mirror of
https://github.com/explosion/spaCy.git
synced 2024-12-26 01:46:28 +03:00
refactor again to clusters of entities and cosine similarity
This commit is contained in:
svlandeg
parent
8c4aa076bc
commit
992fa92b66
|
|
@ -11,7 +11,7 @@ from thinc.neural._classes.convolution import ExtractWindow
|
|||
|
||||
from examples.pipeline.wiki_entity_linking import run_el, training_set_creator, kb_creator
|
||||
|
||||
from spacy._ml import SpacyVectors, create_default_optimizer, zero_init, logistic, Tok2Vec
|
||||
from spacy._ml import SpacyVectors, create_default_optimizer, zero_init, logistic, Tok2Vec, cosine
|
||||
|
||||
from thinc.api import chain, concatenate, flatten_add_lengths, clone, with_flatten
|
||||
from thinc.v2v import Model, Maxout, Affine, ReLu
|
||||
|
|
@ -20,6 +20,7 @@ from thinc.t2t import ParametricAttention
|
|||
from thinc.misc import Residual
|
||||
from thinc.misc import LayerNorm as LN
|
||||
|
||||
from spacy.cli.pretrain import get_cossim_loss
|
||||
from spacy.matcher import PhraseMatcher
|
||||
from spacy.tokens import Doc
|
||||
|
||||
|
|
@ -34,20 +35,20 @@ class EL_Model:
|
|||
CUTOFF = 0.5
|
||||
|
||||
BATCH_SIZE = 5
|
||||
UPSAMPLE = True
|
||||
# UPSAMPLE = True
|
||||
|
||||
DOC_CUTOFF = 300 # number of characters from the doc context
|
||||
INPUT_DIM = 300 # dimension of pre-trained vectors
|
||||
|
||||
# HIDDEN_1_WIDTH = 32 # 10
|
||||
HIDDEN_2_WIDTH = 32 # 6
|
||||
DESC_WIDTH = 64 # 4
|
||||
ARTICLE_WIDTH = 64 # 8
|
||||
HIDDEN_1_WIDTH = 32
|
||||
# HIDDEN_2_WIDTH = 32 # 6
|
||||
DESC_WIDTH = 64
|
||||
ARTICLE_WIDTH = 64
|
||||
SENT_WIDTH = 64
|
||||
|
||||
DROP = 0.1
|
||||
LEARN_RATE = 0.0001
|
||||
EPOCHS = 20
|
||||
EPOCHS = 10
|
||||
L2 = 1e-6
|
||||
|
||||
name = "entity_linker"
|
||||
|
|
@ -57,9 +58,10 @@ class EL_Model:
|
|||
self.nlp = nlp
|
||||
self.kb = kb
|
||||
|
||||
self._build_cnn(desc_width=self.DESC_WIDTH,
|
||||
self._build_cnn(embed_width=self.INPUT_DIM,
|
||||
desc_width=self.DESC_WIDTH,
|
||||
article_width=self.ARTICLE_WIDTH,
|
||||
sent_width=self.SENT_WIDTH)
|
||||
sent_width=self.SENT_WIDTH, hidden_1_width=self.HIDDEN_1_WIDTH)
|
||||
|
||||
def train_model(self, training_dir, entity_descr_output, trainlimit=None, devlimit=None, to_print=True):
|
||||
# raise errors instead of runtime warnings in case of int/float overflow
|
||||
|
|
@ -70,24 +72,28 @@ class EL_Model:
|
|||
|
||||
train_ent, train_gold, train_desc, train_art, train_art_texts, train_sent, train_sent_texts = \
|
||||
self._get_training_data(training_dir, entity_descr_output, False, trainlimit, to_print=False)
|
||||
train_clusters = list(train_ent.keys())
|
||||
|
||||
dev_ent, dev_gold, dev_desc, dev_art, dev_art_texts, dev_sent, dev_sent_texts = \
|
||||
self._get_training_data(training_dir, entity_descr_output, True, devlimit, to_print=False)
|
||||
dev_clusters = list(dev_ent.keys())
|
||||
|
||||
dev_pos_count = len([g for g in dev_gold.values() if g])
|
||||
dev_neg_count = len([g for g in dev_gold.values() if not g])
|
||||
|
||||
# inspect data
|
||||
if self.PRINT_INSPECT:
|
||||
for entity in train_ent:
|
||||
print("entity", entity)
|
||||
print("gold", train_gold[entity])
|
||||
print("desc", train_desc[entity])
|
||||
print("sentence ID", train_sent[entity])
|
||||
print("sentence text", train_sent_texts[train_sent[entity]])
