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Fix entity linker batching (#9669)

Browse Source 
* Partial fix of entity linker batching

* Add import

* Better name

* Add `use_gold_ents` option, docs

* Change to v2, create stub v1, update docs etc.

* Fix error type

Honestly no idea what the right type to use here is.
ConfigValidationError seems wrong. Maybe a NotImplementedError?

* Make mypy happy

* Add hacky fix for init issue

* Add legacy pipeline entity linker

* Fix references to class name

* Add __init__.py for legacy

* Attempted fix for loss issue

* Remove placeholder V1

* formatting

* slightly more interesting train data

* Handle batches with no usable examples

This adds a test for batches that have docs but not entities, and a
check in the component that detects such cases and skips the update step
as thought the batch were empty.

* Remove todo about data verification

Check for empty data was moved further up so this should be OK now - the
case in question shouldn't be possible.

* Fix gradient calculation

The model doesn't know which entities are not in the kb, so it generates
embeddings for the context of all of them.

However, the loss does know which entities aren't in the kb, and it
ignores them, as there's no sensible gradient.

This has the issue that the gradient will not be calculated for some of
the input embeddings, which causes a dimension mismatch in backprop.
That should have caused a clear error, but with numpyops it was causing
nans to happen, which is another problem that should be addressed
separately.

This commit changes the loss to give a zero gradient for entities not in
the kb.

* add failing test for v1 EL legacy architecture

* Add nasty but simple working check for legacy arch

* Clarify why init hack works the way it does

* Clarify use_gold_ents use case

* Fix use gold ents related handling

* Add tests for no gold ents and fix other tests

* Use aligned ents function (not working)

This doesn't actually work because the "aligned" ents are gold-only. But
if I have a different function that returns the intersection, *then*
this will work as desired.

* Use proper matching ent check

This changes the process when gold ents are not used so that the
intersection of ents in the pred and gold is used.

* Move get_matching_ents to Example

* Use model attribute to check for legacy arch

* Rename flag

* bump spacy-legacy to lower 3.0.9

Co-authored-by: svlandeg <svlandeg@github.com>
This commit is contained in:
Paul O'Leary McCann 2022-03-04 17:17:36 +09:00 committed by GitHub
parent 8e93fa8507
commit 91acc3ea75
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12 changed files with 765 additions and 49 deletions
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2
requirements.txt
View File

@ -1,5 +1,5 @@
# Our libraries
spacy-legacy>=3.0.8,<3.1.0
spacy-legacy>=3.0.9,<3.1.0
spacy-loggers>=1.0.0,<2.0.0
cymem>=2.0.2,<2.1.0
preshed>=3.0.2,<3.1.0

2
setup.cfg
View File

@ -41,7 +41,7 @@ setup_requires =
thinc>=8.0.12,<8.1.0
install_requires =
# Our libraries
spacy-legacy>=3.0.8,<3.1.0
spacy-legacy>=3.0.9,<3.1.0
spacy-loggers>=1.0.0,<2.0.0
murmurhash>=0.28.0,<1.1.0
cymem>=2.0.2,<2.1.0

4
spacy/cli/templates/quickstart_training.jinja
View File

@ -131,7 +131,7 @@ incl_context = true
incl_prior = true
[components.entity_linker.model]
@architectures = "spacy.EntityLinker.v1"
@architectures = "spacy.EntityLinker.v2"
nO = null
[components.entity_linker.model.tok2vec]
@ -303,7 +303,7 @@ incl_context = true
incl_prior = true
[components.entity_linker.model]
@architectures = "spacy.EntityLinker.v1"
@architectures = "spacy.EntityLinker.v2"
nO = null
[components.entity_linker.model.tok2vec]

2
spacy/ml/extract_spans.py
View File

@ -63,4 +63,4 @@ def _get_span_indices(ops, spans: Ragged, lengths: Ints1d) -> Ints1d:
def _ensure_cpu(spans: Ragged, lengths: Ints1d) -> Tuple[Ragged, Ints1d]:
return (Ragged(to_numpy(spans.dataXd), to_numpy(spans.lengths)), to_numpy(lengths))
return Ragged(to_numpy(spans.dataXd), to_numpy(spans.lengths)), to_numpy(lengths)

