k, k]
    antecedents_mask = antecedent_offsets >= 1  # [k, k]
    fast_antecedent_scores = tf.expand_dims(top_span_mention_scores, 1) + tf.expand_dims(top_span_mention_scores,
                                                                                         0)  # [k, k]
    fast_antecedent_scores += tf.log(tf.to_float(antecedents_mask))  # [k, k]
    fast_antecedent_scores += self.get_fast_antecedent_scores(top_span_emb)  # [k, k]

    _, top_antecedents = tf.nn.top_k(fast_antecedent_scores, c, sorted=False)  # [k, c]
    top_antecedents_mask = util.batch_gather(antecedents_mask, top_antecedents)  # [k, c]
    top_fast_antecedent_scores = util.batch_gather(fast_antecedent_scores, top_antecedents)  # [k, c]
    top_antecedent_offsets = util.batch_gather(antecedent_offsets, top_antecedents)  # [k, c]
    return top_antecedents, top_antecedents_mask, top_fast_antecedent_scores, top_antecedent_offsets

  def distance_pruning(self, top_span_emb, top_span_mention_scores, c):
    k = util.shape(top_span_emb, 0)
    top_antecedent_offsets = tf.tile(tf.expand_dims(tf.range(c) + 1, 0), [k, 1])  # [k, c]
    raw_top_antecedents = tf.expand_dims(tf.range(k), 1) - top_antecedent_offsets  # [k, c]
    top_antecedents_mask = raw_top_antecedents >= 0  # [k, c]
    top_antecedents = tf.maximum(raw_top_antecedents, 0)  # [k, c]

    top_fast_antecedent_scores = tf.expand_dims(top_span_mention_scores, 1) + tf.gather(top_span_mention_scores,
                                                                                        top_antecedents)  # [k, c]
    top_fast_antecedent_scores += tf.log(tf.to_float(top_antecedents_mask))  # [k, c]
    return top_antecedents, top_antecedents_mask, top_fast_antecedent_scores, top_antecedent_offsets

  def get_predictions_and_loss(self, tokens, context_word_emb, head_word_emb, lm_emb, char_index, text_len, speaker_ids, genre, is_training, gold_starts, gold_ends, cluster_ids,pred_starts, pred_ends,use_pred_mentions):
    self.dropout = self.get_dropout(self.config["dropout_rate"], is_training)
    self.lexical_dropout = self.get_dropout(self.config["lexical_dropout_rate"], is_training)
    self.lstm_dropout = self.get_dropout(self.config["lstm_dropout_rate"], is_training)

    num_sentences = tf.shape(context_word_emb)[0]
    max_sentence_length = tf.shape(context_word_emb)[1]

    context_emb_list = [context_word_emb]
    head_emb_list = [head_word_emb]

    if self.config["char_embedding_size"] > 0:
      char_emb = tf.gather(tf.get_variable("char_embeddings", [len(self.char_dict), self.config["char_embedding_size"]]), char_index) # [num_sentences, max_sentence_length, max_word_length, emb]
      flattened_char_emb = tf.reshape(char_emb, [num_sentences * max_sentence_length, util.shape(char_emb, 2), util.shape(char_emb, 3)]) # [num_sentences * max_sentence_length, max_word_length, emb]
      flattened_aggregated_char_emb = util.cnn(flattened_char_emb, self.config["filter_widths"], self.config["filter_size"]) # [num_sentences * max_sentence_length, emb]
      aggregated_char_emb = tf.reshape(flattened_aggregated_char_emb, [num_sentences, max_sentence_length, util.shape(flattened_aggregated_char_emb, 1)]) # [num_sentences, max_sentence_length, emb]
      context_emb_list.append(aggregated_char_emb)
      head_emb_list.append(aggregated_char_emb)


