mirror of
https://github.com/explosion/spaCy.git
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d61e742960
* Handle docs with no entities If a whole batch contains no entities it won't make it to the model, but it's possible for individual Docs to have no entities. Before this commit, those Docs would cause an error when attempting to concatenate arrays because the dimensions didn't match. It turns out the process of preparing the Ragged at the end of the span maker forward was a little different from list2ragged, which just uses the flatten function directly. Letting list2ragged do the conversion avoids the dimension issue. This did not come up before because in NEL demo projects it's typical for data with no entities to be discarded before it reaches the NEL component. This includes a simple direct test that shows the issue and checks it's resolved. It doesn't check if there are any downstream changes, so a more complete test could be added. A full run was tested by adding an example with no entities to the Emerson sample project. * Add a blank instance to default training data in tests Rather than adding a specific test, since not failing on instances with no entities is basic functionality, it makes sense to add it to the default set. * Fix without modifying architecture If the architecture is modified this would have to be a new version, but this change isn't big enough to merit that.
1219 lines
44 KiB
Python
1219 lines
44 KiB
Python
from typing import Callable, Iterable, Dict, Any
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import pytest
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from numpy.testing import assert_equal
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from spacy import registry, util
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from spacy.attrs import ENT_KB_ID
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from spacy.compat import pickle
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from spacy.kb import Candidate, InMemoryLookupKB, get_candidates, KnowledgeBase
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from spacy.lang.en import English
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from spacy.ml import load_kb
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from spacy.ml.models.entity_linker import build_span_maker
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from spacy.pipeline import EntityLinker
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from spacy.pipeline.legacy import EntityLinker_v1
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from spacy.pipeline.tok2vec import DEFAULT_TOK2VEC_MODEL
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from spacy.scorer import Scorer
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from spacy.tests.util import make_tempdir
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from spacy.tokens import Span, Doc
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from spacy.training import Example
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from spacy.util import ensure_path
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from spacy.vocab import Vocab
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@pytest.fixture
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def nlp():
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return English()
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def assert_almost_equal(a, b):
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delta = 0.0001
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assert a - delta <= b <= a + delta
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@pytest.mark.issue(4674)
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def test_issue4674():
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"""Test that setting entities with overlapping identifiers does not mess up IO"""
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nlp = English()
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kb = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
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vector1 = [0.9, 1.1, 1.01]
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vector2 = [1.8, 2.25, 2.01]
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with pytest.warns(UserWarning):
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kb.set_entities(
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entity_list=["Q1", "Q1"],
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freq_list=[32, 111],
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vector_list=[vector1, vector2],
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)
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assert kb.get_size_entities() == 1
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# dumping to file & loading back in
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with make_tempdir() as d:
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dir_path = ensure_path(d)
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if not dir_path.exists():
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dir_path.mkdir()
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file_path = dir_path / "kb"
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kb.to_disk(str(file_path))
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kb2 = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
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kb2.from_disk(str(file_path))
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assert kb2.get_size_entities() == 1
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@pytest.mark.issue(6730)
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def test_issue6730(en_vocab):
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"""Ensure that the KB does not accept empty strings, but otherwise IO works fine."""
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from spacy.kb.kb_in_memory import InMemoryLookupKB
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kb = InMemoryLookupKB(en_vocab, entity_vector_length=3)
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kb.add_entity(entity="1", freq=148, entity_vector=[1, 2, 3])
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with pytest.raises(ValueError):
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kb.add_alias(alias="", entities=["1"], probabilities=[0.4])
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assert kb.contains_alias("") is False
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kb.add_alias(alias="x", entities=["1"], probabilities=[0.2])
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kb.add_alias(alias="y", entities=["1"], probabilities=[0.1])
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with make_tempdir() as tmp_dir:
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kb.to_disk(tmp_dir)
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kb.from_disk(tmp_dir)
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assert kb.get_size_aliases() == 2
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assert set(kb.get_alias_strings()) == {"x", "y"}
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@pytest.mark.issue(7065)
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def test_issue7065():
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text = "Kathleen Battle sang in Mahler 's Symphony No. 8 at the Cincinnati Symphony Orchestra 's May Festival."
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nlp = English()
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nlp.add_pipe("sentencizer")
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ruler = nlp.add_pipe("entity_ruler")
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patterns = [
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{
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"label": "THING",
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"pattern": [
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{"LOWER": "symphony"},
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{"LOWER": "no"},
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{"LOWER": "."},
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{"LOWER": "8"},
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],
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}
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]
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ruler.add_patterns(patterns)
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doc = nlp(text)
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sentences = [s for s in doc.sents]
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assert len(sentences) == 2
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sent0 = sentences[0]
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ent = doc.ents[0]
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assert ent.start < sent0.end < ent.end
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assert sentences.index(ent.sent) == 0
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@pytest.mark.issue(7065)
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def test_issue7065_b():
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# Test that the NEL doesn't crash when an entity crosses a sentence boundary
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nlp = English()
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vector_length = 3
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nlp.add_pipe("sentencizer")
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text = "Mahler 's Symphony No. 8 was beautiful."