60
spacy/ml/models/entity_linker.py
View File

@ -1,34 +1,82 @@
from pathlib import Path
from typing import Optional, Callable, Iterable, List
from typing import Optional, Callable, Iterable, List, Tuple
from thinc.types import Floats2d
from thinc.api import chain, clone, list2ragged, reduce_mean, residual
from thinc.api import Model, Maxout, Linear
from thinc.api import Model, Maxout, Linear, noop, tuplify, Ragged
from ...util import registry
from ...kb import KnowledgeBase, Candidate, get_candidates
from ...vocab import Vocab
from ...tokens import Span, Doc
from ..extract_spans import extract_spans
from ...errors import Errors
@registry.architectures("spacy.EntityLinker.v1")
@registry.architectures("spacy.EntityLinker.v2")
def build_nel_encoder(
tok2vec: Model, nO: Optional[int] = None
) -> Model[List[Doc], Floats2d]:
with Model.define_operators({">>": chain, "**": clone}):
with Model.define_operators({">>": chain, "&": tuplify}):
token_width = tok2vec.maybe_get_dim("nO")
output_layer = Linear(nO=nO, nI=token_width)
model = (
tok2vec
>> list2ragged()
((tok2vec >> list2ragged()) & build_span_maker())
>> extract_spans()
>> reduce_mean()
>> residual(Maxout(nO=token_width, nI=token_width, nP=2, dropout=0.0)) # type: ignore[arg-type]
>> output_layer
)
model.set_ref("output_layer", output_layer)
model.set_ref("tok2vec", tok2vec)
# flag to show this isn't legacy
model.attrs["include_span_maker"] = True
return model
def build_span_maker(n_sents: int = 0) -> Model:
model: Model = Model("span_maker", forward=span_maker_forward)
model.attrs["n_sents"] = n_sents
return model
def span_maker_forward(model, docs: List[Doc], is_train) -> Tuple[Ragged, Callable]:
ops = model.ops
n_sents = model.attrs["n_sents"]
candidates = []
for doc in docs:
cands = []
try:
sentences = [s for s in doc.sents]
except ValueError:
# no sentence info, normal in initialization
for tok in doc:
tok.is_sent_start = tok.i == 0
sentences = [doc[:]]
for ent in doc.ents:
try:
# find the sentence in the list of sentences.
sent_index = sentences.index(ent.sent)
except AttributeError:
# Catch the exception when ent.sent is None and provide a user-friendly warning
raise RuntimeError(Errors.E030) from None
# get n previous sentences, if there are any
start_sentence = max(0, sent_index - n_sents)
# get n posterior sentences, or as many < n as there are
end_sentence = min(len(sentences) - 1, sent_index + n_sents)
# get token positions
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
# save positions for extraction
cands.append((start_token, end_token))
candidates.append(ops.asarray2i(cands))
candlens = ops.asarray1i([len(cands) for cands in candidates])
candidates = ops.xp.concatenate(candidates)
outputs = Ragged(candidates, candlens)
# because this is just rearranging docs, the backprop does nothing
return outputs, lambda x: []
@registry.misc("spacy.KBFromFile.v1")
def load_kb(kb_path: Path) -> Callable[[Vocab], KnowledgeBase]:
def kb_from_file(vocab):