|
||||
print("article ID", train_art[entity])
|
||||
print("article text", train_art_texts[train_art[entity]])
|
||||
for cluster, entities in train_ent.items():
|
||||
print()
|
||||
for entity in entities:
|
||||
print("entity", entity)
|
||||
print("gold", train_gold[entity])
|
||||
print("desc", train_desc[entity])
|
||||
print("sentence ID", train_sent[entity])
|
||||
print("sentence text", train_sent_texts[train_sent[entity]])
|
||||
print("article ID", train_art[entity])
|
||||
print("article text", train_art_texts[train_art[entity]])
|
||||
print()
|
||||
|
||||
train_pos_entities = [k for k, v in train_gold.items() if v]
|
||||
train_neg_entities = [k for k, v in train_gold.items() if not v]
|
||||
|
|
@ -95,29 +101,29 @@ class EL_Model:
|
|||
train_pos_count = len(train_pos_entities)
|
||||
train_neg_count = len(train_neg_entities)
|
||||
|
||||
if self.UPSAMPLE:
|
||||
if to_print:
|
||||
print()
|
||||
print("Upsampling, original training instances pos/neg:", train_pos_count, train_neg_count)
|
||||
|
||||
# upsample positives to 50-50 distribution
|
||||
while train_pos_count < train_neg_count:
|
||||
train_ent.append(random.choice(train_pos_entities))
|
||||
train_pos_count += 1
|
||||
|
||||
# if self.UPSAMPLE:
|
||||
# if to_print:
|
||||
# print()
|
||||
# print("Upsampling, original training instances pos/neg:", train_pos_count, train_neg_count)
|
||||
#
|
||||
# # upsample positives to 50-50 distribution
|
||||
# while train_pos_count < train_neg_count:
|
||||
# train_ent.append(random.choice(train_pos_entities))
|
||||
# train_pos_count += 1
|
||||
#
|
||||
# upsample negatives to 50-50 distribution
|
||||
while train_neg_count < train_pos_count:
|
||||
train_ent.append(random.choice(train_neg_entities))
|
||||
train_neg_count += 1
|
||||
# while train_neg_count < train_pos_count:
|
||||
# train_ent.append(random.choice(train_neg_entities))
|
||||
# train_neg_count += 1
|
||||
|
||||
self._begin_training()
|
||||
|
||||
if to_print:
|
||||
print()
|
||||
print("Training on", len(train_ent), "entities in", len(train_art_texts), "articles")
|
||||
print("Training on", len(train_clusters), "entity clusters in", len(train_art_texts), "articles")
|
||||
print("Training instances pos/neg:", train_pos_count, train_neg_count)
|
||||
print()
|
||||
print("Dev test on", len(dev_ent), "entities in", len(dev_art_texts), "articles")
|
||||
print("Dev test on", len(dev_clusters), "entity clusters in", len(dev_art_texts), "articles")
|
||||
print("Dev instances pos/neg:", dev_pos_count, dev_neg_count)
|
||||
print()
|
||||
print(" CUTOFF", self.CUTOFF)
|
||||
|
|
@ -138,94 +144,104 @@ class EL_Model:
|
|||
|
||||
self._test_dev(dev_ent, dev_gold, dev_desc, dev_art, dev_art_texts, dev_sent, dev_sent_texts,
|
||||
print_string="dev_pre", avg=True)
|
||||
print()
|
||||
|
||||
processed = 0
|
||||
for i in range(self.EPOCHS):
|
||||
shuffle(train_ent)
|
||||
shuffle(train_clusters)
|
||||
|
||||
start = 0
|
||||
stop = min(self.BATCH_SIZE, len(train_ent))
|
||||
stop = min(self.BATCH_SIZE, len(train_clusters))
|
||||
|
||||
while start < len(train_ent):
|
||||
next_batch = train_ent[start:stop]
|
||||
while start < len(train_clusters):
|
||||
next_batch = {c: train_ent[c] for c in train_clusters[start:stop]}
|
||||
processed += len(next_batch.keys())