    lm_emb_size = util.shape(lm_emb, 2)
    lm_num_layers = util.shape(lm_emb, 3)
    with tf.variable_scope("lm_aggregation"):
      self.lm_weights = tf.nn.softmax(tf.get_variable("lm_scores", [lm_num_layers], initializer=tf.constant_initializer(0.0)))
      self.lm_scaling = tf.get_variable("lm_scaling", [], initializer=tf.constant_initializer(1.0))
    flattened_lm_emb = tf.reshape(lm_emb, [num_sentences * max_sentence_length * lm_emb_size, lm_num_layers])
    flattened_aggregated_lm_emb = tf.matmul(flattened_lm_emb, tf.expand_dims(self.lm_weights, 1)) # [num_sentences * max_sentence_length * emb, 1]
    aggregated_lm_emb = tf.reshape(flattened_aggregated_lm_emb, [num_sentences, max_sentence_length, lm_emb_size])
    aggregated_lm_emb *= self.lm_scaling
    context_emb_list.append(aggregated_lm_emb)

    context_emb = tf.concat(context_emb_list, 2) # [num_sentences, max_sentence_length, emb]
    head_emb = tf.concat(head_emb_list, 2) # [num_sentences, max_sentence_length, emb]
    context_emb = tf.nn.dropout(context_emb, self.lexical_dropout) # [num_sentences, max_sentence_length, emb]
    head_emb = tf.nn.dropout(head_emb, self.lexical_dropout) # [num_sentences, max_sentence_length, emb]

    text_len_mask = tf.sequence_mask(text_len, maxlen=max_sentence_length) # [num_sentence, max_sentence_length]

    context_outputs = self.lstm_contextualize(context_emb, text_len, text_len_mask) # [num_words, emb]
    num_words = util.shape(context_outputs, 0)

    genre_emb = tf.gather(tf.get_variable("genre_embeddings", [len(self.genres), self.config["feature_size"]]), genre) # [emb]

    sentence_indices = tf.tile(tf.expand_dims(tf.range(num_sentences), 1), [1, max_sentence_length]) # [num_sentences, max_sentence_length]
    flattened_sentence_indices = self.flatten_emb_by_sentence(sentence_indices, text_len_mask) # [num_words]
    flattened_head_emb = self.flatten_emb_by_sentence(head_emb, text_len_mask) # [num_words]



    candidate_starts = tf.tile(tf.expand_dims(tf.range(num_words), 1),
                               [1, self.max_span_width])  # [num_words, max_span_width]
    candidate_ends = candidate_starts + tf.expand_dims(tf.range(self.max_span_width), 0)  # [num_words, max_span_width]
    candidate_start_sentence_indices = tf.gather(flattened_sentence_indices,
                                                 candidate_starts)  # [num_words, max_span_width]
    candidate_end_sentence_indices = tf.gather(flattened_sentence_indices,
                                               tf.minimum(candidate_ends, num_words - 1))  # [num_words, max_span_width]
    candidate_mask = tf.logical_and(candidate_ends < num_words, tf.equal(candidate_start_sentence_indices,
                                                                         candidate_end_sentence_indices))  # [num_words, max_span_width]
    flattened_candidate_mask = tf.reshape(candidate_mask, [-1])  # [num_words * max_span_width]
    candidate_starts = tf.boolean_mask(tf.reshape(candidate_starts, [-1]), flattened_candidate_mask)  # [num_candidates]
    candidate_ends = tf.boolean_mask(tf.reshape(candidate_ends, [-1]), flattened_candidate_mask)  # [num_candidates]
    candidate_sentence_indices = tf.boolean_mask(tf.reshape(candidate_start_sentence_indices, [-1]),
                                                 flattened_candidate_mask)  # [num_candidates]

    candidate_starts = tf.cond(use_pred_mentions,lambda : pred_starts,lambda :candidate_starts)
    candidate_ends = tf.cond(use_pred_mentions,lambda :pred_ends,lambda :candidate_ends)

    candidate_cluster_ids = self.get_candidate_labels(candidate_starts, candidate_ends, gold_starts, gold_ends,
                                                      cluster_ids)  # [num_candidates]

