423 lines
18 KiB
Python
423 lines
18 KiB
Python
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# This file is present to provide a prior version of the EntityLinker component
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# for backwards compatability. For details see #9669.
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from typing import Optional, Iterable, Callable, Dict, Union, List, Any
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from thinc.types import Floats2d
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from pathlib import Path
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from itertools import islice
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import srsly
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import random
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from thinc.api import CosineDistance, Model, Optimizer
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from thinc.api import set_dropout_rate
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import warnings
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from spacy.kb import KnowledgeBase, Candidate
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from spacy.ml import empty_kb
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from spacy.tokens import Doc, Span
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from spacy.pipeline.pipe import deserialize_config
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from spacy.pipeline.trainable_pipe import TrainablePipe
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from spacy.language import Language
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from spacy.vocab import Vocab
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from spacy.training import Example, validate_examples, validate_get_examples
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from spacy.errors import Errors, Warnings
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from spacy.util import SimpleFrozenList
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from spacy import util
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from spacy.scorer import Scorer
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# See #9050
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BACKWARD_OVERWRITE = True
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def entity_linker_score(examples, **kwargs):
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return Scorer.score_links(examples, negative_labels=[EntityLinker_v1.NIL], **kwargs)
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class EntityLinker_v1(TrainablePipe):
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"""Pipeline component for named entity linking.
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DOCS: https://spacy.io/api/entitylinker
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"""
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NIL = "NIL" # string used to refer to a non-existing link
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def __init__(
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self,
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vocab: Vocab,
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model: Model,
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name: str = "entity_linker",
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*,
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labels_discard: Iterable[str],
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n_sents: int,
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incl_prior: bool,
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incl_context: bool,
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entity_vector_length: int,
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get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
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overwrite: bool = BACKWARD_OVERWRITE,
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scorer: Optional[Callable] = entity_linker_score,
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) -> None:
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"""Initialize an entity linker.
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vocab (Vocab): The shared vocabulary.
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model (thinc.api.Model): The Thinc Model powering the pipeline component.
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name (str): The component instance name, used to add entries to the
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losses during training.
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labels_discard (Iterable[str]): NER labels that will automatically get a "NIL" prediction.
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n_sents (int): The number of neighbouring sentences to take into account.
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incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
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incl_context (bool): Whether or not to include the local context in the model.
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entity_vector_length (int): Size of encoding vectors in the KB.
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get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
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produces a list of candidates, given a certain knowledge base and a textual mention.
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scorer (Optional[Callable]): The scoring method. Defaults to Scorer.score_links.
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DOCS: https://spacy.io/api/entitylinker#init
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"""
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self.vocab = vocab
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self.model = model
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self.name = name
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self.labels_discard = list(labels_discard)
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self.n_sents = n_sents
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self.incl_prior = incl_prior
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self.incl_context = incl_context
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self.get_candidates = get_candidates
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self.cfg: Dict[str, Any] = {"overwrite": overwrite}
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self.distance = CosineDistance(normalize=False)
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# how many neighbour sentences to take into account
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# create an empty KB by default. If you want to load a predefined one, specify it in 'initialize'.
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self.kb = empty_kb(entity_vector_length)(self.vocab)
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self.scorer = scorer
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def set_kb(self, kb_loader: Callable[[Vocab], KnowledgeBase]):
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"""Define the KB of this pipe by providing a function that will
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create it using this object's vocab."""
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if not callable(kb_loader):
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raise ValueError(Errors.E885.format(arg_type=type(kb_loader)))
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self.kb = kb_loader(self.vocab)
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def validate_kb(self) -> None:
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# Raise an error if the knowledge base is not initialized.
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if self.kb is None:
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raise ValueError(Errors.E1018.format(name=self.name))
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if len(self.kb) == 0:
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raise ValueError(Errors.E139.format(name=self.name))
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def initialize(
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self,
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get_examples: Callable[[], Iterable[Example]],
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*,
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nlp: Optional[Language] = None,
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kb_loader: Optional[Callable[[Vocab], KnowledgeBase]] = None,
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):
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"""Initialize the pipe for training, using a representative set
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of data examples.
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get_examples (Callable[[], Iterable[Example]]): Function that
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returns a representative sample of gold-standard Example objects.
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nlp (Language): The current nlp object the component is part of.
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kb_loader (Callable[[Vocab], KnowledgeBase]): A function that creates an InMemoryLookupKB from a Vocab instance.
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Note that providing this argument, will overwrite all data accumulated in the current KB.
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Use this only when loading a KB as-such from file.
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DOCS: https://spacy.io/api/entitylinker#initialize
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"""
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validate_get_examples(get_examples, "EntityLinker_v1.initialize")
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if kb_loader is not None:
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self.set_kb(kb_loader)
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self.validate_kb()
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nO = self.kb.entity_vector_length
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doc_sample = []
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vector_sample = []
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for example in islice(get_examples(), 10):
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doc_sample.append(example.x)
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vector_sample.append(self.model.ops.alloc1f(nO))
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assert len(doc_sample) > 0, Errors.E923.format(name=self.name)
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assert len(vector_sample) > 0, Errors.E923.format(name=self.name)
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self.model.initialize(
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X=doc_sample, Y=self.model.ops.asarray(vector_sample, dtype="float32")
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)
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def update(
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self,
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examples: Iterable[Example],
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*,
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drop: float = 0.0,
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sgd: Optional[Optimizer] = None,
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losses: Optional[Dict[str, float]] = None,
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) -> Dict[str, float]:
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"""Learn from a batch of documents and gold-standard information,
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updating the pipe's model. Delegates to predict and get_loss.