|
||||
|
||||
golds = [train_gold[e] for e in next_batch]
|
||||
descs = [train_desc[e] for e in next_batch]
|
||||
article_texts = [train_art_texts[train_art[e]] for e in next_batch]
|
||||
sent_texts = [train_sent_texts[train_sent[e]] for e in next_batch]
|
||||
|
||||
self.update(entities=next_batch, golds=golds, descs=descs, art_texts=article_texts, sent_texts=sent_texts)
|
||||
|
||||
processed += len(next_batch)
|
||||
self.update(entity_clusters=next_batch, golds=train_gold, descs=train_desc,
|
||||
art_texts=train_art_texts, arts=train_art,
|
||||
sent_texts=train_sent_texts, sents=train_sent)
|
||||
|
||||
start = start + self.BATCH_SIZE
|
||||
stop = min(stop + self.BATCH_SIZE, len(train_ent))
|
||||
stop = min(stop + self.BATCH_SIZE, len(train_clusters))
|
||||
|
||||
if self.PRINT_TRAIN:
|
||||
print()
|
||||
self._test_dev(train_ent, train_gold, train_desc, train_art, train_art_texts, train_sent, train_sent_texts,
|
||||
print_string="train_inter_epoch " + str(i), avg=True)
|
||||
print_string="train_inter_epoch " + str(i), avg=True)
|
||||
|
||||
self._test_dev(dev_ent, dev_gold, dev_desc, dev_art, dev_art_texts, dev_sent, dev_sent_texts,
|
||||
print_string="dev_inter_epoch " + str(i), avg=True)
|
||||
|
||||
if to_print:
|
||||
print()
|
||||
print("Trained on", processed, "entities across", self.EPOCHS, "epochs")
|
||||
print("Trained on", processed, "entity clusters across", self.EPOCHS, "epochs")
|
||||
|
||||
def _test_dev(self, entities, gold_by_entity, desc_by_entity, art_by_entity, art_texts, sent_by_entity, sent_texts,
|
||||
def _test_dev(self, entity_clusters, golds, descs, arts, art_texts, sents, sent_texts,
|
||||
print_string, avg=True, calc_random=False):
|
||||
golds = [gold_by_entity[e] for e in entities]
|
||||
|
||||
if calc_random:
|
||||
predictions = self._predict_random(entities=entities)
|
||||
correct = 0
|
||||
incorrect = 0
|
||||
|
||||
else:
|
||||
desc_docs = self.nlp.pipe([desc_by_entity[e] for e in entities])
|
||||
article_docs = self.nlp.pipe([art_texts[art_by_entity[e]] for e in entities])
|
||||
sent_docs = self.nlp.pipe([sent_texts[sent_by_entity[e]] for e in entities])
|
||||
predictions = self._predict(entities=entities, article_docs=article_docs, sent_docs=sent_docs,
|
||||
desc_docs=desc_docs, avg=avg)
|
||||
for cluster, entities in entity_clusters.items():
|
||||
correct_entities = [e for e in entities if golds[e]]
|
||||
incorrect_entities = [e for e in entities if not golds[e]]
|
||||
assert len(correct_entities) == 1
|
||||
|
||||
# TODO: combine with prior probability
|
||||
p, r, f, acc = run_el.evaluate(predictions, golds, to_print=False, times_hundred=False)
|
||||
loss, gradient = self.get_loss(self.model.ops.asarray(predictions), self.model.ops.asarray(golds))
|
||||
entities = list(entities)
|
||||
shuffle(entities)
|
||||
|
||||
print("p/r/F/acc/loss", print_string, round(p, 2), round(r, 2), round(f, 2), round(acc, 2), round(loss, 2))
|
||||
if calc_random:
|
||||
predicted_entity = random.choice(entities)
|
||||
if predicted_entity in correct_entities:
|
||||
correct += 1
|
||||
else:
|
||||
incorrect += 1
|
||||
|
||||
return loss, p, r, f
|
||||
else:
|
||||
desc_docs = self.nlp.pipe([descs[e] for e in entities])
|
||||
# article_texts = [art_texts[arts[e]] for e in entities]
|
||||