    candidate_span_emb = self.get_span_emb(flattened_head_emb, context_outputs, candidate_starts,
                                           candidate_ends)  # [num_candidates, emb]
    candidate_mention_scores = self.get_mention_scores(candidate_span_emb)  # [k, 1]
    candidate_mention_scores = tf.squeeze(candidate_mention_scores, 1)  # [k]



    if self.use_joint_coref:
      k = tf.to_int32(tf.floor(tf.to_float(tf.shape(context_outputs)[0]) * self.config["top_span_ratio"]))
      k = tf.cond(use_pred_mentions,lambda :tf.minimum(util.shape(candidate_starts,0),k),lambda :k)
      top_span_indices = coref_ops.extract_spans(tf.expand_dims(candidate_mention_scores, 0),
                                                 tf.expand_dims(candidate_starts, 0),
                                                 tf.expand_dims(candidate_ends, 0),
                                                 tf.expand_dims(k, 0),
                                                 util.shape(context_outputs, 0),
                                                 True)  # [1, k]
      top_span_indices.set_shape([1, None])
      top_span_indices = tf.squeeze(top_span_indices, 0)  # [k]

      top_span_starts = tf.gather(candidate_starts, top_span_indices) # [k]
      top_span_ends = tf.gather(candidate_ends, top_span_indices)  # [k]
      top_span_emb = tf.gather(candidate_span_emb, top_span_indices)  # [k, emb]
      top_span_cluster_ids = tf.gather(candidate_cluster_ids, top_span_indices)  # [k]
      top_span_mention_scores = tf.gather(candidate_mention_scores, top_span_indices)  # [k]
      top_span_speaker_ids = tf.gather(speaker_ids, top_span_starts)  # [k]
    else:
      k = util.shape(candidate_starts,0)
      top_span_starts = candidate_starts
      top_span_ends = candidate_ends
      top_span_emb = candidate_span_emb
      top_span_cluster_ids = candidate_cluster_ids
      top_span_mention_scores = candidate_mention_scores
      top_span_speaker_ids = tf.gather(speaker_ids, top_span_starts)


    c = tf.minimum(self.config["max_top_antecedents"], k)

    if self.config["coarse_to_fine"]:
      top_antecedents, top_antecedents_mask, top_fast_antecedent_scores, top_antecedent_offsets = self.coarse_to_fine_pruning(
        top_span_emb, top_span_mention_scores, c)
    else:
      top_antecedents, top_antecedents_mask, top_fast_antecedent_scores, top_antecedent_offsets = self.distance_pruning(
        top_span_emb, top_span_mention_scores, c)

    dummy_scores = tf.zeros([k, 1])  # [k, 1]
    for i in range(self.config["coref_depth"]):
      with tf.variable_scope("coref_layer", reuse=(i > 0)):
        top_antecedent_emb = tf.gather(top_span_emb, top_antecedents)  # [k, c, emb]
        top_antecedent_scores = top_fast_antecedent_scores + self.get_slow_antecedent_scores(top_span_emb,
                                                                                             top_antecedents,
                                                                                             top_antecedent_emb,
                                                                                             top_antecedent_offsets,
                                                                                             top_span_speaker_ids,
                                                                                             genre_emb)  # [k, c]
        top_antecedent_weights = tf.nn.softmax(tf.concat([dummy_scores, top_antecedent_scores], 1))  # [k, c + 1]
        top_antecedent_emb = tf.concat([tf.expand_dims(top_span_emb, 1), top_antecedent_emb], 1)  # [k, c + 1, emb]
        attended_span_emb = tf.reduce_sum(tf.expand_dims(top_antecedent_weights, 2) * top_antecedent_emb, 1)  # [k, emb]
        with tf.variable_scope("f"):
          f = tf.sigmoid(
            util.projection(tf.concat([top_span_emb, attended_span_emb], 1), util.shape(top_span_emb, -1)))  # [k, emb]
          top_span_emb = f * attended_span_emb + (1 - f) * top_span_emb  # [k, emb]