135
spacy/pipeline/entity_linker.py
View File

@ -6,17 +6,17 @@ import srsly
import random
from thinc.api import CosineDistance, Model, Optimizer, Config
from thinc.api import set_dropout_rate
import warnings
from ..kb import KnowledgeBase, Candidate
from ..ml import empty_kb
from ..tokens import Doc, Span
from .pipe import deserialize_config
from .legacy.entity_linker import EntityLinker_v1
from .trainable_pipe import TrainablePipe
from ..language import Language
from ..vocab import Vocab
from ..training import Example, validate_examples, validate_get_examples
from ..errors import Errors, Warnings
from ..errors import Errors
from ..util import SimpleFrozenList, registry
from .. import util
from ..scorer import Scorer
@ -26,7 +26,7 @@ BACKWARD_OVERWRITE = True
default_model_config = """
[model]
@architectures = "spacy.EntityLinker.v1"
@architectures = "spacy.EntityLinker.v2"
[model.tok2vec]
@architectures = "spacy.HashEmbedCNN.v2"
@ -55,6 +55,7 @@ DEFAULT_NEL_MODEL = Config().from_str(default_model_config)["model"]
"get_candidates": {"@misc": "spacy.CandidateGenerator.v1"},
"overwrite": True,
"scorer": {"@scorers": "spacy.entity_linker_scorer.v1"},
"use_gold_ents": True,
},
default_score_weights={
"nel_micro_f": 1.0,
@ -75,6 +76,7 @@ def make_entity_linker(
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
overwrite: bool,
scorer: Optional[Callable],
use_gold_ents: bool,
):
"""Construct an EntityLinker component.
@ -90,6 +92,22 @@ def make_entity_linker(
produces a list of candidates, given a certain knowledge base and a textual mention.
scorer (Optional[Callable]): The scoring method.
"""
if not model.attrs.get("include_span_maker", False):
# The only difference in arguments here is that use_gold_ents is not available
return EntityLinker_v1(
nlp.vocab,
model,
name,
labels_discard=labels_discard,
n_sents=n_sents,
incl_prior=incl_prior,
incl_context=incl_context,
entity_vector_length=entity_vector_length,
get_candidates=get_candidates,
overwrite=overwrite,
scorer=scorer,
)
return EntityLinker(
nlp.vocab,
model,
@ -102,6 +120,7 @@ def make_entity_linker(
get_candidates=get_candidates,
overwrite=overwrite,
scorer=scorer,
use_gold_ents=use_gold_ents,
)
@ -136,6 +155,7 @@ class EntityLinker(TrainablePipe):
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
overwrite: bool = BACKWARD_OVERWRITE,
scorer: Optional[Callable] = entity_linker_score,
use_gold_ents: bool,
) -> None:
"""Initialize an entity linker.
@ -152,6 +172,8 @@ class EntityLinker(TrainablePipe):
produces a list of candidates, given a certain knowledge base and a textual mention.
scorer (Optional[Callable]): The scoring method. Defaults to
Scorer.score_links.
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
component must provide entity annotations.
DOCS: https://spacy.io/api/entitylinker#init
"""
@ -169,6 +191,7 @@ class EntityLinker(TrainablePipe):
# create an empty KB by default. If you want to load a predefined one, specify it in 'initialize'.
self.kb = empty_kb(entity_vector_length)(self.vocab)
self.scorer = scorer
self.use_gold_ents = use_gold_ents
def set_kb(self, kb_loader: Callable[[Vocab], KnowledgeBase]):
"""Define the KB of this pipe by providing a function that will
@ -212,14 +235,48 @@ class EntityLinker(TrainablePipe):
doc_sample = []
vector_sample = []
for example in islice(get_examples(), 10):
doc_sample.append(example.x)
doc = example.x
if self.use_gold_ents:
doc.ents = example.y.ents
doc_sample.append(doc)
vector_sample.append(self.model.ops.alloc1f(nO))
assert len(doc_sample) > 0, Errors.E923.format(name=self.name)
assert len(vector_sample) > 0, Errors.E923.format(name=self.name)
# XXX In order for size estimation to work, there has to be at least
# one entity. It's not used for training so it doesn't have to be real,
# so we add a fake one if none are present.
# We can't use Doc.has_annotation here because it can be True for docs
# that have been through an NER component but got no entities.
has_annotations = any([doc.ents for doc in doc_sample])