|
||||
def _predict(self, entities, article_docs, sent_docs, desc_docs, avg=True, apply_threshold=True):
|
||||
sent_doc = self.nlp(sent_texts[sents[cluster]])
|
||||
article_doc = self.nlp(art_texts[arts[cluster]])
|
||||
|
||||
predicted_index = self._predict(article_doc=article_doc, sent_doc=sent_doc,
|
||||
desc_docs=desc_docs, avg=avg)
|
||||
if entities[predicted_index] in correct_entities:
|
||||
correct += 1
|
||||
else:
|
||||
incorrect += 1
|
||||
|
||||
if correct == incorrect == 0:
|
||||
print("acc", print_string, "NA")
|
||||
return 0
|
||||
|
||||
acc = correct / (correct + incorrect)
|
||||
print("acc", print_string, round(acc, 2))
|
||||
return acc
|
||||
|
||||
def _predict(self, article_doc, sent_doc, desc_docs, avg=True, apply_threshold=True):
|
||||
if avg:
|
||||
with self.article_encoder.use_params(self.sgd_article.averages) \
|
||||
and self.desc_encoder.use_params(self.sgd_desc.averages):
|
||||
doc_encodings = self.article_encoder(article_docs)
|
||||
and self.desc_encoder.use_params(self.sgd_desc.averages)\
|
||||
and self.sent_encoder.use_params(self.sgd_sent.averages):
|
||||
# doc_encoding = self.article_encoder(article_doc)
|
||||
desc_encodings = self.desc_encoder(desc_docs)
|
||||
sent_encodings = self.sent_encoder(sent_docs)
|
||||
sent_encoding = self.sent_encoder([sent_doc])
|
||||
|
||||
else:
|
||||
doc_encodings = self.article_encoder(article_docs)
|
||||
# doc_encodings = self.article_encoder(article_docs)
|
||||
desc_encodings = self.desc_encoder(desc_docs)
|
||||
sent_encodings = self.sent_encoder(sent_docs)
|
||||
sent_encoding = self.sent_encoder([sent_doc])
|
||||
|
||||
concat_encodings = [list(doc_encodings[i]) + list(sent_encodings[i]) + list(desc_encodings[i]) for i in
|
||||
range(len(entities))]
|
||||
sent_enc = np.transpose(sent_encoding)
|
||||
highest_sim = -5
|
||||
best_i = -1
|
||||
for i, desc_enc in enumerate(desc_encodings):
|
||||
sim = cosine(desc_enc, sent_enc)
|
||||
if sim >= highest_sim:
|
||||
best_i = i
|
||||
highest_sim = sim
|
||||
|
||||
np_array_list = np.asarray(concat_encodings)
|
||||
|
||||
if avg:
|
||||
with self.model.use_params(self.sgd.averages):
|
||||
predictions = self.model(np_array_list)
|
||||
else:
|
||||
predictions = self.model(np_array_list)
|
||||
|
||||
predictions = self.model.ops.flatten(predictions)
|
||||
predictions = [float(p) for p in predictions]
|
||||
if apply_threshold:
|
||||
predictions = [float(1.0) if p > self.CUTOFF else float(0.0) for p in predictions]
|
||||
|
||||
return predictions
|
||||
return best_i
|
||||
|
||||
def _predict_random(self, entities, apply_threshold=True):
|
||||
if not apply_threshold:
|
||||
|
|
@ -233,47 +249,23 @@ class EL_Model:
|
|||
else:
|
||||
return [float(1.0) if random.uniform(0, 1) > self.CUTOFF else float(0.0) for _ in entities]
|
||||
|
||||
def _build_cnn_depr(self, embed_width, desc_width, article_width, sent_width, hidden_1_width, hidden_2_width):
|
||||
def _build_cnn(self, embed_width, desc_width, article_width, sent_width, hidden_1_width):
|
||||
with Model.define_operators({">>": chain, "|": concatenate, "**": clone}):
|
||||
self.desc_encoder = self._encoder_depr(in_width=embed_width, hidden_with=hidden_1_width, end_width=desc_width)
|
||||
self.article_encoder = self._encoder_depr(in_width=embed_width, hidden_with=hidden_1_width, end_width=article_width)