    top_antecedent_scores = tf.concat([dummy_scores, top_antecedent_scores], 1)  # [k, c + 1]

    top_antecedent_cluster_ids = tf.gather(top_span_cluster_ids, top_antecedents)  # [k, c]
    top_antecedent_cluster_ids += tf.to_int32(tf.log(tf.to_float(top_antecedents_mask)))  # [k, c]
    same_cluster_indicator = tf.equal(top_antecedent_cluster_ids, tf.expand_dims(top_span_cluster_ids, 1))  # [k, c]
    non_dummy_indicator = tf.expand_dims(top_span_cluster_ids > 0, 1)  # [k, 1]
    pairwise_labels = tf.logical_and(same_cluster_indicator, non_dummy_indicator)  # [k, c]
    dummy_labels = tf.logical_not(tf.reduce_any(pairwise_labels, 1, keepdims=True))  # [k, 1]
    top_antecedent_labels = tf.concat([dummy_labels, pairwise_labels], 1)  # [k, c + 1]
    loss = self.softmax_loss(top_antecedent_scores, top_antecedent_labels)  # [k]
    loss = tf.reduce_sum(loss)  # []
    #loss = tf.Print(loss,[loss])
    return [top_span_starts, top_span_ends, top_antecedents, top_antecedent_scores], loss

  def get_span_emb(self, head_emb, context_outputs, span_starts, span_ends):
    span_emb_list = []

    span_start_emb = tf.gather(context_outputs, span_starts) # [k, emb]
    span_emb_list.append(span_start_emb)

    span_end_emb = tf.gather(context_outputs, span_ends) # [k, emb]
    span_emb_list.append(span_end_emb)


    #in case the span from MD is longer than max_span_width,  we compute the head attentions for the last max_span_width tokens
    span_starts = tf.maximum(span_starts, 1 + span_ends - self.config["max_span_width"]) #[k]
    span_width = 1 + span_ends - span_starts # [k]

    if self.config["use_features"]:
      span_width_index = span_width - 1 # [k]
      span_width_emb = tf.gather(tf.get_variable("span_width_embeddings", [self.config["max_span_width"], self.config["feature_size"]]), span_width_index) # [k, emb]
      span_width_emb = tf.nn.dropout(span_width_emb, self.dropout)
      span_emb_list.append(span_width_emb)

    if self.config["model_heads"]:
      span_indices = tf.expand_dims(tf.range(self.config["max_span_width"]), 0) + tf.expand_dims(span_starts, 1) # [k, max_span_width]
      span_indices = tf.minimum(util.shape(context_outputs, 0) - 1, span_indices) # [k, max_span_width]
      span_text_emb = tf.gather(head_emb, span_indices) # [k, max_span_width, emb]
      with tf.variable_scope("head_scores"):
        self.head_scores = util.projection(context_outputs, 1) # [num_words, 1]
      span_head_scores = tf.gather(self.head_scores, span_indices) # [k, max_span_width, 1]
      span_mask = tf.expand_dims(tf.sequence_mask(span_width, self.config["max_span_width"], dtype=tf.float32), 2) # [k, max_span_width, 1]
      span_head_scores += tf.log(span_mask) # [k, max_span_width, 1]
      span_attention = tf.nn.softmax(span_head_scores, 1) # [k, max_span_width, 1]
      span_head_emb = tf.reduce_sum(span_attention * span_text_emb, 1) # [k, emb]
      span_emb_list.append(span_head_emb)

    span_emb = tf.concat(span_emb_list, 1) # [k, emb]
    return span_emb # [k, emb]

  def get_mention_scores(self, span_emb,scope_name = 'mention_scores'):
    with tf.variable_scope(scope_name):
      return util.ffnn(span_emb, self.config["ffnn_depth"], self.config["ffnn_size"], 1, self.dropout) # [k, 1]


