fix EL scorer

This commit is contained in:
svlandeg 2024-03-27 18:09:51 +01:00
parent 76d77f0f2e
commit 7ea8c4aaa5
2 changed files with 130 additions and 29 deletions

View File

@ -235,7 +235,6 @@ class EntityLinker(TrainablePipe):
self.cfg: Dict[str, Any] = {"overwrite": overwrite}
self.distance = CosineDistance(normalize=False)
self.kb = generate_empty_kb(self.vocab, entity_vector_length)
self.scorer = scorer
self.use_gold_ents = use_gold_ents
self.candidates_batch_size = candidates_batch_size
self.threshold = threshold
@ -243,6 +242,33 @@ class EntityLinker(TrainablePipe):
if candidates_batch_size < 1:
raise ValueError(Errors.E1044)
def _score_augmented(examples, **kwargs):
# Because of how spaCy works, we can't just score immediately, because Language.evaluate
# calls pipe() on the predicted docs, which won't have entities if there is no NER in the pipeline.
if not self.use_gold_ents:
return scorer(examples, **kwargs)
else:
examples = self._augment_examples(examples)
docs = self.pipe(
(eg.predicted for eg in examples),
)
for eg, doc in zip(examples, docs):
eg.predicted = doc
return scorer(examples, **kwargs)
self.scorer = _score_augmented
def _augment_examples(self, examples: Iterable[Example]) -> Iterable[Example]:
"""If use_gold_ents is true, set the gold entities to eg.predicted.
"""
new_examples = []
for eg in examples:
if self.use_gold_ents:
ents, _ = eg.get_aligned_ents_and_ner()
eg.predicted.ents = ents
new_examples.append(eg)
return new_examples
def set_kb(self, kb_loader: Callable[[Vocab], KnowledgeBase]):
"""Define the KB of this pipe by providing a function that will
create it using this object's vocab."""
@ -284,13 +310,9 @@ class EntityLinker(TrainablePipe):
nO = self.kb.entity_vector_length
doc_sample = []
vector_sample = []
orig_ents = []
for eg in islice(get_examples(), 10):
examples = self._augment_examples(islice(get_examples(), 10))
for eg in examples:
doc = eg.x
if self.use_gold_ents:
orig_ents.append(doc.ents)
ents, _ = eg.get_aligned_ents_and_ner()
doc.ents = ents
doc_sample.append(doc)
vector_sample.append(self.model.ops.alloc1f(nO))
assert len(doc_sample) > 0, Errors.E923.format(name=self.name)
@ -315,10 +337,6 @@ class EntityLinker(TrainablePipe):
if not has_annotations:
# Clean up dummy annotation
doc.ents = []
if self.use_gold_ents:
assert len(doc_sample) == len(orig_ents)
for doc, orig_ent in zip(doc_sample, orig_ents):
doc.ents = orig_ent
def batch_has_learnable_example(self, examples):
"""Check if a batch contains a learnable example.
@ -360,25 +378,15 @@ class EntityLinker(TrainablePipe):
losses.setdefault(self.name, 0.0)
if not examples:
return losses
examples = self._augment_examples(examples)
validate_examples(examples, "EntityLinker.update")
set_dropout_rate(self.model, drop)
docs = [eg.predicted for eg in examples]
# save to restore later
old_ents = [doc.ents for doc in docs]
for doc, ex in zip(docs, examples):
if self.use_gold_ents:
ents, _ = ex.get_aligned_ents_and_ner()
doc.ents = ents
else:
# only keep matching ents
doc.ents = ex.get_matching_ents()
# make sure we have something to learn from, if not, short-circuit
if not self.batch_has_learnable_example(examples):
return losses
set_dropout_rate(self.model, drop)
docs = [eg.predicted for eg in examples]
sentence_encodings, bp_context = self.model.begin_update(docs)
loss, d_scores = self.get_loss(
@ -389,14 +397,10 @@ class EntityLinker(TrainablePipe):
self.finish_update(sgd)
losses[self.name] += loss
# now restore the ents
assert len(docs) == len(old_ents)
for doc, old in zip(docs, old_ents):
doc.ents = old
return losses
def get_loss(self, examples: Iterable[Example], sentence_encodings: Floats2d):
""" Here, we assume that get_loss is called with augmented examples if need be"""
validate_examples(examples, "EntityLinker.get_loss")
entity_encodings = []
eidx = 0 # indices in gold entities to keep

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@ -807,6 +807,103 @@ def test_overfitting_IO_gold_entities():
assert_equal(batch_deps_1, batch_deps_2)
assert_equal(batch_deps_1, no_batch_deps)
eval = nlp.evaluate(train_examples)
assert "nel_macro_p" in eval
assert "nel_macro_r" in eval
assert "nel_macro_f" in eval
assert "nel_micro_p" in eval
assert "nel_micro_r" in eval
assert "nel_micro_f" in eval
assert "nel_f_per_type" in eval
assert "PERSON" in eval["nel_f_per_type"]
assert eval["nel_macro_f"] > 0
assert eval["nel_micro_f"] > 0
def test_overfitting_IO_with_ner():
# Simple test to try and overfit the NER and NEL component in combination - 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 NER and EL components and add them to the pipeline
ner = nlp.add_pipe("ner", first=True)
entity_linker = nlp.add_pipe("entity_linker", last=True, config={"use_gold_ents": False})
entity_linker.set_kb(create_kb)
train_examples = []
for text, annotations in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
for ent in annotations.get("entities"):
ner.add_label(ent[2])
optimizer = nlp.initialize()
# train the NER and NEL pipes
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
assert losses["ner"] < 0.001
assert losses["entity_linker"] < 0.001
# adding additional components that are required for the entity_linker
nlp.add_pipe("sentencizer", first=True)
# test the trained model
test_text = "Russ Cochran was a member of a golf team."
doc = nlp(test_text)
ents = doc.ents
assert len(ents) == 1
assert ents[0].text == "Russ Cochran"
assert ents[0].label_ == "PERSON"
assert ents[0].kb_id_ == "Q2146908"
# 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
doc2 = nlp2(test_text)
ents2 = doc2.ents
assert len(ents2) == 1
assert ents2[0].text == "Russ Cochran"
assert ents2[0].label_ == "PERSON"
assert ents2[0].kb_id_ == "Q2146908"
eval = nlp.evaluate(train_examples)
print(eval)
assert "nel_macro_f" in eval
assert "nel_micro_f" in eval
assert "ents_f" in eval
assert "nel_f_per_type" in eval
assert "ents_per_type" in eval
assert "PERSON" in eval["nel_f_per_type"]
assert "PERSON" in eval["ents_per_type"]
assert eval["nel_macro_f"] > 0
assert eval["nel_micro_f"] > 0
assert eval["ents_f"] > 0
def test_kb_serialization():
# Test that the KB can be used in a pipeline with a different vocab