|
||||
self.sent_encoder = self._encoder_depr(in_width=embed_width, hidden_with=hidden_1_width, end_width=sent_width)
|
||||
self.desc_encoder = self._encoder(in_width=embed_width, hidden_with=hidden_1_width,
|
||||
end_width=desc_width)
|
||||
self.article_encoder = self._encoder(in_width=embed_width, hidden_with=hidden_1_width,
|
||||
end_width=article_width)
|
||||
self.sent_encoder = self._encoder(in_width=embed_width, hidden_with=hidden_1_width,
|
||||
end_width=sent_width)
|
||||
|
||||
in_width = article_width + sent_width + desc_width
|
||||
out_width = hidden_2_width
|
||||
|
||||
self.model = Affine(out_width, in_width) \
|
||||
>> LN(Maxout(out_width, out_width)) \
|
||||
>> Affine(1, out_width) \
|
||||
>> logistic
|
||||
|
||||
def _build_cnn(self, desc_width, article_width, sent_width):
|
||||
with Model.define_operators({">>": chain, "|": concatenate, "**": clone}):
|
||||
self.desc_encoder = self._encoder(width=desc_width)
|
||||
self.article_encoder = self._encoder(width=article_width)
|
||||
self.sent_encoder = self._encoder(width=sent_width)
|
||||
|
||||
in_width = desc_width + article_width + sent_width
|
||||
|
||||
self.model = Affine(self.HIDDEN_2_WIDTH, in_width) \
|
||||
>> LN(Maxout(self.HIDDEN_2_WIDTH, self.HIDDEN_2_WIDTH)) \
|
||||
>> Affine(1, self.HIDDEN_2_WIDTH) \
|
||||
>> logistic
|
||||
|
||||
# output_layer = (
|
||||
# zero_init(Affine(1, in_width, drop_factor=0.0)) >> logistic
|
||||
# )
|
||||
# self.model = output_layer
|
||||
self.model.nO = 1
|
||||
|
||||
def _encoder(self, width):
|
||||
tok2vec = Tok2Vec(width=width, embed_size=2000, pretrained_vectors=self.nlp.vocab.vectors.name, cnn_maxout_pieces=3,
|
||||
subword_features=False, conv_depth=4, bilstm_depth=0)
|
||||
|
||||
return tok2vec >> flatten_add_lengths >> Pooling(mean_pool)
|
||||
# def _encoder(self, width):
|
||||
# tok2vec = Tok2Vec(width=width, embed_size=2000, pretrained_vectors=self.nlp.vocab.vectors.name, cnn_maxout_pieces=3,
|
||||
# subword_features=False, conv_depth=4, bilstm_depth=0)
|
||||
#
|
||||
# return tok2vec >> flatten_add_lengths >> Pooling(mean_pool)
|
||||
|
||||
@staticmethod
|
||||
def _encoder_depr(in_width, hidden_with, end_width):
|
||||
def _encoder(in_width, hidden_with, end_width):
|
||||
conv_depth = 2
|
||||
cnn_maxout_pieces = 3
|
||||
|
||||
|
|
@ -307,64 +299,58 @@ class EL_Model:
|
|||
self.sgd_desc.learn_rate = self.LEARN_RATE
|
||||
self.sgd_desc.L2 = self.L2
|
||||
|
||||
self.sgd = create_default_optimizer(self.model.ops)
|
||||
self.sgd.learn_rate = self.LEARN_RATE
|
||||
self.sgd.L2 = self.L2
|
||||
# self.sgd = create_default_optimizer(self.model.ops)
|
||||
# self.sgd.learn_rate = self.LEARN_RATE
|
||||
# self.sgd.L2 = self.L2
|
||||
|
||||
@staticmethod
|
||||
def get_loss(predictions, golds):
|
||||
d_scores = (predictions - golds)
|
||||
gradient = d_scores.mean()
|
||||
loss = (d_scores ** 2).mean()
|
||||
return loss, gradient
|
||||
loss, gradients = get_cossim_loss(predictions, golds)
|
||||
return loss, gradients
|
||||
|
||||
def update(self, entities, golds, descs, art_texts, sent_texts):
|
||||
golds = self.model.ops.asarray(golds)
|
||||
def update(self, entity_clusters, golds, descs, art_texts, arts, sent_texts, sents):
|
||||