if not has_annotations:
doc = doc_sample[0]
ent = doc[0:1]
ent.label_ = "XXX"
doc.ents = (ent,)
self.model.initialize(
X=doc_sample, Y=self.model.ops.asarray(vector_sample, dtype="float32")
)
if not has_annotations:
# Clean up dummy annotation
doc.ents = []
def batch_has_learnable_example(self, examples):
"""Check if a batch contains a learnable example.
If one isn't present, then the update step needs to be skipped.
"""
for eg in examples:
for ent in eg.predicted.ents:
candidates = list(self.get_candidates(self.kb, ent))
if candidates:
return True
return False
def update(
self,
examples: Iterable[Example],
@ -247,35 +304,29 @@ class EntityLinker(TrainablePipe):
if not examples:
return losses
validate_examples(examples, "EntityLinker.update")
sentence_docs = []
for eg in examples:
sentences = [s for s in eg.reference.sents]
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
for ent in eg.reference.ents:
# KB ID of the first token is the same as the whole span
kb_id = kb_ids[ent.start]
if kb_id:
try:
# find the sentence in the list of sentences.
sent_index = sentences.index(ent.sent)
except AttributeError:
# Catch the exception when ent.sent is None and provide a user-friendly warning
raise RuntimeError(Errors.E030) from None
# get n previous sentences, if there are any
start_sentence = max(0, sent_index - self.n_sents)
# get n posterior sentences, or as many < n as there are
end_sentence = min(len(sentences) - 1, sent_index + self.n_sents)
# get token positions
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
# append that span as a doc to training
sent_doc = eg.predicted[start_token:end_token].as_doc()
sentence_docs.append(sent_doc)
set_dropout_rate(self.model, drop)
if not sentence_docs:
warnings.warn(Warnings.W093.format(name="Entity Linker"))
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:
doc.ents = ex.reference.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
sentence_encodings, bp_context = self.model.begin_update(sentence_docs)
sentence_encodings, bp_context = self.model.begin_update(docs)
# now restore the ents
for doc, old in zip(docs, old_ents):
doc.ents = old
loss, d_scores = self.get_loss(
sentence_encodings=sentence_encodings, examples=examples
)
@ -288,24 +339,38 @@ class EntityLinker(TrainablePipe):
def get_loss(self, examples: Iterable[Example], sentence_encodings: Floats2d):
validate_examples(examples, "EntityLinker.get_loss")
entity_encodings = []
eidx = 0 # indices in gold entities to keep
keep_ents = [] # indices in sentence_encodings to keep
for eg in examples:
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
for ent in eg.reference.ents:
kb_id = kb_ids[ent.start]
if kb_id:
entity_encoding = self.kb.get_vector(kb_id)
entity_encodings.append(entity_encoding)
keep_ents.append(eidx)
eidx += 1
entity_encodings = self.model.ops.asarray(entity_encodings, dtype="float32")
if sentence_encodings.shape != entity_encodings.shape:
selected_encodings = sentence_encodings[keep_ents]
# If the entity encodings list is empty, then
if selected_encodings.shape != entity_encodings.shape:
err = Errors.E147.format(
method="get_loss", msg="gold entities do not match up"
)
raise RuntimeError(err)
# TODO: fix typing issue here
gradients = self.distance.get_grad(sentence_encodings, entity_encodings) # type: ignore
loss = self.distance.get_loss(sentence_encodings, entity_encodings) # type: ignore
gradients = self.distance.get_grad(selected_encodings, entity_encodings) # type: ignore
# to match the input size, we need to give a zero gradient for items not in the kb
out = self.model.ops.alloc2f(*sentence_encodings.shape)
out[keep_ents] = gradients
loss = self.distance.get_loss(selected_encodings, entity_encodings) # type: ignore
loss = loss / len(entity_encodings)
return float(loss), gradients
return float(loss), out
def predict(self, docs: Iterable[Doc]) -> List[str]:
"""Apply the pipeline's model to a batch of docs, without modifying them.