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entities = [(0, 6, "PERSON"), (10, 24, "WORK")]
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links = {
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(0, 6): {"Q7304": 1.0, "Q270853": 0.0},
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(10, 24): {"Q7304": 0.0, "Q270853": 1.0},
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}
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sent_starts = [1, -1, 0, 0, 0, 0, 0, 0, 0]
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doc = nlp(text)
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example = Example.from_dict(
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doc, {"entities": entities, "links": links, "sent_starts": sent_starts}
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)
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train_examples = [example]
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def create_kb(vocab):
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# create artificial KB
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mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
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mykb.add_entity(entity="Q270853", freq=12, entity_vector=[9, 1, -7])
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mykb.add_alias(
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alias="No. 8",
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entities=["Q270853"],
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probabilities=[1.0],
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)
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mykb.add_entity(entity="Q7304", freq=12, entity_vector=[6, -4, 3])
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mykb.add_alias(
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alias="Mahler",
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entities=["Q7304"],
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probabilities=[1.0],
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)
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return mykb
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# Create the Entity Linker component and add it to the pipeline
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entity_linker = nlp.add_pipe("entity_linker", last=True)
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entity_linker.set_kb(create_kb)
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# train the NEL pipe
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optimizer = nlp.initialize(get_examples=lambda: train_examples)
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for i in range(2):
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losses = {}
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nlp.update(train_examples, sgd=optimizer, losses=losses)
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# Add a custom rule-based component to mimick NER
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patterns = [
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{"label": "PERSON", "pattern": [{"LOWER": "mahler"}]},
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{
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"label": "WORK",
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"pattern": [
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{"LOWER": "symphony"},
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{"LOWER": "no"},
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{"LOWER": "."},
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{"LOWER": "8"},
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],
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},
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]
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ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
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ruler.add_patterns(patterns)
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# test the trained model - this should not throw E148
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doc = nlp(text)
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assert doc
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def test_no_entities():
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# Test that having no entities doesn't crash the model
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TRAIN_DATA = [
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(
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"The sky is blue.",
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{
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"sent_starts": [1, 0, 0, 0, 0],
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},
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)
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]
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nlp = English()
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vector_length = 3
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train_examples = []
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for text, annotation in TRAIN_DATA:
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doc = nlp(text)
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train_examples.append(Example.from_dict(doc, annotation))
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def create_kb(vocab):
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# create artificial KB
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mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
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mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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mykb.add_alias("Russ Cochran", ["Q2146908"], [0.9])
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return mykb
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# Create and train the Entity Linker
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entity_linker = nlp.add_pipe("entity_linker", last=True)
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entity_linker.set_kb(create_kb)
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optimizer = nlp.initialize(get_examples=lambda: train_examples)
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for i in range(2):
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losses = {}
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nlp.update(train_examples, sgd=optimizer, losses=losses)
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# adding additional components that are required for the entity_linker
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nlp.add_pipe("sentencizer", first=True)
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# this will run the pipeline on the examples and shouldn't crash
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nlp.evaluate(train_examples)
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def test_partial_links():
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# Test that having some entities on the doc without gold links, doesn't crash
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TRAIN_DATA = [
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(
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"Russ Cochran his reprints include EC Comics.",
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{
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"links": {(0, 12): {"Q2146908": 1.0}},
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"entities": [(0, 12, "PERSON")],
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"sent_starts": [1, -1, 0, 0, 0, 0, 0, 0],
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},
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)
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]
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nlp = English()
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vector_length = 3
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train_examples = []
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for text, annotation in TRAIN_DATA:
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doc = nlp(text)
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train_examples.append(Example.from_dict(doc, annotation))
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def create_kb(vocab):
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# create artificial KB
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mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
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mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
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mykb.add_alias("Russ Cochran", ["Q2146908"], [0.9])
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return mykb
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# Create and train the Entity Linker
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entity_linker = nlp.add_pipe("entity_linker", last=True)
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entity_linker.set_kb(create_kb)
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optimizer = nlp.initialize(get_examples=lambda: train_examples)
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for i in range(2):
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losses = {}
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nlp.update(train_examples, sgd=optimizer, losses=losses)
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# adding additional components that are required for the entity_linker
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nlp.add_pipe("sentencizer", first=True)
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patterns = [
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{"label": "PERSON", "pattern": [{"LOWER": "russ"}, {"LOWER": "cochran"}]},
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{"label": "ORG", "pattern": [{"LOWER": "ec"}, {"LOWER": "comics"}]},
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]
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ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
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ruler.add_patterns(patterns)
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# this will run the pipeline on the examples and shouldn't crash
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results = nlp.evaluate(train_examples)
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assert "PERSON" in results["ents_per_type"]
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assert "PERSON" in results["nel_f_per_type"]
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assert "ORG" in results["ents_per_type"]
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assert "ORG" not in results["nel_f_per_type"]
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def test_kb_valid_entities(nlp):
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"""Test the valid construction of a KB with 3 entities and two aliases"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
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# adding entities
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[8, 4, 3])
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2, 1, 0])
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mykb.add_entity(entity="Q3", freq=25, entity_vector=[-1, -6, 5])
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# adding aliases
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mykb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.2])
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mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
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# test the size of the corresponding KB
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assert mykb.get_size_entities() == 3
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assert mykb.get_size_aliases() == 2
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# test retrieval of the entity vectors
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assert mykb.get_vector("Q1") == [8, 4, 3]
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assert mykb.get_vector("Q2") == [2, 1, 0]
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assert mykb.get_vector("Q3") == [-1, -6, 5]