for cluster, entities in entity_clusters.items():
|
||||
correct_entities = [e for e in entities if golds[e]]
|
||||
incorrect_entities = [e for e in entities if not golds[e]]
|
||||
|
||||
art_docs = self.nlp.pipe(art_texts)
|
||||
sent_docs = self.nlp.pipe(sent_texts)
|
||||
desc_docs = self.nlp.pipe(descs)
|
||||
assert len(correct_entities) == 1
|
||||
entities = list(entities)
|
||||
shuffle(entities)
|
||||
|
||||
doc_encodings, bp_doc = self.article_encoder.begin_update(art_docs, drop=self.DROP)
|
||||
sent_encodings, bp_sent = self.sent_encoder.begin_update(sent_docs, drop=self.DROP)
|
||||
desc_encodings, bp_desc = self.desc_encoder.begin_update(desc_docs, drop=self.DROP)
|
||||
# article_text = art_texts[arts[cluster]]
|
||||
cluster_sent = sent_texts[sents[cluster]]
|
||||
|
||||
concat_encodings = [list(doc_encodings[i]) + list(sent_encodings[i]) + list(desc_encodings[i])
|
||||
for i in range(len(entities))]
|
||||
# art_docs = self.nlp.pipe(article_text)
|
||||
sent_doc = self.nlp(cluster_sent)
|
||||
|
||||
predictions, bp_model = self.model.begin_update(np.asarray(concat_encodings), drop=self.DROP)
|
||||
predictions = self.model.ops.flatten(predictions)
|
||||
for e in entities:
|
||||
if golds[e]:
|
||||
# TODO: more appropriate loss for the whole cluster (currently only pos entities)
|
||||
# TODO: speed up
|
||||
desc_doc = self.nlp(descs[e])
|
||||
|
||||
# print("entities", entities)
|
||||
# print("predictions", predictions)
|
||||
# print("golds", golds)
|
||||
# doc_encodings, bp_doc = self.article_encoder.begin_update(art_docs, drop=self.DROP)
|
||||
sent_encodings, bp_sent = self.sent_encoder.begin_update([sent_doc], drop=self.DROP)
|
||||
desc_encodings, bp_desc = self.desc_encoder.begin_update([desc_doc], drop=self.DROP)
|
||||
|
||||
loss, gradient = self.get_loss(predictions, golds)
|
||||
sent_encoding = sent_encodings[0]
|
||||
desc_encoding = desc_encodings[0]
|
||||
|
||||
gradient = float(gradient)
|
||||
# print("gradient", gradient)
|
||||
# print("loss", loss)
|
||||
sent_enc = self.sent_encoder.ops.asarray([sent_encoding])
|
||||
desc_enc = self.sent_encoder.ops.asarray([desc_encoding])
|
||||
|
||||
model_gradient = bp_model(gradient, sgd=self.sgd)
|
||||
# print("model_gradient", model_gradient)
|
||||
# print("sent_encoding", type(sent_encoding), sent_encoding)
|
||||
# print("desc_encoding", type(desc_encoding), desc_encoding)
|
||||
# print("getting los for entity", e)
|
||||
|
||||
# concat = doc + sent + desc, but doc is the same within this function
|
||||
sent_start = self.ARTICLE_WIDTH
|
||||
desc_start = self.ARTICLE_WIDTH + self.SENT_WIDTH
|
||||
doc_gradient = model_gradient[0][0:sent_start]
|
||||
sent_gradients = list()
|
||||
desc_gradients = list()
|
||||
for x in model_gradient:
|
||||
sent_gradients.append(list(x[sent_start:desc_start]))
|
||||
desc_gradients.append(list(x[desc_start:]))
|
||||
loss, gradient = self.get_loss(sent_enc, desc_enc)
|
||||
|
||||
# print("doc_gradient", doc_gradient)
|
||||
# print("sent_gradients", sent_gradients)
|
||||
# print("desc_gradients", desc_gradients)
|
||||
# print("gradient", gradient)
|
||||
# print("loss", loss)
|
||||
|
||||
bp_doc([doc_gradient], sgd=self.sgd_article)
|
||||
bp_sent(sent_gradients, sgd=self.sgd_sent)
|
||||
bp_desc(desc_gradients, sgd=self.sgd_desc)
|
||||
