spaCy/spacy/tests/pipeline/test_entity_linker.py

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# coding: utf-8
from __future__ import unicode_literals
import pytest
from spacy.kb import KnowledgeBase
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from spacy.lang.en import English
from spacy.pipeline import EntityRuler
from spacy.tokens import Span
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@pytest.fixture
def nlp():
return English()
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def assert_almost_equal(a, b):
delta = 0.0001
assert a - delta <= b <= a + delta
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def test_kb_valid_entities(nlp):
"""Test the valid construction of a KB with 3 entities and two aliases"""
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mykb = KnowledgeBase(nlp.vocab, entity_vector_length=3)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[8, 4, 3])
mykb.add_entity(entity="Q2", freq=5, entity_vector=[2, 1, 0])
mykb.add_entity(entity="Q3", freq=25, entity_vector=[-1, -6, 5])
# adding aliases
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mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.2])
mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
# test the size of the corresponding KB
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assert mykb.get_size_entities() == 3
assert mykb.get_size_aliases() == 2
# test retrieval of the entity vectors
assert mykb.get_vector("Q1") == [8, 4, 3]
assert mykb.get_vector("Q2") == [2, 1, 0]
assert mykb.get_vector("Q3") == [-1, -6, 5]
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# test retrieval of prior probabilities
assert_almost_equal(mykb.get_prior_prob(entity="Q2", alias="douglas"), 0.8)
assert_almost_equal(mykb.get_prior_prob(entity="Q3", alias="douglas"), 0.2)
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assert_almost_equal(mykb.get_prior_prob(entity="Q342", alias="douglas"), 0.0)
assert_almost_equal(mykb.get_prior_prob(entity="Q3", alias="douglassssss"), 0.0)
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def test_kb_invalid_entities(nlp):
"""Test the invalid construction of a KB with an alias linked to a non-existing entity"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
# adding aliases - should fail because one of the given IDs is not valid
with pytest.raises(ValueError):
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mykb.add_alias(
alias="douglas", entities=["Q2", "Q342"], probabilities=[0.8, 0.2]
)
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def test_kb_invalid_probabilities(nlp):
"""Test the invalid construction of a KB with wrong prior probabilities"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
# adding aliases - should fail because the sum of the probabilities exceeds 1
with pytest.raises(ValueError):
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mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.4])
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def test_kb_invalid_combination(nlp):
"""Test the invalid construction of a KB with non-matching entity and probability lists"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
# adding aliases - should fail because the entities and probabilities vectors are not of equal length
with pytest.raises(ValueError):
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mykb.add_alias(
alias="douglas", entities=["Q2", "Q3"], probabilities=[0.3, 0.4, 0.1]
)
def test_kb_invalid_entity_vector(nlp):
"""Test the invalid construction of a KB with non-matching entity vector lengths"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=3)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1, 2, 3])
# this should fail because the kb's expected entity vector length is 3
with pytest.raises(ValueError):
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
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def test_candidate_generation(nlp):
"""Test correct candidate generation"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=27, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=12, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=5, entity_vector=[3])
# adding aliases
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mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.1])
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mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
# test the size of the relevant candidates
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assert len(mykb.get_candidates("douglas")) == 2
assert len(mykb.get_candidates("adam")) == 1
assert len(mykb.get_candidates("shrubbery")) == 0
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# test the content of the candidates
assert mykb.get_candidates("adam")[0].entity_ == "Q2"
assert mykb.get_candidates("adam")[0].alias_ == "adam"
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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assert_almost_equal(mykb.get_candidates("adam")[0].entity_freq, 12)
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assert_almost_equal(mykb.get_candidates("adam")[0].prior_prob, 0.9)
def test_append_alias(nlp):
"""Test that we can append additional alias-entity pairs"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
mykb.add_entity(entity="Q1", freq=27, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=12, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=5, entity_vector=[3])
