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using entity descriptions and article texts as input embedding vectors for training

This commit is contained in:
svlandeg 2019-05-07 16:03:42 +02:00
parent 7e348d7f7f
commit 9f33732b96
6 changed files with 147 additions and 108 deletions
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50
examples/pipeline/wiki_entity_linking/kb_creator.py
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@ -4,13 +4,16 @@ from __future__ import unicode_literals
import spacy
from spacy.kb import KnowledgeBase
import csv
import datetime
from . import wikipedia_processor as wp
from . import wikidata_processor as wd
def create_kb(vocab, max_entities_per_alias, min_occ, entity_output, count_input, prior_prob_input,
def create_kb(vocab, max_entities_per_alias, min_occ,
entity_def_output, entity_descr_output,
count_input, prior_prob_input,
to_print=False, write_entity_defs=True):
""" Create the knowledge base from Wikidata entries """
kb = KnowledgeBase(vocab=vocab)
@ -18,15 +21,11 @@ def create_kb(vocab, max_entities_per_alias, min_occ, entity_output, count_input
print()
print("1. _read_wikidata_entities", datetime.datetime.now())
print()
# title_to_id = _read_wikidata_entities_regex_depr(limit=1000)
title_to_id = wd.read_wikidata_entities_json(limit=None)
title_to_id, id_to_descr = wd.read_wikidata_entities_json(limit=None)
# write the title-ID mapping to file
# write the title-ID and ID-description mappings to file
if write_entity_defs:
with open(entity_output, mode='w', encoding='utf8') as entity_file:
entity_file.write("WP_title" + "|" + "WD_id" + "\n")
for title, qid in title_to_id.items():
entity_file.write(title + "|" + str(qid) + "\n")
_write_entity_files(entity_def_output, entity_descr_output, title_to_id, id_to_descr)
title_list = list(title_to_id.keys())
entity_list = [title_to_id[x] for x in title_list]
@ -57,6 +56,41 @@ def create_kb(vocab, max_entities_per_alias, min_occ, entity_output, count_input
return kb
def _write_entity_files(entity_def_output, entity_descr_output, title_to_id, id_to_descr):
with open(entity_def_output, mode='w', encoding='utf8') as id_file:
id_file.write("WP_title" + "|" + "WD_id" + "\n")
for title, qid in title_to_id.items():
id_file.write(title + "|" + str(qid) + "\n")
with open(entity_descr_output, mode='w', encoding='utf8') as descr_file:
descr_file.write("WD_id" + "|" + "description" + "\n")
for qid, descr in id_to_descr.items():
descr_file.write(str(qid) + "|" + descr + "\n")
def _get_entity_to_id(entity_def_output):
entity_to_id = dict()
with open(entity_def_output, 'r', encoding='utf8') as csvfile:
csvreader = csv.reader(csvfile, delimiter='|')
# skip header
next(csvreader)
for row in csvreader:
entity_to_id[row[0]] = row[1]
return entity_to_id
def _get_id_to_description(entity_descr_output):
id_to_desc = dict()
with open(entity_descr_output, 'r', encoding='utf8') as csvfile:
csvreader = csv.reader(csvfile, delimiter='|')
# skip header
next(csvreader)
for row in csvreader:
id_to_desc[row[0]] = row[1]
return id_to_desc
def _add_aliases(kb, title_to_id, max_entities_per_alias, min_occ, prior_prob_input, to_print=False):
wp_titles = title_to_id.keys()