bp_sent(gradient, sgd=self.sgd_sent)
|
||||
# bp_desc(desc_gradients, sgd=self.sgd_desc) TODO
|
||||
# print()
|
||||
|
||||
def _get_training_data(self, training_dir, entity_descr_output, dev, limit, to_print):
|
||||
id_to_descr = kb_creator._get_id_to_description(entity_descr_output)
|
||||
|
|
@ -373,13 +359,14 @@ class EL_Model:
|
|||
collect_correct=True,
|
||||
collect_incorrect=True)
|
||||
|
||||
entities = set()
|
||||
entities_by_cluster = dict()
|
||||
gold_by_entity = dict()
|
||||
desc_by_entity = dict()
|
||||
article_by_entity = dict()
|
||||
article_by_cluster = dict()
|
||||
text_by_article = dict()
|
||||
sentence_by_entity = dict()
|
||||
sentence_by_cluster = dict()
|
||||
text_by_sentence = dict()
|
||||
sentence_by_text = dict()
|
||||
|
||||
cnt = 0
|
||||
next_entity_nr = 1
|
||||
|
|
@ -402,74 +389,69 @@ class EL_Model:
|
|||
text_by_article[article_id] = truncated_text
|
||||
|
||||
# process all positive and negative entities, collect all relevant mentions in this article
|
||||
article_terms = set()
|
||||
entities_by_mention = dict()
|
||||
|
||||
for mention, entity_pos in correct_entries[article_id].items():
|
||||
cluster = article_id + "_" + mention
|
||||
descr = id_to_descr.get(entity_pos)
|
||||
entities = set()
|
||||
if descr:
|
||||
entity = "E_" + str(next_entity_nr) + "_" + article_id + "_" + mention
|
||||
entity = "E_" + str(next_entity_nr) + "_" + cluster
|
||||
next_entity_nr += 1
|
||||
gold_by_entity[entity] = 1
|
||||
desc_by_entity[entity] = descr
|
||||
article_terms.add(mention)
|
||||
mention_entities = entities_by_mention.get(mention, set())
|
||||
mention_entities.add(entity)
|
||||
entities_by_mention[mention] = mention_entities
|
||||
|
||||
for mention, entity_negs in incorrect_entries[article_id].items():
|
||||
for entity_neg in entity_negs:
|
||||
descr = id_to_descr.get(entity_neg)
|
||||
if descr:
|
||||
entity = "E_" + str(next_entity_nr) + "_" + article_id + "_" + mention
|
||||
next_entity_nr += 1
|
||||
gold_by_entity[entity] = 0
|
||||
desc_by_entity[entity] = descr
|
||||
article_terms.add(mention)
|
||||
mention_entities = entities_by_mention.get(mention, set())
|
||||
mention_entities.add(entity)
|
||||
entities_by_mention[mention] = mention_entities
|
||||
|
||||
# find all matches in the doc for the mentions
|
||||
# TODO: fix this - doesn't look like all entities are found
|
||||
matcher = PhraseMatcher(self.nlp.vocab)
|
||||
patterns = list(self.nlp.tokenizer.pipe(article_terms))
|
||||
|
||||
matcher.add("TerminologyList", None, *patterns)
|
||||
matches = matcher(article_doc)
|
||||
|
||||
# store sentences
|
||||
sentence_to_id = dict()
|
||||
for match_id, start, end in matches:
|
||||
span = article_doc[start:end]
|
||||
sent_text = span.sent.text
|
||||
sent_nr = sentence_to_id.get(sent_text, None)
|
||||
mention = span.text
|
||||
if sent_nr is None:
|
||||
sent_nr = "S_" + str(next_sent_nr) + article_id
|
||||
next_sent_nr += 1
|
||||
text_by_sentence[sent_nr] = sent_text
|
||||
sentence_to_id[sent_text] = sent_nr
|
||||
mention_entities = entities_by_mention[mention]
|
||||
for entity in mention_entities:
|
||||
entities.add(entity)
|
||||
sentence_by_entity[entity] = sent_nr
|
||||
article_by_entity[entity] = article_id
|
||||
|
||||
# remove entities that didn't have all data
|