3
spacy/pipeline/legacy/__init__.py Normal file
View File

@ -0,0 +1,3 @@
from .entity_linker import EntityLinker_v1
__all__ = ["EntityLinker_v1"]

427
spacy/pipeline/legacy/entity_linker.py Normal file
View File

@ -0,0 +1,427 @@
# This file is present to provide a prior version of the EntityLinker component
# for backwards compatability. For details see #9669.
from typing import Optional, Iterable, Callable, Dict, Union, List, Any
from thinc.types import Floats2d
from pathlib import Path
from itertools import islice
import srsly
import random
from thinc.api import CosineDistance, Model, Optimizer, Config
from thinc.api import set_dropout_rate
import warnings
from ...kb import KnowledgeBase, Candidate
from ...ml import empty_kb
from ...tokens import Doc, Span
from ..pipe import deserialize_config
from ..trainable_pipe import TrainablePipe
from ...language import Language
from ...vocab import Vocab
from ...training import Example, validate_examples, validate_get_examples
from ...errors import Errors, Warnings
from ...util import SimpleFrozenList, registry
from ... import util
from ...scorer import Scorer
# See #9050
BACKWARD_OVERWRITE = True
def entity_linker_score(examples, **kwargs):
return Scorer.score_links(examples, negative_labels=[EntityLinker_v1.NIL], **kwargs)
class EntityLinker_v1(TrainablePipe):
"""Pipeline component for named entity linking.
DOCS: https://spacy.io/api/entitylinker
"""
NIL = "NIL" # string used to refer to a non-existing link
def __init__(
self,
vocab: Vocab,
model: Model,
name: str = "entity_linker",
*,
labels_discard: Iterable[str],
n_sents: int,
incl_prior: bool,
incl_context: bool,
entity_vector_length: int,
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
overwrite: bool = BACKWARD_OVERWRITE,
scorer: Optional[Callable] = entity_linker_score,
) -> None:
"""Initialize an entity linker.
vocab (Vocab): The shared vocabulary.
model (thinc.api.Model): The Thinc Model powering the pipeline component.
name (str): The component instance name, used to add entries to the
losses during training.
labels_discard (Iterable[str]): NER labels that will automatically get a "NIL" prediction.
n_sents (int): The number of neighbouring sentences to take into account.
incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
incl_context (bool): Whether or not to include the local context in the model.
entity_vector_length (int): Size of encoding vectors in the KB.
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
produces a list of candidates, given a certain knowledge base and a textual mention.
scorer (Optional[Callable]): The scoring method. Defaults to
Scorer.score_links.
DOCS: https://spacy.io/api/entitylinker#init
"""
self.vocab = vocab
self.model = model
self.name = name
self.labels_discard = list(labels_discard)
self.n_sents = n_sents
self.incl_prior = incl_prior
self.incl_context = incl_context
self.get_candidates = get_candidates
self.cfg: Dict[str, Any] = {"overwrite": overwrite}
self.distance = CosineDistance(normalize=False)
# how many neighbour sentences to take into account
# create an empty KB by default. If you want to load a predefined one, specify it in 'initialize'.
self.kb = empty_kb(entity_vector_length)(self.vocab)
self.scorer = scorer
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."""
if not callable(kb_loader):
raise ValueError(Errors.E885.format(arg_type=type(kb_loader)))
self.kb = kb_loader(self.vocab)
def validate_kb(self) -> None:
# Raise an error if the knowledge base is not initialized.
if self.kb is None:
raise ValueError(Errors.E1018.format(name=self.name))
if len(self.kb) == 0:
raise ValueError(Errors.E139.format(name=self.name))
def initialize(
self,
get_examples: Callable[[], Iterable[Example]],
*,
nlp: Optional[Language] = None,
kb_loader: Optional[Callable[[Vocab], KnowledgeBase]] = None,
):
"""Initialize the pipe for training, using a representative set
of data examples.
get_examples (Callable[[], Iterable[Example]]): Function that
returns a representative sample of gold-standard Example objects.
nlp (Language): The current nlp object the component is part of.
kb_loader (Callable[[Vocab], KnowledgeBase]): A function that creates a KnowledgeBase from a Vocab instance.
Note that providing this argument, will overwrite all data accumulated in the current KB.
Use this only when loading a KB as-such from file.
DOCS: https://spacy.io/api/entitylinker#initialize
"""
validate_get_examples(get_examples, "EntityLinker_v1.initialize")
if kb_loader is not None:
self.set_kb(kb_loader)
self.validate_kb()
nO = self.kb.entity_vector_length
doc_sample = []
vector_sample = []
for example in islice(get_examples(), 10):
doc_sample.append(example.x)
vector_sample.append(self.model.ops.alloc1f(nO))
assert len(doc_sample) > 0, Errors.E923.format(name=self.name)
assert len(vector_sample) > 0, Errors.E923.format(name=self.name)