4
examples/pipeline/wiki_entity_linking/run_el.py
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@ -32,7 +32,7 @@ def run_el_toy_example(nlp, kb):
print("ent", ent.text, ent.label_, ent.kb_id_)
def run_el_training(nlp, kb, training_dir, limit=None):
def run_el_dev(nlp, kb, training_dir, limit=None):
_prepare_pipeline(nlp, kb)
correct_entries_per_article, _ = training_set_creator.read_training_entities(training_output=training_dir,
@ -48,7 +48,7 @@ def run_el_training(nlp, kb, training_dir, limit=None):
if is_dev(f):
article_id = f.replace(".txt", "")
if cnt % 500 == 0:
print(datetime.datetime.now(), "processed", cnt, "files in the training dataset")
print(datetime.datetime.now(), "processed", cnt, "files in the dev dataset")
cnt += 1
with open(os.path.join(training_dir, f), mode="r", encoding='utf8') as file:
text = file.read()

58
examples/pipeline/wiki_entity_linking/train_el.py Normal file
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@ -0,0 +1,58 @@
# coding: utf-8
from __future__ import unicode_literals
import os
import datetime
from os import listdir
from examples.pipeline.wiki_entity_linking import run_el, training_set_creator, kb_creator
from examples.pipeline.wiki_entity_linking import wikidata_processor as wd
""" TODO: this code needs to be implemented in pipes.pyx"""
def train_model(kb, nlp, training_dir, entity_descr_output, limit=None):
run_el._prepare_pipeline(nlp, kb)
correct_entries, incorrect_entries = training_set_creator.read_training_entities(training_output=training_dir,
collect_correct=True,
collect_incorrect=True)
entities = kb.get_entity_strings()
id_to_descr = kb_creator._get_id_to_description(entity_descr_output)
cnt = 0
for f in listdir(training_dir):
if not limit or cnt < limit:
if not run_el.is_dev(f):
article_id = f.replace(".txt", "")
if cnt % 500 == 0:
print(datetime.datetime.now(), "processed", cnt, "files in the dev dataset")
cnt += 1
with open(os.path.join(training_dir, f), mode="r", encoding='utf8') as file:
text = file.read()
print()
doc = nlp(text)
doc_vector = doc.vector
print("FILE", f, len(doc_vector), "D vector")
for mention_pos, entity_pos in correct_entries[article_id].items():
descr = id_to_descr.get(entity_pos)
if descr:
doc_descr = nlp(descr)
descr_vector = doc_descr.vector
print("GOLD POS", mention_pos, entity_pos, len(descr_vector), "D vector")
for mention_neg, entity_negs in incorrect_entries[article_id].items():
for entity_neg in entity_negs:
descr = id_to_descr.get(entity_neg)
if descr:
doc_descr = nlp(descr)
descr_vector = doc_descr.vector
print("GOLD NEG", mention_neg, entity_neg, len(descr_vector), "D vector")
print()
print("Processed", cnt, "dev articles")
print()

19
examples/pipeline/wiki_entity_linking/training_set_creator.py
View File

@ -6,7 +6,7 @@ import csv
import bz2
import datetime
from . import wikipedia_processor as wp
from . import wikipedia_processor as wp, kb_creator
"""
Process Wikipedia interlinks to generate a training dataset for the EL algorithm
@ -14,26 +14,15 @@ Process Wikipedia interlinks to generate a training dataset for the EL algorithm
ENTITY_FILE = "gold_entities.csv"
def create_training(kb, entity_input, training_output):
def create_training(kb, entity_def_input, training_output):
if not kb:
raise ValueError("kb should be defined")
# nlp = spacy.load('en_core_web_sm')
wp_to_id = _get_entity_to_id(entity_input)
wp_to_id = kb_creator._get_entity_to_id(entity_def_input)
_process_wikipedia_texts(kb, wp_to_id, training_output, limit=100000000) # TODO: full dataset
def _get_entity_to_id(entity_input):
entity_to_id = dict()
with open(entity_input, 'r', encoding='utf8') as csvfile:
csvreader = csv.reader(csvfile, delimiter='|')
# skip header
next(csvreader)
for row in csvreader:
entity_to_id[row[0]] = row[1]
return entity_to_id
def _process_wikipedia_texts(kb, wp_to_id, training_output, limit=None):
"""
Read the XML wikipedia data to parse out training data:

34
examples/pipeline/wiki_entity_linking/wiki_nel_pipeline.py
View File

@ -1,7 +1,7 @@
# coding: utf-8
from __future__ import unicode_literals
from examples.pipeline.wiki_entity_linking import wikipedia_processor as wp, kb_creator, training_set_creator, run_el
from examples.pipeline.wiki_entity_linking import wikipedia_processor as wp, kb_creator, training_set_creator, run_el, train_el
import spacy
from spacy.vocab import Vocab
@ -15,11 +15,12 @@ Demonstrate how to build a knowledge base from WikiData and run an Entity Linkin
PRIOR_PROB = 'C:/Users/Sofie/Documents/data/wikipedia/prior_prob.csv'
ENTITY_COUNTS = 'C:/Users/Sofie/Documents/data/wikipedia/entity_freq.csv'
ENTITY_DEFS = 'C:/Users/Sofie/Documents/data/wikipedia/entity_defs.csv'
ENTITY_DESCR = 'C:/Users/Sofie/Documents/data/wikipedia/entity_descriptions.csv'
KB_FILE = 'C:/Users/Sofie/Documents/data/wikipedia/kb'
VOCAB_DIR = 'C:/Users/Sofie/Documents/data/wikipedia/vocab'
TRAINING_DIR = 'C:/Users/Sofie/Documents/data/wikipedia/training_nel/'
TRAINING_DIR = 'C:/Users/Sofie/Documents/data/wikipedia/training_data_nel/'
if __name__ == "__main__":
@ -30,17 +31,20 @@ if __name__ == "__main__":
# one-time methods to create KB and write to file
to_create_prior_probs = False
to_create_entity_counts = False
to_create_kb = False
to_create_kb = True
# read KB back in from file
to_read_kb = True
to_test_kb = False
to_test_kb = True
# create training dataset
create_wp_training = False
# apply named entity linking to the training dataset
apply_to_training = True
# run training
run_training = False
# apply named entity linking to the dev dataset
apply_to_dev = False
# STEP 1 : create prior probabilities from WP
# run only once !
@ -65,7 +69,8 @@ if __name__ == "__main__":
my_kb = kb_creator.create_kb(my_vocab,
max_entities_per_alias=10,
min_occ=5,
entity_output=ENTITY_DEFS,
entity_def_output=ENTITY_DEFS,
entity_descr_output=ENTITY_DESCR,
count_input=ENTITY_COUNTS,
prior_prob_input=PRIOR_PROB,
to_print=False)
@ -98,12 +103,19 @@ if __name__ == "__main__":
# STEP 5: create a training dataset from WP
if create_wp_training:
print("STEP 5: create training dataset", datetime.datetime.now())
training_set_creator.create_training(kb=my_kb, entity_input=ENTITY_DEFS, training_output=TRAINING_DIR)
training_set_creator.create_training(kb=my_kb, entity_def_input=ENTITY_DEFS, training_output=TRAINING_DIR)
# STEP 6: apply the EL algorithm on the training dataset
if apply_to_training:
# STEP 7: apply the EL algorithm on the training dataset
if run_training:
print("STEP 6: training ", datetime.datetime.now())
my_nlp = spacy.load('en_core_web_sm')
run_el.run_el_training(kb=my_kb, nlp=my_nlp, training_dir=TRAINING_DIR, limit=1000)
train_el.train_model(kb=my_kb, nlp=my_nlp, training_dir=TRAINING_DIR, entity_descr_output=ENTITY_DESCR, limit=5)
print()
# STEP 8: apply the EL algorithm on the dev dataset
if apply_to_dev:
my_nlp = spacy.load('en_core_web_sm')
run_el.run_el_dev(kb=my_kb, nlp=my_nlp, training_dir=TRAINING_DIR, limit=2000)
print()