  def softmax_loss(self, antecedent_scores, antecedent_labels):
    gold_scores = antecedent_scores + tf.log(tf.to_float(antecedent_labels)) # [k, max_ant + 1]
    marginalized_gold_scores = tf.reduce_logsumexp(gold_scores, [1]) # [k]
    log_norm = tf.reduce_logsumexp(antecedent_scores, [1]) # [k]
    return log_norm - marginalized_gold_scores # [k]


  def bucket_distance(self, distances):
    """
    Places the given values (designed for distances) into 10 semi-logscale buckets:
    [0, 1, 2, 3, 4, 5-7, 8-15, 16-31, 32-63, 64+].
    """
    logspace_idx = tf.to_int32(tf.floor(tf.log(tf.to_float(distances))/math.log(2))) + 3
    use_identity = tf.to_int32(distances <= 4)
    combined_idx = use_identity * distances + (1 - use_identity) * logspace_idx
    return tf.clip_by_value(combined_idx, 0, 9)

  def get_slow_antecedent_scores(self, top_span_emb, top_antecedents, top_antecedent_emb, top_antecedent_offsets, top_span_speaker_ids, genre_emb):
    k = util.shape(top_span_emb, 0)
    c = util.shape(top_antecedents, 1)

    feature_emb_list = []

    if self.config["use_metadata"]:
      top_antecedent_speaker_ids = tf.gather(top_span_speaker_ids, top_antecedents) # [k, c]
      same_speaker = tf.equal(tf.expand_dims(top_span_speaker_ids, 1), top_antecedent_speaker_ids) # [k, c]
      speaker_pair_emb = tf.gather(tf.get_variable("same_speaker_emb", [2, self.config["feature_size"]]), tf.to_int32(same_speaker)) # [k, c, emb]
      feature_emb_list.append(speaker_pair_emb)

      tiled_genre_emb = tf.tile(tf.expand_dims(tf.expand_dims(genre_emb, 0), 0), [k, c, 1]) # [k, c, emb]
      feature_emb_list.append(tiled_genre_emb)

    if self.config["use_features"]:
      antecedent_distance_buckets = self.bucket_distance(top_antecedent_offsets) # [k, c]
      antecedent_distance_emb = tf.gather(tf.get_variable("antecedent_distance_emb", [10, self.config["feature_size"]]), antecedent_distance_buckets) # [k, c]
      feature_emb_list.append(antecedent_distance_emb)

    feature_emb = tf.concat(feature_emb_list, 2) # [k, c, emb]
    feature_emb = tf.nn.dropout(feature_emb, self.dropout) # [k, c, emb]

    target_emb = tf.expand_dims(top_span_emb, 1) # [k, 1, emb]
    similarity_emb = top_antecedent_emb * target_emb # [k, c, emb]
    target_emb = tf.tile(target_emb, [1, c, 1]) # [k, c, emb]

    pair_emb = tf.concat([target_emb, top_antecedent_emb, similarity_emb, feature_emb], 2) # [k, c, emb]

    with tf.variable_scope("slow_antecedent_scores"):
      slow_antecedent_scores = util.ffnn(pair_emb, self.config["ffnn_depth"], self.config["ffnn_size"], 1, self.dropout) # [k, c, 1]
    slow_antecedent_scores = tf.squeeze(slow_antecedent_scores, 2) # [k, c]
    return slow_antecedent_scores # [k, c]

  def get_fast_antecedent_scores(self, top_span_emb):
    with tf.variable_scope("src_projection"):
      source_top_span_emb = tf.nn.dropout(util.projection(top_span_emb, util.shape(top_span_emb, -1)), self.dropout) # [k, emb]
    target_top_span_emb = tf.nn.dropout(top_span_emb, self.dropout) # [k, emb]
    return tf.matmul(source_top_span_emb, target_top_span_emb, transpose_b=True) # [k, k]