self.model.initialize(
X=doc_sample, Y=self.model.ops.asarray(vector_sample, dtype="float32")
)
def update(
self,
examples: Iterable[Example],
*,
drop: float = 0.0,
sgd: Optional[Optimizer] = None,
losses: Optional[Dict[str, float]] = None,
) -> Dict[str, float]:
"""Learn from a batch of documents and gold-standard information,
updating the pipe's model. Delegates to predict and get_loss.
examples (Iterable[Example]): A batch of Example objects.
drop (float): The dropout rate.
sgd (thinc.api.Optimizer): The optimizer.
losses (Dict[str, float]): Optional record of the loss during training.
Updated using the component name as the key.
RETURNS (Dict[str, float]): The updated losses dictionary.
DOCS: https://spacy.io/api/entitylinker#update
"""
self.validate_kb()
if losses is None:
losses = {}
losses.setdefault(self.name, 0.0)
if not examples:
return losses
validate_examples(examples, "EntityLinker_v1.update")
sentence_docs = []
for eg in examples:
sentences = [s for s in eg.reference.sents]
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
for ent in eg.reference.ents:
# KB ID of the first token is the same as the whole span
kb_id = kb_ids[ent.start]
if kb_id:
try:
# find the sentence in the list of sentences.
sent_index = sentences.index(ent.sent)
except AttributeError:
# Catch the exception when ent.sent is None and provide a user-friendly warning
raise RuntimeError(Errors.E030) from None
# get n previous sentences, if there are any
start_sentence = max(0, sent_index - self.n_sents)
# get n posterior sentences, or as many < n as there are
end_sentence = min(len(sentences) - 1, sent_index + self.n_sents)
# get token positions
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
# append that span as a doc to training
sent_doc = eg.predicted[start_token:end_token].as_doc()
sentence_docs.append(sent_doc)
set_dropout_rate(self.model, drop)
if not sentence_docs:
warnings.warn(Warnings.W093.format(name="Entity Linker"))
return losses
sentence_encodings, bp_context = self.model.begin_update(sentence_docs)
loss, d_scores = self.get_loss(
sentence_encodings=sentence_encodings, examples=examples
)
bp_context(d_scores)
if sgd is not None:
self.finish_update(sgd)
losses[self.name] += loss
return losses
def get_loss(self, examples: Iterable[Example], sentence_encodings: Floats2d):
validate_examples(examples, "EntityLinker_v1.get_loss")
entity_encodings = []
for eg in examples:
kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
for ent in eg.reference.ents:
kb_id = kb_ids[ent.start]
if kb_id:
entity_encoding = self.kb.get_vector(kb_id)
entity_encodings.append(entity_encoding)
entity_encodings = self.model.ops.asarray(entity_encodings, dtype="float32")
if sentence_encodings.shape != entity_encodings.shape:
err = Errors.E147.format(
method="get_loss", msg="gold entities do not match up"
)
raise RuntimeError(err)
# TODO: fix typing issue here
gradients = self.distance.get_grad(sentence_encodings, entity_encodings) # type: ignore
loss = self.distance.get_loss(sentence_encodings, entity_encodings) # type: ignore
loss = loss / len(entity_encodings)
return float(loss), gradients
def predict(self, docs: Iterable[Doc]) -> List[str]:
"""Apply the pipeline's model to a batch of docs, without modifying them.
Returns the KB IDs for each entity in each doc, including NIL if there is
no prediction.
docs (Iterable[Doc]): The documents to predict.
RETURNS (List[str]): The models prediction for each document.
DOCS: https://spacy.io/api/entitylinker#predict
"""
self.validate_kb()
entity_count = 0
final_kb_ids: List[str] = []
if not docs:
return final_kb_ids
if isinstance(docs, Doc):
docs = [docs]
for i, doc in enumerate(docs):
sentences = [s for s in doc.sents]
if len(doc) > 0:
# Looping through each entity (TODO: rewrite)
for ent in doc.ents:
sent = ent.sent
sent_index = sentences.index(sent)
assert sent_index >= 0
# get n_neighbour sentences, clipped to the length of the document
start_sentence = max(0, sent_index - self.n_sents)
end_sentence = min(len(sentences) - 1, sent_index + self.n_sents)
start_token = sentences[start_sentence].start
end_token = sentences[end_sentence].end
sent_doc = doc[start_token:end_token].as_doc()
# currently, the context is the same for each entity in a sentence (should be refined)
xp = self.model.ops.xp
if self.incl_context:
sentence_encoding = self.model.predict([sent_doc])[0]
sentence_encoding_t = sentence_encoding.T
sentence_norm = xp.linalg.norm(sentence_encoding_t)
entity_count += 1
if ent.label_ in self.labels_discard:
# ignoring this entity - setting to NIL
final_kb_ids.append(self.NIL)
else:
candidates = list(self.get_candidates(self.kb, ent))
if not candidates:
# no prediction possible for this entity - setting to NIL
final_kb_ids.append(self.NIL)
elif len(candidates) == 1:
# shortcut for efficiency reasons: take the 1 candidate
# TODO: thresholding
final_kb_ids.append(candidates[0].entity_)
else:
random.shuffle(candidates)
# set all prior probabilities to 0 if incl_prior=False
prior_probs = xp.asarray([c.prior_prob for c in candidates])
if not self.incl_prior:
prior_probs = xp.asarray([0.0 for _ in candidates])
scores = prior_probs
# add in similarity from the context
if self.incl_context:
entity_encodings = xp.asarray(
[c.entity_vector for c in candidates]
)
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
if len(entity_encodings) != len(prior_probs):
raise RuntimeError(
Errors.E147.format(
method="predict",
msg="vectors not of equal length",
)
)
# cosine similarity
sims = xp.dot(entity_encodings, sentence_encoding_t) / (
sentence_norm * entity_norm
)
if sims.shape != prior_probs.shape:
raise ValueError(Errors.E161)
scores = prior_probs + sims - (prior_probs * sims)
# TODO: thresholding
best_index = scores.argmax().item()
best_candidate = candidates[best_index]
final_kb_ids.append(best_candidate.entity_)
if not (len(final_kb_ids) == entity_count):
err = Errors.E147.format(
method="predict", msg="result variables not of equal length"
)
raise RuntimeError(err)
return final_kb_ids
def set_annotations(self, docs: Iterable[Doc], kb_ids: List[str]) -> None:
"""Modify a batch of documents, using pre-computed scores.
docs (Iterable[Doc]): The documents to modify.
kb_ids (List[str]): The IDs to set, produced by EntityLinker.predict.
DOCS: https://spacy.io/api/entitylinker#set_annotations
"""
count_ents = len([ent for doc in docs for ent in doc.ents])
if count_ents != len(kb_ids):
raise ValueError(Errors.E148.format(ents=count_ents, ids=len(kb_ids)))
i = 0
overwrite = self.cfg["overwrite"]
for doc in docs:
for ent in doc.ents:
kb_id = kb_ids[i]
i += 1
for token in ent:
if token.ent_kb_id == 0 or overwrite:
token.ent_kb_id_ = kb_id
def to_bytes(self, *, exclude=tuple()):
"""Serialize the pipe to a bytestring.
exclude (Iterable[str]): String names of serialization fields to exclude.
RETURNS (bytes): The serialized object.
DOCS: https://spacy.io/api/entitylinker#to_bytes
"""
self._validate_serialization_attrs()
serialize = {}
if hasattr(self, "cfg") and self.cfg is not None:
serialize["cfg"] = lambda: srsly.json_dumps(self.cfg)
serialize["vocab"] = lambda: self.vocab.to_bytes(exclude=exclude)
serialize["kb"] = self.kb.to_bytes
serialize["model"] = self.model.to_bytes
return util.to_bytes(serialize, exclude)
def from_bytes(self, bytes_data, *, exclude=tuple()):
"""Load the pipe from a bytestring.
exclude (Iterable[str]): String names of serialization fields to exclude.
RETURNS (TrainablePipe): The loaded object.
DOCS: https://spacy.io/api/entitylinker#from_bytes
"""
self._validate_serialization_attrs()
def load_model(b):
try:
self.model.from_bytes(b)
except AttributeError:
raise ValueError(Errors.E149) from None
deserialize = {}
if hasattr(self, "cfg") and self.cfg is not None:
deserialize["cfg"] = lambda b: self.cfg.update(srsly.json_loads(b))
deserialize["vocab"] = lambda b: self.vocab.from_bytes(b, exclude=exclude)
deserialize["kb"] = lambda b: self.kb.from_bytes(b)
deserialize["model"] = load_model
util.from_bytes(bytes_data, deserialize, exclude)
return self
def to_disk(
self, path: Union[str, Path], *, exclude: Iterable[str] = SimpleFrozenList()
) -> None:
"""Serialize the pipe to disk.
path (str / Path): Path to a directory.
exclude (Iterable[str]): String names of serialization fields to exclude.
DOCS: https://spacy.io/api/entitylinker#to_disk
"""
serialize = {}
serialize["vocab"] = lambda p: self.vocab.to_disk(p, exclude=exclude)
serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg)
serialize["kb"] = lambda p: self.kb.to_disk(p)
serialize["model"] = lambda p: self.model.to_disk(p)
util.to_disk(path, serialize, exclude)
def from_disk(
self, path: Union[str, Path], *, exclude: Iterable[str] = SimpleFrozenList()
) -> "EntityLinker_v1":
"""Load the pipe from disk. Modifies the object in place and returns it.
path (str / Path): Path to a directory.
exclude (Iterable[str]): String names of serialization fields to exclude.
RETURNS (EntityLinker): The modified EntityLinker object.
DOCS: https://spacy.io/api/entitylinker#from_disk
"""
def load_model(p):
try:
with p.open("rb") as infile:
self.model.from_bytes(infile.read())
except AttributeError:
raise ValueError(Errors.E149) from None
deserialize: Dict[str, Callable[[Any], Any]] = {}
deserialize["cfg"] = lambda p: self.cfg.update(deserialize_config(p))
deserialize["vocab"] = lambda p: self.vocab.from_disk(p, exclude=exclude)
deserialize["kb"] = lambda p: self.kb.from_disk(p)
deserialize["model"] = load_model
util.from_disk(path, deserialize, exclude)
return self
def rehearse(self, examples, *, sgd=None, losses=None, **config):
raise NotImplementedError
def add_label(self, label):
raise NotImplementedError