# adding aliases
mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.4, 0.1])
mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
# test the size of the relevant candidates
assert len(mykb.get_candidates("douglas")) == 2
# append an alias
mykb.append_alias(alias="douglas", entity="Q1", prior_prob=0.2)
# test the size of the relevant candidates has been incremented
assert len(mykb.get_candidates("douglas")) == 3
# append the same alias-entity pair again should not work (will throw a warning)
mykb.append_alias(alias="douglas", entity="Q1", prior_prob=0.3)
# test the size of the relevant candidates remained unchanged
assert len(mykb.get_candidates("douglas")) == 3
def test_append_invalid_alias(nlp):
"""Test that append an alias will throw an error if prior probs are exceeding 1"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
mykb.add_entity(entity="Q1", freq=27, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=12, entity_vector=[2])
mykb.add_entity(entity="Q3", freq=5, entity_vector=[3])
# adding aliases
mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.1])
mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
# append an alias - should fail because the entities and probabilities vectors are not of equal length
with pytest.raises(ValueError):
mykb.append_alias(alias="douglas", entity="Q1", prior_prob=0.2)
def test_preserving_links_asdoc(nlp):
"""Test that Span.as_doc preserves the existing entity links"""
mykb = KnowledgeBase(nlp.vocab, entity_vector_length=1)
# adding entities
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
mykb.add_entity(entity="Q2", freq=8, entity_vector=[1])
# adding aliases
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mykb.add_alias(alias="Boston", entities=["Q1"], probabilities=[0.7])
mykb.add_alias(alias="Denver", entities=["Q2"], probabilities=[0.6])
# set up pipeline with NER (Entity Ruler) and NEL (prior probability only, model not trained)
sentencizer = nlp.create_pipe("sentencizer")
nlp.add_pipe(sentencizer)
ruler = EntityRuler(nlp)
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patterns = [
{"label": "GPE", "pattern": "Boston"},
{"label": "GPE", "pattern": "Denver"},
]
ruler.add_patterns(patterns)
nlp.add_pipe(ruler)
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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el_pipe = nlp.create_pipe(name="entity_linker")
el_pipe.set_kb(mykb)
el_pipe.begin_training()
CLI scripts for entity linking (wikipedia & generic) (#4091) * document token ent_kb_id * document span kb_id * update pipeline documentation * prior and context weights as bool's instead * entitylinker api documentation * drop for both models * finish entitylinker documentation * small fixes * documentation for KB * candidate documentation * links to api pages in code * small fix * frequency examples as counts for consistency * consistent documentation about tensors returned by predict * add entity linking to usage 101 * add entity linking infobox and KB section to 101 * entity-linking in linguistic features * small typo corrections * training example and docs for entity_linker * predefined nlp and kb * revert back to similarity encodings for simplicity (for now) * set prior probabilities to 0 when excluded * code clean up * bugfix: deleting kb ID from tokens when entities were removed * refactor train el example to use either model or vocab * pretrain_kb example for example kb generation * add to training docs for KB + EL example scripts * small fixes * error numbering * ensure the language of vocab and nlp stay consistent across serialization * equality with = * avoid conflict in errors file * add error 151 * final adjustements to the train scripts - consistency * update of goldparse documentation * small corrections * push commit * turn kb_creator into CLI script (wip) * proper parameters for training entity vectors * wikidata pipeline split up into two executable scripts * remove context_width * move wikidata scripts in bin directory, remove old dummy script * refine KB script with logs and preprocessing options * small edits * small improvements to logging of EL CLI script
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el_pipe.incl_context = False
el_pipe.incl_prior = True
nlp.add_pipe(el_pipe, last=True)
# test whether the entity links are preserved by the `as_doc()` function
text = "She lives in Boston. He lives in Denver."
doc = nlp(text)
for ent in doc.ents:
orig_text = ent.text
orig_kb_id = ent.kb_id_
sent_doc = ent.sent.as_doc()
for s_ent in sent_doc.ents:
if s_ent.text == orig_text:
assert s_ent.kb_id_ == orig_kb_id
def test_preserving_links_ents(nlp):
"""Test that doc.ents preserves KB annotations"""
text = "She lives in Boston. He lives in Denver."
doc = nlp(text)
assert len(list(doc.ents)) == 0
boston_ent = Span(doc, 3, 4, label="LOC", kb_id="Q1")
doc.ents = [boston_ent]
assert len(list(doc.ents)) == 1
assert list(doc.ents)[0].label_ == "LOC"
assert list(doc.ents)[0].kb_id_ == "Q1"
def test_preserving_links_ents_2(nlp):
"""Test that doc.ents preserves KB annotations"""
text = "She lives in Boston. He lives in Denver."
doc = nlp(text)
assert len(list(doc.ents)) == 0
loc = doc.vocab.strings.add("LOC")
q1 = doc.vocab.strings.add("Q1")
doc.ents = [(loc, q1, 3, 4)]
assert len(list(doc.ents)) == 1
assert list(doc.ents)[0].label_ == "LOC"
assert list(doc.ents)[0].kb_id_ == "Q1"