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# test retrieval of prior probabilities
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assert_almost_equal(mykb.get_prior_prob(entity="Q2", alias="douglas"), 0.8)
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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)
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assert_almost_equal(mykb.get_prior_prob(entity="Q3", alias="douglassssss"), 0.0)
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def test_kb_invalid_entities(nlp):
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"""Test the invalid construction of a KB with an alias linked to a non-existing entity"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
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# adding entities
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
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mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
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# adding aliases - should fail because one of the given IDs is not valid
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with pytest.raises(ValueError):
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mykb.add_alias(
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alias="douglas", entities=["Q2", "Q342"], probabilities=[0.8, 0.2]
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)
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def test_kb_invalid_probabilities(nlp):
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"""Test the invalid construction of a KB with wrong prior probabilities"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
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# adding entities
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
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mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
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# adding aliases - should fail because the sum of the probabilities exceeds 1
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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):
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"""Test the invalid construction of a KB with non-matching entity and probability lists"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
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# adding entities
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
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mykb.add_entity(entity="Q3", freq=25, entity_vector=[3])
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# adding aliases - should fail because the entities and probabilities vectors are not of equal length
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with pytest.raises(ValueError):
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mykb.add_alias(
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alias="douglas", entities=["Q2", "Q3"], probabilities=[0.3, 0.4, 0.1]
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)
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def test_kb_invalid_entity_vector(nlp):
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"""Test the invalid construction of a KB with non-matching entity vector lengths"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
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# adding entities
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mykb.add_entity(entity="Q1", freq=19, entity_vector=[1, 2, 3])
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# this should fail because the kb's expected entity vector length is 3
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with pytest.raises(ValueError):
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mykb.add_entity(entity="Q2", freq=5, entity_vector=[2])
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def test_kb_default(nlp):
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"""Test that the default (empty) KB is loaded upon construction"""
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entity_linker = nlp.add_pipe("entity_linker", config={})
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assert len(entity_linker.kb) == 0
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assert entity_linker.kb.get_size_entities() == 0
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assert entity_linker.kb.get_size_aliases() == 0
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# 64 is the default value from pipeline.entity_linker
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assert entity_linker.kb.entity_vector_length == 64
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def test_kb_custom_length(nlp):
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"""Test that the default (empty) KB can be configured with a custom entity length"""
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entity_linker = nlp.add_pipe("entity_linker", config={"entity_vector_length": 35})
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assert len(entity_linker.kb) == 0
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assert entity_linker.kb.get_size_entities() == 0
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assert entity_linker.kb.get_size_aliases() == 0
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assert entity_linker.kb.entity_vector_length == 35
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def test_kb_initialize_empty(nlp):
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"""Test that the EL can't initialize without examples"""
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entity_linker = nlp.add_pipe("entity_linker")
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with pytest.raises(TypeError):
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entity_linker.initialize(lambda: [])
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def test_kb_serialize(nlp):
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"""Test serialization of the KB"""
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mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
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with make_tempdir() as d:
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# normal read-write behaviour
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mykb.to_disk(d / "kb")
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mykb.from_disk(d / "kb")
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mykb.to_disk(d / "new" / "kb")
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mykb.from_disk(d / "new" / "kb")
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# allow overwriting an existing file
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mykb.to_disk(d / "kb")
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with pytest.raises(ValueError):
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# can not read from an unknown file
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mykb.from_disk(d / "unknown" / "kb")
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@pytest.mark.issue(9137)
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def test_kb_serialize_2(nlp):
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v = [5, 6, 7, 8]
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kb1 = InMemoryLookupKB(vocab=nlp.vocab, entity_vector_length=4)
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kb1.set_entities(["E1"], [1], [v])
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assert kb1.get_vector("E1") == v
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with make_tempdir() as d:
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kb1.to_disk(d / "kb")
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kb2 = InMemoryLookupKB(vocab=nlp.vocab, entity_vector_length=4)
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kb2.from_disk(d / "kb")
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assert kb2.get_vector("E1") == v
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def test_kb_set_entities(nlp):
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"""Test that set_entities entirely overwrites the previous set of entities"""
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v = [5, 6, 7, 8]
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v1 = [1, 1, 1, 0]
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v2 = [2, 2, 2, 3]
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kb1 = InMemoryLookupKB(vocab=nlp.vocab, entity_vector_length=4)
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kb1.set_entities(["E0"], [1], [v])
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assert kb1.get_entity_strings() == ["E0"]
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kb1.set_entities(["E1", "E2"], [1, 9], [v1, v2])
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assert set(kb1.get_entity_strings()) == {"E1", "E2"}
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assert kb1.get_vector("E1") == v1
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assert kb1.get_vector("E2") == v2
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with make_tempdir() as d:
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kb1.to_disk(d / "kb")
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kb2 = InMemoryLookupKB(vocab=nlp.vocab, entity_vector_length=4)
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kb2.from_disk(d / "kb")
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assert set(kb2.get_entity_strings()) == {"E1", "E2"}
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assert kb2.get_vector("E1") == v1
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assert kb2.get_vector("E2") == v2
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def test_kb_serialize_vocab(nlp):
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"""Test serialization of the KB and custom strings"""
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entity = "MyFunnyID"
|
|
assert entity not in nlp.vocab.strings
|
|
mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
|
|
assert not mykb.contains_entity(entity)
|
|
mykb.add_entity(entity, freq=342, entity_vector=[3])
|
|
assert mykb.contains_entity(entity)
|
|
assert entity in mykb.vocab.strings
|
|
with make_tempdir() as d:
|
|
# normal read-write behaviour
|
|
mykb.to_disk(d / "kb")
|
|
mykb_new = InMemoryLookupKB(Vocab(), entity_vector_length=1)
|
|
mykb_new.from_disk(d / "kb")
|
|
assert entity in mykb_new.vocab.strings
|
|
|
|
|
|
def test_candidate_generation(nlp):
|
|
"""Test correct candidate generation"""
|
|
mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
|
|
doc = nlp("douglas adam Adam shrubbery")
|
|
|
|
douglas_ent = doc[0:1]
|
|
adam_ent = doc[1:2]
|
|
Adam_ent = doc[2:3]
|
|
shrubbery_ent = doc[3:4]
|
|
|
|
# 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])
|
|
|
|
# test the size of the relevant candidates
|
|
assert len(get_candidates(mykb, douglas_ent)) == 2
|
|
assert len(get_candidates(mykb, adam_ent)) == 1
|
|
assert len(get_candidates(mykb, Adam_ent)) == 0 # default case sensitive
|
|
assert len(get_candidates(mykb, shrubbery_ent)) == 0
|
|
|
|
# test the content of the candidates
|
|
assert get_candidates(mykb, adam_ent)[0].entity_ == "Q2"
|
|
assert get_candidates(mykb, adam_ent)[0].alias_ == "adam"
|
|
assert_almost_equal(get_candidates(mykb, adam_ent)[0].entity_freq, 12)
|
|
assert_almost_equal(get_candidates(mykb, adam_ent)[0].prior_prob, 0.9)
|
|
|
|
|
|
def test_el_pipe_configuration(nlp):
|
|
"""Test correct candidate generation as part of the EL pipe"""
|
|
nlp.add_pipe("sentencizer")
|
|
pattern = {"label": "PERSON", "pattern": [{"LOWER": "douglas"}]}
|
|
ruler = nlp.add_pipe("entity_ruler")
|
|
ruler.add_patterns([pattern])
|
|
|
|
def create_kb(vocab):
|
|
kb = InMemoryLookupKB(vocab, entity_vector_length=1)
|
|
kb.add_entity(entity="Q2", freq=12, entity_vector=[2])
|
|
kb.add_entity(entity="Q3", freq=5, entity_vector=[3])
|
|
kb.add_alias(alias="douglas", entities=["Q2", "Q3"], probabilities=[0.8, 0.1])
|
|
return kb
|
|
|
|
# run an EL pipe without a trained context encoder, to check the candidate generation step only
|
|
entity_linker = nlp.add_pipe("entity_linker", config={"incl_context": False})
|
|
entity_linker.set_kb(create_kb)
|
|
# With the default get_candidates function, matching is case-sensitive
|
|
text = "Douglas and douglas are not the same."