151
spacy/tests/pipeline/test_entity_linker.py
View File

@ -9,6 +9,9 @@ from spacy.compat import pickle
from spacy.kb import Candidate, KnowledgeBase, get_candidates
from spacy.lang.en import English
from spacy.ml import load_kb
from spacy.pipeline import EntityLinker
from spacy.pipeline.legacy import EntityLinker_v1
from spacy.pipeline.tok2vec import DEFAULT_TOK2VEC_MODEL
from spacy.scorer import Scorer
from spacy.tests.util import make_tempdir
from spacy.tokens import Span
@ -168,6 +171,45 @@ def test_issue7065_b():
assert doc
def test_no_entities():
# Test that having no entities doesn't crash the model
TRAIN_DATA = [
(
"The sky is blue.",
{
"sent_starts": [1, 0, 0, 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))
def create_kb(vocab):
# create artificial KB
mykb = KnowledgeBase(vocab, entity_vector_length=vector_length)
mykb.add_entity(entity="Q2146908", freq=12, entity_vector=[6, -4, 3])
mykb.add_alias("Russ Cochran", ["Q2146908"], [0.9])
return mykb
# Create and train the Entity Linker
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)
# 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
results = nlp.evaluate(train_examples)
def test_partial_links():
# Test that having some entities on the doc without gold links, doesn't crash
TRAIN_DATA = [
@ -650,7 +692,7 @@ TRAIN_DATA = [
"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")],
"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}},
@ -693,6 +735,7 @@ def test_overfitting_IO():
# 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
@ -922,3 +965,109 @@ def test_scorer_links():
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 = KnowledgeBase(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)
def create_kb(vocab):
# create artificial KB
mykb = KnowledgeBase(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 == 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
results = nlp.evaluate(train_examples)

23
spacy/training/example.pyx
View File

@ -256,6 +256,29 @@ cdef class Example:
x_ents, x_tags = self.get_aligned_ents_and_ner()
return x_tags
def get_matching_ents(self, check_label=True):
"""Return entities that are shared between predicted and reference docs.
If `check_label` is True, entities must have matching labels to be
kept. Otherwise only the character indices need to match.
"""
gold = {}
for ent in self.reference:
gold[(ent.start_char, ent.end_char)] = ent.label
keep = []
for ent in self.predicted:
key = (ent.start_char, ent.end_char)
if key not in gold:
continue
if check_label and ent.label != gold[key]:
continue
keep.append(ent)
return keep
def to_dict(self):
return {
"doc_annotation": {

4
website/docs/api/architectures.md
View File

@ -858,13 +858,13 @@ into the "real world". This requires 3 main components:
- A machine learning [`Model`](https://thinc.ai/docs/api-model) that picks the
most plausible ID from the set of candidates.
### spacy.EntityLinker.v1 {#EntityLinker}
### spacy.EntityLinker.v2 {#EntityLinker}
> #### Example Config
>
> ```ini
> [model]
> @architectures = "spacy.EntityLinker.v1"
> @architectures = "spacy.EntityLinker.v2"
> nO = null
>
> [model.tok2vec]

1
website/docs/api/entitylinker.md
View File

@ -59,6 +59,7 @@ architectures and their arguments and hyperparameters.
| `incl_context` | Whether or not to include the local context in the model. Defaults to `True`. ~~bool~~ |
| `model` | The [`Model`](https://thinc.ai/docs/api-model) powering the pipeline component. Defaults to [EntityLinker](/api/architectures#EntityLinker). ~~Model~~ |
| `entity_vector_length` | Size of encoding vectors in the KB. Defaults to `64`. ~~int~~ |
| `use_gold_ents` | Whether to copy entities from the gold docs or not. Defaults to `True`. If `False`, entities must be set in the training data or by an annotating component in the pipeline. ~~int~~ |
| `get_candidates` | Function that generates plausible candidates for a given `Span` object. Defaults to [CandidateGenerator](/api/architectures#CandidateGenerator), a function looking up exact, case-dependent aliases in the KB. ~~Callable[[KnowledgeBase, Span], Iterable[Candidate]]~~ |
| `overwrite` <Tag variant="new">3.2</Tag> | Whether existing annotation is overwritten. Defaults to `True`. ~~bool~~ |
| `scorer` <Tag variant="new">3.2</Tag> | The scoring method. Defaults to [`Scorer.score_links`](/api/scorer#score_links). ~~Optional[Callable]~~ |