||||
gold_by_entity = {k: v for k, v in gold_by_entity.items() if k in entities}
|
||||
desc_by_entity = {k: v for k, v in desc_by_entity.items() if k in entities}
|
||||
entity_negs = incorrect_entries[article_id][mention]
|
||||
for entity_neg in entity_negs:
|
||||
descr = id_to_descr.get(entity_neg)
|
||||
if descr:
|
||||
entity = "E_" + str(next_entity_nr) + "_" + cluster
|
||||
next_entity_nr += 1
|
||||
gold_by_entity[entity] = 0
|
||||
desc_by_entity[entity] = descr
|
||||
entities.add(entity)
|
||||
|
||||
article_by_entity = {k: v for k, v in article_by_entity.items() if k in entities}
|
||||
text_by_article = {k: v for k, v in text_by_article.items() if k in article_by_entity.values()}
|
||||
found_matches = 0
|
||||
if len(entities) > 1:
|
||||
entities_by_cluster[cluster] = entities
|
||||
|
||||
# find all matches in the doc for the mentions
|
||||
# TODO: fix this - doesn't look like all entities are found
|
||||
matcher = PhraseMatcher(self.nlp.vocab)
|
||||
patterns = list(self.nlp.tokenizer.pipe([mention]))
|
||||
|
||||
matcher.add("TerminologyList", None, *patterns)
|
||||
matches = matcher(article_doc)
|
||||
|
||||
|
||||
# store sentences
|
||||
for match_id, start, end in matches:
|
||||
found_matches += 1
|
||||
span = article_doc[start:end]
|
||||
assert mention == span.text
|
||||
sent_text = span.sent.text
|
||||
sent_nr = sentence_by_text.get(sent_text, None)
|
||||
if sent_nr is None:
|
||||
sent_nr = "S_" + str(next_sent_nr) + article_id
|
||||
next_sent_nr += 1
|
||||
text_by_sentence[sent_nr] = sent_text
|
||||
sentence_by_text[sent_text] = sent_nr
|
||||
article_by_cluster[cluster] = article_id
|
||||
sentence_by_cluster[cluster] = sent_nr
|
||||
|
||||
if found_matches == 0:
|
||||
# TODO print("Could not find neg instances or sentence matches for", mention, "in", article_id)
|
||||
entities_by_cluster.pop(cluster, None)
|
||||
article_by_cluster.pop(cluster, None)
|
||||
sentence_by_cluster.pop(cluster, None)
|
||||
for entity in entities:
|
||||
gold_by_entity.pop(entity, None)
|
||||
desc_by_entity.pop(entity, None)
|
||||
|
||||
sentence_by_entity = {k: v for k, v in sentence_by_entity.items() if k in entities}
|
||||
text_by_sentence = {k: v for k, v in text_by_sentence.items() if k in sentence_by_entity.values()}
|
||||
|
||||
if to_print:
|
||||
print()
|
||||
print("Processed", cnt, "training articles, dev=" + str(dev))
|
||||
print()
|
||||
return list(entities), gold_by_entity, desc_by_entity, article_by_entity, text_by_article, \
|
||||
sentence_by_entity, text_by_sentence
|
||||
return entities_by_cluster, gold_by_entity, desc_by_entity, article_by_cluster, text_by_article, \
|
||||
sentence_by_cluster, text_by_sentence
|
||||
|
||||
|
|
|
|||
|
|
@ -111,7 +111,7 @@ if __name__ == "__main__":
|
|||
print("STEP 6: training", datetime.datetime.now())
|
||||
my_nlp = spacy.load('en_core_web_md')
|
||||
trainer = EL_Model(kb=my_kb, nlp=my_nlp)
|
||||
trainer.train_model(training_dir=TRAINING_DIR, entity_descr_output=ENTITY_DESCR, trainlimit=100, devlimit=20)
|
||||
trainer.train_model(training_dir=TRAINING_DIR, entity_descr_output=ENTITY_DESCR, trainlimit=1000, devlimit=100)
|
||||
print()
|
||||
|
||||
# STEP 7: apply the EL algorithm on the dev dataset
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user