  def flatten_emb_by_sentence(self, emb, text_len_mask):
    num_sentences = tf.shape(emb)[0]
    max_sentence_length = tf.shape(emb)[1]

    emb_rank = len(emb.get_shape())
    if emb_rank  == 2:
      flattened_emb = tf.reshape(emb, [num_sentences * max_sentence_length])
    elif emb_rank == 3:
      flattened_emb = tf.reshape(emb, [num_sentences * max_sentence_length, util.shape(emb, 2)])
    else:
      raise ValueError("Unsupported rank: {}".format(emb_rank))
    return tf.boolean_mask(flattened_emb, tf.reshape(text_len_mask, [num_sentences * max_sentence_length]))

  def lstm_contextualize(self, text_emb, text_len, text_len_mask):
    num_sentences = tf.shape(text_emb)[0]

    current_inputs = text_emb # [num_sentences, max_sentence_length, emb]

    for layer in range(self.config["contextualization_layers"]):
      with tf.variable_scope("layer_{}".format(layer)):
        with tf.variable_scope("fw_cell"):
          cell_fw = util.CustomLSTMCell(self.config["contextualization_size"], num_sentences, self.lstm_dropout)
        with tf.variable_scope("bw_cell"):
          cell_bw = util.CustomLSTMCell(self.config["contextualization_size"], num_sentences, self.lstm_dropout)
        state_fw = tf.contrib.rnn.LSTMStateTuple(tf.tile(cell_fw.initial_state.c, [num_sentences, 1]), tf.tile(cell_fw.initial_state.h, [num_sentences, 1]))
        state_bw = tf.contrib.rnn.LSTMStateTuple(tf.tile(cell_bw.initial_state.c, [num_sentences, 1]), tf.tile(cell_bw.initial_state.h, [num_sentences, 1]))

        (fw_outputs, bw_outputs), _ = tf.nn.bidirectional_dynamic_rnn(
          cell_fw=cell_fw,
          cell_bw=cell_bw,
          inputs=current_inputs,
          sequence_length=text_len,
          initial_state_fw=state_fw,
          initial_state_bw=state_bw)

        text_outputs = tf.concat([fw_outputs, bw_outputs], 2) # [num_sentences, max_sentence_length, emb]
        text_outputs = tf.nn.dropout(text_outputs, self.lstm_dropout)
        if layer > 0:
          highway_gates = tf.sigmoid(util.projection(text_outputs, util.shape(text_outputs, 2))) # [num_sentences, max_sentence_length, emb]
          text_outputs = highway_gates * text_outputs + (1 - highway_gates) * current_inputs
        current_inputs = text_outputs

    return self.flatten_emb_by_sentence(text_outputs, text_len_mask)

  def get_predicted_antecedents(self, antecedents, antecedent_scores):
    predicted_antecedents = []
    for i, index in enumerate(np.argmax(antecedent_scores, axis=1) - 1):
      if index < 0:
        predicted_antecedents.append(-1)
      else:
        predicted_antecedents.append(antecedents[i, index])
    return predicted_antecedents

  def get_predicted_clusters(self, top_span_starts, top_span_ends, predicted_antecedents):
    mention_to_predicted = {}
    predicted_clusters = []
    for i, predicted_index in enumerate(predicted_antecedents):
      if predicted_index < 0:
        continue
      assert i > predicted_index
      predicted_antecedent = (int(top_span_starts[predicted_index]), int(top_span_ends[predicted_index]))
      if predicted_antecedent in mention_to_predicted:
        predicted_cluster = mention_to_predicted[predicted_antecedent]
      else:
        predicted_cluster = len(predicted_clusters)
        predicted_clusters.append([predicted_antecedent])
        mention_to_predicted[predicted_antecedent] = predicted_cluster

      mention = (int(top_span_starts[i]), int(top_span_ends[i]))
      predicted_clusters[predicted_cluster].append(mention)
      mention_to_predicted[mention] = predicted_cluster