|
|
doc = nlp(text)
|
|
assert doc[0].ent_kb_id_ == "NIL"
|
|
assert doc[1].ent_kb_id_ == ""
|
|
assert doc[2].ent_kb_id_ == "Q2"
|
|
|
|
def get_lowercased_candidates(kb, span):
|
|
return kb.get_alias_candidates(span.text.lower())
|
|
|
|
def get_lowercased_candidates_batch(kb, spans):
|
|
return [get_lowercased_candidates(kb, span) for span in spans]
|
|
|
|
@registry.misc("spacy.LowercaseCandidateGenerator.v1")
|
|
def create_candidates() -> Callable[
|
|
[InMemoryLookupKB, "Span"], Iterable[Candidate]
|
|
]:
|
|
return get_lowercased_candidates
|
|
|
|
@registry.misc("spacy.LowercaseCandidateBatchGenerator.v1")
|
|
def create_candidates_batch() -> Callable[
|
|
[InMemoryLookupKB, Iterable["Span"]], Iterable[Iterable[Candidate]]
|
|
]:
|
|
return get_lowercased_candidates_batch
|
|
|
|
# replace the pipe with a new one with with a different candidate generator
|
|
entity_linker = nlp.replace_pipe(
|
|
"entity_linker",
|
|
"entity_linker",
|
|
config={
|
|
"incl_context": False,
|
|
"get_candidates": {"@misc": "spacy.LowercaseCandidateGenerator.v1"},
|
|
"get_candidates_batch": {
|
|
"@misc": "spacy.LowercaseCandidateBatchGenerator.v1"
|
|
},
|
|
},
|
|
)
|
|
entity_linker.set_kb(create_kb)
|
|
doc = nlp(text)
|
|
assert doc[0].ent_kb_id_ == "Q2"
|
|
assert doc[1].ent_kb_id_ == ""
|
|
assert doc[2].ent_kb_id_ == "Q2"
|
|
|
|
|
|
def test_nel_nsents(nlp):
|
|
"""Test that n_sents can be set through the configuration"""
|
|
entity_linker = nlp.add_pipe("entity_linker", config={})
|
|
assert entity_linker.n_sents == 0
|
|
entity_linker = nlp.replace_pipe(
|
|
"entity_linker", "entity_linker", config={"n_sents": 2}
|
|
)
|
|
assert entity_linker.n_sents == 2
|
|
|
|
|
|
def test_vocab_serialization(nlp):
|
|
"""Test that string information is retained across storage"""
|
|
mykb = InMemoryLookupKB(nlp.vocab, entity_vector_length=1)
|
|
|
|
# adding entities
|
|
mykb.add_entity(entity="Q1", freq=27, entity_vector=[1])
|
|
q2_hash = 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])
|
|
adam_hash = mykb.add_alias(alias="adam", entities=["Q2"], probabilities=[0.9])
|
|
|
|
candidates = mykb.get_alias_candidates("adam")
|
|
assert len(candidates) == 1
|
|
assert candidates[0].entity == q2_hash
|
|
assert candidates[0].entity_ == "Q2"
|
|
assert candidates[0].alias == adam_hash
|
|
assert candidates[0].alias_ == "adam"
|
|
|
|
with make_tempdir() as d:
|
|
mykb.to_disk(d / "kb")
|
|
kb_new_vocab = InMemoryLookupKB(Vocab(), entity_vector_length=1)
|
|
kb_new_vocab.from_disk(d / "kb")
|
|
|
|
candidates = kb_new_vocab.get_alias_candidates("adam")
|
|
assert len(candidates) == 1
|
|
assert candidates[0].entity == q2_hash
|
|
assert candidates[0].entity_ == "Q2"
|
|
assert candidates[0].alias == adam_hash
|
|
assert candidates[0].alias_ == "adam"
|
|
|
|
assert kb_new_vocab.get_vector("Q2") == [2]
|
|
assert_almost_equal(kb_new_vocab.get_prior_prob("Q2", "douglas"), 0.4)
|
|
|
|
|
|
def test_append_alias(nlp):
|
|
"""Test that we can append additional alias-entity pairs"""
|
|
mykb = InMemoryLookupKB(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_alias_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_alias_candidates("douglas")) == 3
|
|
|
|
# append the same alias-entity pair again should not work (will throw a warning)
|
|
with pytest.warns(UserWarning):
|
|
mykb.append_alias(alias="douglas", entity="Q1", prior_prob=0.3)
|
|
|
|
# test the size of the relevant candidates remained unchanged
|
|
assert len(mykb.get_alias_candidates("douglas")) == 3
|
|
|
|
|
|
@pytest.mark.filterwarnings("ignore:\\[W036")
|
|
def test_append_invalid_alias(nlp):
|
|
"""Test that append an alias will throw an error if prior probs are exceeding 1"""
|
|
mykb = InMemoryLookupKB(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)
|
|
|
|
|
|
@pytest.mark.filterwarnings("ignore:\\[W036")
|
|
def test_preserving_links_asdoc(nlp):
|
|
"""Test that Span.as_doc preserves the existing entity links"""
|
|
vector_length = 1
|
|
|
|
def create_kb(vocab):
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
|
# adding entities
|
|
mykb.add_entity(entity="Q1", freq=19, entity_vector=[1])
|
|
mykb.add_entity(entity="Q2", freq=8, entity_vector=[1])
|
|
# adding aliases
|
|
mykb.add_alias(alias="Boston", entities=["Q1"], probabilities=[0.7])
|
|
mykb.add_alias(alias="Denver", entities=["Q2"], probabilities=[0.6])
|
|
return mykb
|
|
|
|
# set up pipeline with NER (Entity Ruler) and NEL (prior probability only, model not trained)
|
|
nlp.add_pipe("sentencizer")
|
|
patterns = [
|
|
{"label": "GPE", "pattern": "Boston"},
|
|
{"label": "GPE", "pattern": "Denver"},
|
|
]
|
|
ruler = nlp.add_pipe("entity_ruler")
|
|
ruler.add_patterns(patterns)
|
|
config = {"incl_prior": False}
|
|
entity_linker = nlp.add_pipe("entity_linker", config=config, last=True)
|
|
entity_linker.set_kb(create_kb)
|
|
nlp.initialize()
|
|
assert entity_linker.model.get_dim("nO") == vector_length
|
|
|
|
# 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"
|
|
|
|
|
|
# fmt: off
|
|
TRAIN_DATA = [