64
examples/pipeline/wiki_entity_linking/wikidata_processor.py
View File

@ -13,17 +13,18 @@ WIKIDATA_JSON = 'C:/Users/Sofie/Documents/data/wikidata/wikidata-20190304-all.js
def read_wikidata_entities_json(limit=None, to_print=False):
""" Read the JSON wiki data and parse out the entities. Takes about 7u30 to parse 55M lines. """
languages = {'en', 'de'}
lang = 'en'
prop_filter = {'P31': {'Q5', 'Q15632617'}} # currently defined as OR: one property suffices to be selected
site_filter = 'enwiki'
title_to_id = dict()
id_to_descr = dict()
# parse appropriate fields - depending on what we need in the KB
parse_properties = False
parse_sitelinks = True
parse_labels = False
parse_descriptions = False
parse_descriptions = True
parse_aliases = False
with bz2.open(WIKIDATA_JSON, mode='rb') as file:
@ -76,12 +77,10 @@ def read_wikidata_entities_json(limit=None, to_print=False):
if to_print:
print(site_filter, ":", site)
title_to_id[site] = unique_id
# print(site, "for", unique_id)
if parse_labels:
labels = obj["labels"]
if labels:
for lang in languages:
lang_label = labels.get(lang, None)
if lang_label:
if to_print:
@ -90,16 +89,15 @@ def read_wikidata_entities_json(limit=None, to_print=False):
if parse_descriptions:
descriptions = obj["descriptions"]
if descriptions:
for lang in languages:
lang_descr = descriptions.get(lang, None)
if lang_descr:
if to_print:
print("description (" + lang + "):", lang_descr["value"])
id_to_descr[unique_id] = lang_descr["value"]
if parse_aliases:
aliases = obj["aliases"]
if aliases:
for lang in languages:
lang_aliases = aliases.get(lang, None)
if lang_aliases:
for item in lang_aliases:
@ -111,56 +109,4 @@ def read_wikidata_entities_json(limit=None, to_print=False):
line = file.readline()
cnt += 1
return title_to_id
def _read_wikidata_entities_regex_depr(limit=None):
"""
Read the JSON wiki data and parse out the entities with regular expressions. Takes XXX to parse 55M lines.
TODO: doesn't work yet. may be deleted ?
"""
regex_p31 = re.compile(r'mainsnak[^}]*\"P31\"[^}]*}', re.UNICODE)
regex_id = re.compile(r'\"id\":"Q[0-9]*"', re.UNICODE)
regex_enwiki = re.compile(r'\"enwiki\":[^}]*}', re.UNICODE)
regex_title = re.compile(r'\"title\":"[^"]*"', re.UNICODE)
title_to_id = dict()
with bz2.open(WIKIDATA_JSON, mode='rb') as file:
line = file.readline()
cnt = 0
while line and (not limit or cnt < limit):
if cnt % 500000 == 0:
print(datetime.datetime.now(), "processed", cnt, "lines of WikiData dump")
clean_line = line.strip()
if clean_line.endswith(b","):
clean_line = clean_line[:-1]
if len(clean_line) > 1:
clean_line = line.strip().decode("utf-8")
keep = False
p31_matches = regex_p31.findall(clean_line)
if p31_matches:
for p31_match in p31_matches:
id_matches = regex_id.findall(p31_match)
for id_match in id_matches:
id_match = id_match[6:][:-1]
if id_match == "Q5" or id_match == "Q15632617":
keep = True
if keep:
id_match = regex_id.search(clean_line).group(0)
id_match = id_match[6:][:-1]
enwiki_matches = regex_enwiki.findall(clean_line)
if enwiki_matches:
for enwiki_match in enwiki_matches:
title_match = regex_title.search(enwiki_match).group(0)
title = title_match[9:][:-1]
title_to_id[title] = id_match
line = file.readline()
cnt += 1
return title_to_id
return title_to_id, id_to_descr