    predicted_clusters = [tuple(pc) for pc in predicted_clusters]
    mention_to_predicted = { m:predicted_clusters[i] for m,i in mention_to_predicted.items() }

    return predicted_clusters, mention_to_predicted

  def evaluate_coref(self, top_span_starts, top_span_ends, predicted_antecedents, gold_clusters, evaluator):
    gold_clusters = [tuple(tuple(m) for m in gc) for gc in gold_clusters]
    mention_to_gold = {}
    for gc in gold_clusters:
      for mention in gc:
        mention_to_gold[mention] = gc

    predicted_clusters, mention_to_predicted = self.get_predicted_clusters(top_span_starts, top_span_ends, predicted_antecedents)
    evaluator.update(predicted_clusters, gold_clusters, mention_to_predicted, mention_to_gold)
    return predicted_clusters

  def load_eval_data(self):
    if self.eval_data is None:
      def load_line(line):
        example = json.loads(line)
        use_pred_mentions = True if not self.use_joint_coref or self.use_e2e_annealing else False
        return self.tensorize_example(example, False,use_pred_mentions), example
      with open(self.config["eval_path"]) as f:
        self.eval_data = [load_line(l) for l in f.readlines()]
      print("Loaded {} eval examples.".format(len(self.eval_data)))

  def evaluate(self, session, official_stdout=False):
    self.load_eval_data()

    tp,fn,fp = 0,0,0
    coref_predictions = {}
    coref_evaluator = metrics.CorefEvaluator()

    for example_num, (tensorized_example, example) in enumerate(self.eval_data):
      _, _, _, _, _, _, _, _, _, gold_starts, gold_ends, _, _,_,_ = tensorized_example
      feed_dict = {i:t for i,t in zip(self.input_tensors, tensorized_example)}
      top_span_starts, top_span_ends, top_antecedents, top_antecedent_scores = session.run(self.predictions, feed_dict=feed_dict)
      predicted_antecedents = self.get_predicted_antecedents(top_antecedents, top_antecedent_scores)
      coref_predictions[example["doc_key"]] = self.evaluate_coref(top_span_starts, top_span_ends, predicted_antecedents, example["clusters"], coref_evaluator)

      gold_mentions = set([(s, e) for cl in example["clusters"] for s, e in cl])
      pred_mentions = set([(s, e) for s, e in zip(top_span_starts, top_span_ends)])
      tp += len(gold_mentions & pred_mentions)
      fn += len(gold_mentions - pred_mentions)
      fp += len(pred_mentions - gold_mentions)
      if example_num % 10 == 0:
        print("Evaluated {}/{} examples.".format(example_num + 1, len(self.eval_data)))

    m_r = float(tp) / (tp + fn)
    m_p = float(tp) / (tp + fp)
    m_f1 = 2.0 * m_r * m_p / (m_r + m_p)
    print("Mention F1: {:.2f}%".format(m_f1 * 100))
    print("Mention recall: {:.2f}%".format(m_r * 100))
    print("Mention precision: {:.2f}%".format(m_p * 100))
    
    summary_dict = {}
    if official_stdout:
      conll_results = conll.evaluate_conll(self.config["conll_eval_path"], coref_predictions, official_stdout)
      average_f1 = sum(results["f"] for results in conll_results.values()) / len(conll_results)
      summary_dict["Average F1 (conll)"] = average_f1
      print("Average F1 (conll): {:.2f}%".format(average_f1))

    p,r,f = coref_evaluator.get_prf()
    summary_dict["Average F1 (py)"] = f
    print("Average F1 (py): {:.2f}%".format(f * 100))
    summary_dict["Average precision (py)"] = p
    print("Average precision (py): {:.2f}%".format(p * 100))
    summary_dict["Average recall (py)"] = r
    print("Average recall (py): {:.2f}%".format(r * 100))
    average_f1 = average_f1 if official_stdout else f*100
    return util.make_summary(summary_dict), average_f1