|
|
("Russ Cochran captured his first major title with his son as caddie.",
|
|
{"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}},
|
|
"entities": [(0, 12, "PERSON")],
|
|
"sent_starts": [1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]}),
|
|
("Russ Cochran his reprints include EC Comics.",
|
|
{"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}},
|
|
"entities": [(0, 12, "PERSON"), (34, 43, "ART")],
|
|
"sent_starts": [1, -1, 0, 0, 0, 0, 0, 0]}),
|
|
("Russ Cochran has been publishing comic art.",
|
|
{"links": {(0, 12): {"Q7381115": 1.0, "Q2146908": 0.0}},
|
|
"entities": [(0, 12, "PERSON")],
|
|
"sent_starts": [1, -1, 0, 0, 0, 0, 0, 0]}),
|
|
("Russ Cochran was a member of University of Kentucky's golf team.",
|
|
{"links": {(0, 12): {"Q7381115": 0.0, "Q2146908": 1.0}},
|
|
"entities": [(0, 12, "PERSON"), (43, 51, "LOC")],
|
|
"sent_starts": [1, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]}),
|
|
# having a blank instance shouldn't break things
|
|
("The weather is nice today.",
|
|
{"links": {}, "entities": [],
|
|
"sent_starts": [1, -1, 0, 0, 0, 0]})
|
|
]
|
|
GOLD_entities = ["Q2146908", "Q7381115", "Q7381115", "Q2146908"]
|
|
# fmt: on
|
|
|
|
|
|
def test_overfitting_IO():
|
|
# Simple test to try and quickly overfit the NEL component - ensuring the ML models work correctly
|
|
nlp = English()
|
|
vector_length = 3
|
|
assert "Q2146908" not in nlp.vocab.strings
|
|
|
|
# Convert the texts to docs to make sure we have doc.ents set for the training examples
|
|
train_examples = []
|
|
for text, annotation in TRAIN_DATA:
|
|
doc = nlp(text)
|
|
train_examples.append(Example.from_dict(doc, annotation))
|
|
|
|
def create_kb(vocab):
|
|
# create artificial KB - assign same prior weight to the two russ cochran's
|
|
# Q2146908 (Russ Cochran): American golfer
|
|
# Q7381115 (Russ Cochran): publisher
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
|
mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_entity(entity="Q7381115", freq=12, entity_vector=[9, 1, -7])
|
|
mykb.add_alias(
|
|
alias="Russ Cochran",
|
|
entities=["Q2146908", "Q7381115"],
|
|
probabilities=[0.5, 0.5],
|
|
)
|
|
return mykb
|
|
|
|
# Create the Entity Linker component and add it to the pipeline
|
|
entity_linker = nlp.add_pipe("entity_linker", last=True)
|
|
assert isinstance(entity_linker, EntityLinker)
|
|
entity_linker.set_kb(create_kb)
|
|
assert "Q2146908" in entity_linker.vocab.strings
|
|
assert "Q2146908" in entity_linker.kb.vocab.strings
|
|
|
|
# train the NEL pipe
|
|
optimizer = nlp.initialize(get_examples=lambda: train_examples)
|
|
assert entity_linker.model.get_dim("nO") == vector_length
|
|
assert entity_linker.model.get_dim("nO") == entity_linker.kb.entity_vector_length
|
|
|
|
for i in range(50):
|
|
losses = {}
|
|
nlp.update(train_examples, sgd=optimizer, losses=losses)
|
|
assert losses["entity_linker"] < 0.001
|
|
|
|
# adding additional components that are required for the entity_linker
|
|
nlp.add_pipe("sentencizer", first=True)
|
|
|
|
# Add a custom component to recognize "Russ Cochran" as an entity for the example training data
|
|
patterns = [
|
|
{"label": "PERSON", "pattern": [{"LOWER": "russ"}, {"LOWER": "cochran"}]}
|
|
]
|
|
ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
|
|
ruler.add_patterns(patterns)
|
|
|
|
# test the trained model
|
|
predictions = []
|
|
for text, annotation in TRAIN_DATA:
|
|
doc = nlp(text)
|
|
for ent in doc.ents:
|
|
predictions.append(ent.kb_id_)
|
|
assert predictions == GOLD_entities
|
|
|
|
# Also test the results are still the same after IO
|
|
with make_tempdir() as tmp_dir:
|
|
nlp.to_disk(tmp_dir)
|
|
nlp2 = util.load_model_from_path(tmp_dir)
|
|
assert nlp2.pipe_names == nlp.pipe_names
|
|
assert "Q2146908" in nlp2.vocab.strings
|
|
entity_linker2 = nlp2.get_pipe("entity_linker")
|
|
assert "Q2146908" in entity_linker2.vocab.strings
|
|
assert "Q2146908" in entity_linker2.kb.vocab.strings
|
|
predictions = []
|
|
for text, annotation in TRAIN_DATA:
|
|
doc2 = nlp2(text)
|
|
for ent in doc2.ents:
|
|
predictions.append(ent.kb_id_)
|
|
assert predictions == GOLD_entities
|
|
|
|
# Make sure that running pipe twice, or comparing to call, always amounts to the same predictions
|
|
texts = [
|
|
"Russ Cochran captured his first major title with his son as caddie.",
|
|
"Russ Cochran his reprints include EC Comics.",
|
|
"Russ Cochran has been publishing comic art.",
|
|
"Russ Cochran was a member of University of Kentucky's golf team.",
|
|
]
|
|
batch_deps_1 = [doc.to_array([ENT_KB_ID]) for doc in nlp.pipe(texts)]
|
|
batch_deps_2 = [doc.to_array([ENT_KB_ID]) for doc in nlp.pipe(texts)]
|
|
no_batch_deps = [doc.to_array([ENT_KB_ID]) for doc in [nlp(text) for text in texts]]
|
|
assert_equal(batch_deps_1, batch_deps_2)
|
|
assert_equal(batch_deps_1, no_batch_deps)
|
|
|
|
|
|
def test_kb_serialization():
|
|
# Test that the KB can be used in a pipeline with a different vocab
|
|
vector_length = 3
|
|
with make_tempdir() as tmp_dir:
|
|
kb_dir = tmp_dir / "kb"
|
|
nlp1 = English()
|
|
assert "Q2146908" not in nlp1.vocab.strings
|
|
mykb = InMemoryLookupKB(nlp1.vocab, entity_vector_length=vector_length)
|
|
mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
|
|
assert "Q2146908" in nlp1.vocab.strings
|
|
mykb.to_disk(kb_dir)
|
|
|
|
nlp2 = English()
|
|
assert "RandomWord" not in nlp2.vocab.strings
|
|
nlp2.vocab.strings.add("RandomWord")
|
|
assert "RandomWord" in nlp2.vocab.strings
|
|
assert "Q2146908" not in nlp2.vocab.strings
|
|
|
|
# Create the Entity Linker component with the KB from file, and check the final vocab
|
|
entity_linker = nlp2.add_pipe("entity_linker", last=True)
|
|
entity_linker.set_kb(load_kb(kb_dir))
|
|
assert "Q2146908" in nlp2.vocab.strings
|
|
assert "RandomWord" in nlp2.vocab.strings
|
|
|
|
|
|
@pytest.mark.xfail(reason="Needs fixing")
|
|
def test_kb_pickle():
|
|
# Test that the KB can be pickled
|
|
nlp = English()
|
|
kb_1 = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
|
|
kb_1.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
assert not kb_1.contains_alias("Russ Cochran")
|
|
kb_1.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
|
|
assert kb_1.contains_alias("Russ Cochran")
|
|
data = pickle.dumps(kb_1)
|
|
kb_2 = pickle.loads(data)
|
|
assert kb_2.contains_alias("Russ Cochran")
|
|
|
|
|
|
@pytest.mark.xfail(reason="Needs fixing")
|
|
def test_nel_pickle():
|
|
# Test that a pipeline with an EL component can be pickled
|
|
def create_kb(vocab):
|
|
kb = InMemoryLookupKB(vocab, entity_vector_length=3)
|
|
kb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
kb.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
|
|
return kb
|
|
|
|
nlp_1 = English()
|
|
nlp_1.add_pipe("ner")
|
|
entity_linker_1 = nlp_1.add_pipe("entity_linker", last=True)
|
|
entity_linker_1.set_kb(create_kb)
|
|
assert nlp_1.pipe_names == ["ner", "entity_linker"]
|
|
assert entity_linker_1.kb.contains_alias("Russ Cochran")
|
|
|
|
data = pickle.dumps(nlp_1)
|
|
nlp_2 = pickle.loads(data)
|
|
assert nlp_2.pipe_names == ["ner", "entity_linker"]
|
|
entity_linker_2 = nlp_2.get_pipe("entity_linker")
|
|
assert entity_linker_2.kb.contains_alias("Russ Cochran")
|
|
|
|
|
|
def test_kb_to_bytes():
|
|
# Test that the KB's to_bytes method works correctly
|
|
nlp = English()
|
|
kb_1 = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
|
|
kb_1.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
kb_1.add_entity(entity="Q66", freq=9, entity_vector=[1, 2, 3])
|
|
kb_1.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
|
|
kb_1.add_alias(alias="Boeing", entities=["Q66"], probabilities=[0.5])
|
|
kb_1.add_alias(
|
|
alias="Randomness", entities=["Q66", "Q2146908"], probabilities=[0.1, 0.2]
|
|
)
|
|
assert kb_1.contains_alias("Russ Cochran")
|
|
kb_bytes = kb_1.to_bytes()
|
|
kb_2 = InMemoryLookupKB(nlp.vocab, entity_vector_length=3)
|
|
assert not kb_2.contains_alias("Russ Cochran")
|
|
kb_2 = kb_2.from_bytes(kb_bytes)
|
|
# check that both KBs are exactly the same
|
|
assert kb_1.get_size_entities() == kb_2.get_size_entities()
|
|
assert kb_1.entity_vector_length == kb_2.entity_vector_length
|
|
assert kb_1.get_entity_strings() == kb_2.get_entity_strings()
|
|
assert kb_1.get_vector("Q2146908") == kb_2.get_vector("Q2146908")
|
|
assert kb_1.get_vector("Q66") == kb_2.get_vector("Q66")
|
|
assert kb_2.contains_alias("Russ Cochran")
|
|
assert kb_1.get_size_aliases() == kb_2.get_size_aliases()
|
|
assert kb_1.get_alias_strings() == kb_2.get_alias_strings()
|
|
assert len(kb_1.get_alias_candidates("Russ Cochran")) == len(
|
|
kb_2.get_alias_candidates("Russ Cochran")
|
|
)
|
|
assert len(kb_1.get_alias_candidates("Randomness")) == len(
|
|
kb_2.get_alias_candidates("Randomness")
|
|
)
|
|
|
|
|
|
def test_nel_to_bytes():
|
|
# Test that a pipeline with an EL component can be converted to bytes
|
|
def create_kb(vocab):
|
|
kb = InMemoryLookupKB(vocab, entity_vector_length=3)
|
|
kb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
kb.add_alias(alias="Russ Cochran", entities=["Q2146908"], probabilities=[0.8])
|
|
return kb
|
|
|
|
nlp_1 = English()
|
|
nlp_1.add_pipe("ner")
|
|
entity_linker_1 = nlp_1.add_pipe("entity_linker", last=True)
|
|
entity_linker_1.set_kb(create_kb)
|
|
assert entity_linker_1.kb.contains_alias("Russ Cochran")
|
|
assert nlp_1.pipe_names == ["ner", "entity_linker"]
|
|
|
|
nlp_bytes = nlp_1.to_bytes()
|
|
nlp_2 = English()
|
|
nlp_2.add_pipe("ner")
|
|
nlp_2.add_pipe("entity_linker", last=True)
|
|
assert nlp_2.pipe_names == ["ner", "entity_linker"]
|
|
assert not nlp_2.get_pipe("entity_linker").kb.contains_alias("Russ Cochran")
|
|
nlp_2 = nlp_2.from_bytes(nlp_bytes)
|
|
kb_2 = nlp_2.get_pipe("entity_linker").kb
|
|
assert kb_2.contains_alias("Russ Cochran")
|
|
assert kb_2.get_vector("Q2146908") == [6, -4, 3]
|
|
assert_almost_equal(
|
|
kb_2.get_prior_prob(entity="Q2146908", alias="Russ Cochran"), 0.8
|
|
)
|
|
|
|
|
|
def test_scorer_links():
|
|
train_examples = []
|
|
nlp = English()
|
|
ref1 = nlp("Julia lives in London happily.")
|
|
ref1.ents = [
|
|
Span(ref1, 0, 1, label="PERSON", kb_id="Q2"),
|
|
Span(ref1, 3, 4, label="LOC", kb_id="Q3"),
|
|
]
|
|
pred1 = nlp("Julia lives in London happily.")
|
|
pred1.ents = [
|
|
Span(pred1, 0, 1, label="PERSON", kb_id="Q70"),
|
|
Span(pred1, 3, 4, label="LOC", kb_id="Q3"),
|
|
]
|
|
train_examples.append(Example(pred1, ref1))
|
|
|
|
ref2 = nlp("She loves London.")
|
|
ref2.ents = [
|
|
Span(ref2, 0, 1, label="PERSON", kb_id="Q2"),
|
|
Span(ref2, 2, 3, label="LOC", kb_id="Q13"),
|
|
]
|
|
pred2 = nlp("She loves London.")
|
|
pred2.ents = [
|
|
Span(pred2, 0, 1, label="PERSON", kb_id="Q2"),
|
|
Span(pred2, 2, 3, label="LOC", kb_id="NIL"),
|
|
]
|
|
train_examples.append(Example(pred2, ref2))
|
|
|
|
ref3 = nlp("London is great.")
|
|
ref3.ents = [Span(ref3, 0, 1, label="LOC", kb_id="NIL")]
|
|
pred3 = nlp("London is great.")
|
|
pred3.ents = [Span(pred3, 0, 1, label="LOC", kb_id="NIL")]
|
|
train_examples.append(Example(pred3, ref3))
|
|
|
|
scores = Scorer().score_links(train_examples, negative_labels=["NIL"])
|
|
assert scores["nel_f_per_type"]["PERSON"]["p"] == 1 / 2
|
|
assert scores["nel_f_per_type"]["PERSON"]["r"] == 1 / 2
|
|
assert scores["nel_f_per_type"]["LOC"]["p"] == 1 / 1
|
|
assert scores["nel_f_per_type"]["LOC"]["r"] == 1 / 2
|
|
|
|
assert scores["nel_micro_p"] == 2 / 3
|
|
assert scores["nel_micro_r"] == 2 / 4
|
|
|
|
|
|
# fmt: off
|
|
@pytest.mark.parametrize(
|
|
"name,config",
|
|
[
|
|
("entity_linker", {"@architectures": "spacy.EntityLinker.v1", "tok2vec": DEFAULT_TOK2VEC_MODEL}),
|
|
("entity_linker", {"@architectures": "spacy.EntityLinker.v2", "tok2vec": DEFAULT_TOK2VEC_MODEL}),
|
|
],
|
|
)
|
|
# fmt: on
|
|
def test_legacy_architectures(name, config):
|
|
# Ensure that the legacy architectures still work
|
|
vector_length = 3
|
|
nlp = English()
|
|
|
|
train_examples = []
|
|
for text, annotation in TRAIN_DATA:
|
|
doc = nlp.make_doc(text)
|
|
train_examples.append(Example.from_dict(doc, annotation))
|
|
|
|
def create_kb(vocab):
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
|
mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_entity(entity="Q7381115", freq=12, entity_vector=[9, 1, -7])
|
|
mykb.add_alias(
|
|
alias="Russ Cochran",
|
|
entities=["Q2146908", "Q7381115"],
|
|
probabilities=[0.5, 0.5],
|
|
)
|
|
return mykb
|
|
|
|
entity_linker = nlp.add_pipe(name, config={"model": config})
|
|
if config["@architectures"] == "spacy.EntityLinker.v1":
|
|
assert isinstance(entity_linker, EntityLinker_v1)
|
|
else:
|
|
assert isinstance(entity_linker, EntityLinker)
|
|
entity_linker.set_kb(create_kb)
|
|
optimizer = nlp.initialize(get_examples=lambda: train_examples)
|
|
|
|
for i in range(2):
|
|
losses = {}
|
|
nlp.update(train_examples, sgd=optimizer, losses=losses)
|
|
|
|
|
|
@pytest.mark.parametrize(
|
|
"patterns",
|
|
[
|
|
# perfect case
|
|
[{"label": "CHARACTER", "pattern": "Kirby"}],
|
|
# typo for false negative
|
|
[{"label": "PERSON", "pattern": "Korby"}],
|
|
# random stuff for false positive
|
|
[{"label": "IS", "pattern": "is"}, {"label": "COLOR", "pattern": "pink"}],
|
|
],
|
|
)
|
|
def test_no_gold_ents(patterns):
|
|
# test that annotating components work
|
|
TRAIN_DATA = [
|
|
(
|
|
"Kirby is pink",
|
|
{
|
|
"links": {(0, 5): {"Q613241": 1.0}},
|
|
"entities": [(0, 5, "CHARACTER")],
|
|
"sent_starts": [1, 0, 0],
|
|
},
|
|
)
|
|
]
|
|
nlp = English()
|
|
vector_length = 3
|
|
train_examples = []
|
|
for text, annotation in TRAIN_DATA:
|
|
doc = nlp(text)
|
|
train_examples.append(Example.from_dict(doc, annotation))
|
|
|
|
# Create a ruler to mark entities
|
|
ruler = nlp.add_pipe("entity_ruler")
|
|
ruler.add_patterns(patterns)
|
|
|
|
# Apply ruler to examples. In a real pipeline this would be an annotating component.
|
|
for eg in train_examples:
|
|
eg.predicted = ruler(eg.predicted)
|
|
|
|
# Entity ruler is no longer needed (initialization below wipes out the
|
|
# patterns and causes warnings)
|
|
nlp.remove_pipe("entity_ruler")
|
|
|
|
def create_kb(vocab):
|
|
# create artificial KB
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
|
mykb.add_entity(entity="Q613241", freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_alias("Kirby", ["Q613241"], [0.9])
|
|
# Placeholder
|
|
mykb.add_entity(entity="pink", freq=12, entity_vector=[7, 2, -5])
|
|
mykb.add_alias("pink", ["pink"], [0.9])
|
|
return mykb
|
|
|
|
# Create and train the Entity Linker
|
|
entity_linker = nlp.add_pipe(
|
|
"entity_linker", config={"use_gold_ents": False}, last=True
|
|
)
|
|
entity_linker.set_kb(create_kb)
|
|
assert entity_linker.use_gold_ents is False
|
|
|
|
optimizer = nlp.initialize(get_examples=lambda: train_examples)
|
|
for i in range(2):
|
|
losses = {}
|
|
nlp.update(train_examples, sgd=optimizer, losses=losses)
|
|
|
|
# adding additional components that are required for the entity_linker
|
|
nlp.add_pipe("sentencizer", first=True)
|
|
|
|
# this will run the pipeline on the examples and shouldn't crash
|
|
nlp.evaluate(train_examples)
|
|
|
|
|
|
@pytest.mark.issue(9575)
|
|
def test_tokenization_mismatch():
|
|
nlp = English()
|
|
# include a matching entity so that update isn't skipped
|
|
doc1 = Doc(
|
|
nlp.vocab,
|
|
words=["Kirby", "123456"],
|
|
spaces=[True, False],
|
|
ents=["B-CHARACTER", "B-CARDINAL"],
|
|
)
|
|
doc2 = Doc(
|
|
nlp.vocab,
|
|
words=["Kirby", "123", "456"],
|
|
spaces=[True, False, False],
|
|
ents=["B-CHARACTER", "B-CARDINAL", "B-CARDINAL"],
|
|
)
|
|
|
|
eg = Example(doc1, doc2)
|
|
train_examples = [eg]
|
|
vector_length = 3
|
|
|
|
def create_kb(vocab):
|
|
# create placeholder KB
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
|
mykb.add_entity(entity="Q613241", freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_alias("Kirby", ["Q613241"], [0.9])
|
|
return mykb
|
|
|
|
entity_linker = nlp.add_pipe("entity_linker", last=True)
|
|
entity_linker.set_kb(create_kb)
|
|
|
|
optimizer = nlp.initialize(get_examples=lambda: train_examples)
|
|
for i in range(2):
|
|
losses = {}
|
|
nlp.update(train_examples, sgd=optimizer, losses=losses)
|
|
|
|
nlp.add_pipe("sentencizer", first=True)
|
|
nlp.evaluate(train_examples)
|
|
|
|
|
|
def test_abstract_kb_instantiation():
|
|
"""Test whether instantiation of abstract KB base class fails."""
|
|
with pytest.raises(TypeError):
|
|
KnowledgeBase(None, 3)
|
|
|
|
|
|
# fmt: off
|
|
@pytest.mark.parametrize(
|
|
"meet_threshold,config",
|
|
[
|
|
(False, {"@architectures": "spacy.EntityLinker.v2", "tok2vec": DEFAULT_TOK2VEC_MODEL}),
|
|
(True, {"@architectures": "spacy.EntityLinker.v2", "tok2vec": DEFAULT_TOK2VEC_MODEL}),
|
|
],
|
|
)
|
|
# fmt: on
|
|
def test_threshold(meet_threshold: bool, config: Dict[str, Any]):
|
|
"""Tests abstention threshold.
|
|
meet_threshold (bool): Whether to configure NEL setup so that confidence threshold is met.
|
|
config (Dict[str, Any]): NEL architecture config.
|
|
"""
|
|
nlp = English()
|
|
nlp.add_pipe("sentencizer")
|
|
text = "Mahler's Symphony No. 8 was beautiful."
|
|
entities = [(0, 6, "PERSON")]
|
|
links = {(0, 6): {"Q7304": 1.0}}
|
|
sent_starts = [1, -1, 0, 0, 0, 0, 0, 0, 0]
|
|
entity_id = "Q7304"
|
|
doc = nlp(text)
|
|
train_examples = [
|
|
Example.from_dict(
|
|
doc, {"entities": entities, "links": links, "sent_starts": sent_starts}
|
|
)
|
|
]
|
|
|
|
def create_kb(vocab):
|
|
# create artificial KB
|
|
mykb = InMemoryLookupKB(vocab, entity_vector_length=3)
|
|
mykb.add_entity(entity=entity_id, freq=12, entity_vector=[6, -4, 3])
|
|
mykb.add_alias(
|
|
alias="Mahler",
|
|
entities=[entity_id],
|
|
probabilities=[1 if meet_threshold else 0.01],
|
|
)
|
|
return mykb
|
|
|
|
# Create the Entity Linker component and add it to the pipeline
|
|
entity_linker = nlp.add_pipe(
|
|
"entity_linker",
|
|
last=True,
|
|
config={"threshold": 0.99, "model": config},
|
|
)
|
|
entity_linker.set_kb(create_kb) # type: ignore
|
|
nlp.initialize(get_examples=lambda: train_examples)
|
|
|
|
# Add a custom rule-based component to mimick NER
|
|
ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
|
|
ruler.add_patterns([{"label": "PERSON", "pattern": [{"LOWER": "mahler"}]}]) # type: ignore
|
|
doc = nlp(text)
|
|
|
|
assert len(doc.ents) == 1
|
|
assert doc.ents[0].kb_id_ == entity_id if meet_threshold else EntityLinker.NIL
|
|
|
|
|
|
def test_span_maker_forward_with_empty():
|
|
"""The forward pass of the span maker may have a doc with no entities."""
|
|
nlp = English()
|
|
doc1 = nlp("a b c")
|
|
ent = doc1[0:1]
|
|
ent.label_ = "X"
|
|
doc1.ents = [ent]
|
|
# no entities
|
|
doc2 = nlp("x y z")
|
|
|
|
# just to get a model
|
|
span_maker = build_span_maker()
|
|
span_maker([doc1, doc2], False)
|