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examples (Iterable[Example]): A batch of Example objects.
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drop (float): The dropout rate.
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sgd (thinc.api.Optimizer): The optimizer.
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losses (Dict[str, float]): Optional record of the loss during training.
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Updated using the component name as the key.
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RETURNS (Dict[str, float]): The updated losses dictionary.
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DOCS: https://spacy.io/api/entitylinker#update
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"""
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self.validate_kb()
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if losses is None:
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losses = {}
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losses.setdefault(self.name, 0.0)
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if not examples:
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return losses
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validate_examples(examples, "EntityLinker_v1.update")
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sentence_docs = []
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for eg in examples:
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sentences = [s for s in eg.reference.sents]
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kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
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for ent in eg.reference.ents:
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# KB ID of the first token is the same as the whole span
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kb_id = kb_ids[ent.start]
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if kb_id:
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try:
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# find the sentence in the list of sentences.
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sent_index = sentences.index(ent.sent)
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except AttributeError:
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# Catch the exception when ent.sent is None and provide a user-friendly warning
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raise RuntimeError(Errors.E030) from None
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# get n previous sentences, if there are any
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start_sentence = max(0, sent_index - self.n_sents)
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# get n posterior sentences, or as many < n as there are
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end_sentence = min(len(sentences) - 1, sent_index + self.n_sents)
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# get token positions
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start_token = sentences[start_sentence].start
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end_token = sentences[end_sentence].end
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# append that span as a doc to training
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sent_doc = eg.predicted[start_token:end_token].as_doc()
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sentence_docs.append(sent_doc)
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set_dropout_rate(self.model, drop)
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if not sentence_docs:
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warnings.warn(Warnings.W093.format(name="Entity Linker"))
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return losses
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sentence_encodings, bp_context = self.model.begin_update(sentence_docs)
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loss, d_scores = self.get_loss(
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sentence_encodings=sentence_encodings, examples=examples
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)
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bp_context(d_scores)
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if sgd is not None:
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self.finish_update(sgd)
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losses[self.name] += loss
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return losses
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def get_loss(self, examples: Iterable[Example], sentence_encodings: Floats2d):
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validate_examples(examples, "EntityLinker_v1.get_loss")
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entity_encodings = []
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for eg in examples:
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kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True)
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for ent in eg.reference.ents:
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kb_id = kb_ids[ent.start]
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if kb_id:
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entity_encoding = self.kb.get_vector(kb_id)
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entity_encodings.append(entity_encoding)
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entity_encodings = self.model.ops.asarray2f(entity_encodings)
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if sentence_encodings.shape != entity_encodings.shape:
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err = Errors.E147.format(
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method="get_loss", msg="gold entities do not match up"
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)
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raise RuntimeError(err)
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gradients = self.distance.get_grad(sentence_encodings, entity_encodings)
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loss = self.distance.get_loss(sentence_encodings, entity_encodings)
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loss = loss / len(entity_encodings)
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return float(loss), gradients
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def predict(self, docs: Iterable[Doc]) -> List[str]:
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"""Apply the pipeline's model to a batch of docs, without modifying them.
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Returns the KB IDs for each entity in each doc, including NIL if there is
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no prediction.
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docs (Iterable[Doc]): The documents to predict.
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RETURNS (List[str]): The models prediction for each document.
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DOCS: https://spacy.io/api/entitylinker#predict
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"""
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self.validate_kb()
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entity_count = 0
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final_kb_ids: List[str] = []
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if not docs:
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return final_kb_ids
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if isinstance(docs, Doc):
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docs = [docs]
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for i, doc in enumerate(docs):
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sentences = [s for s in doc.sents]
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if len(doc) > 0:
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# Looping through each entity (TODO: rewrite)
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for ent in doc.ents:
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sent = ent.sent
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sent_index = sentences.index(sent)
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assert sent_index >= 0
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# get n_neighbour sentences, clipped to the length of the document
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start_sentence = max(0, sent_index - self.n_sents)
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end_sentence = min(len(sentences) - 1, sent_index + self.n_sents)
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start_token = sentences[start_sentence].start
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end_token = sentences[end_sentence].end
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sent_doc = doc[start_token:end_token].as_doc()
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# currently, the context is the same for each entity in a sentence (should be refined)
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xp = self.model.ops.xp
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if self.incl_context:
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sentence_encoding = self.model.predict([sent_doc])[0]
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sentence_encoding_t = sentence_encoding.T
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sentence_norm = xp.linalg.norm(sentence_encoding_t)
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entity_count += 1
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if ent.label_ in self.labels_discard:
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# ignoring this entity - setting to NIL
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final_kb_ids.append(self.NIL)
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else:
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candidates = list(self.get_candidates(self.kb, ent))
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if not candidates:
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# no prediction possible for this entity - setting to NIL
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final_kb_ids.append(self.NIL)
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elif len(candidates) == 1:
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# shortcut for efficiency reasons: take the 1 candidate
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final_kb_ids.append(candidates[0].entity_)
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else:
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random.shuffle(candidates)
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# set all prior probabilities to 0 if incl_prior=False
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prior_probs = xp.asarray([c.prior_prob for c in candidates])
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if not self.incl_prior:
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prior_probs = xp.asarray([0.0 for _ in candidates])
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scores = prior_probs
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# add in similarity from the context
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if self.incl_context:
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entity_encodings = xp.asarray(
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[c.entity_vector for c in candidates]
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)
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entity_norm = xp.linalg.norm(entity_encodings, axis=1)
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if len(entity_encodings) != len(prior_probs):
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raise RuntimeError(
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Errors.E147.format(
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method="predict",
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msg="vectors not of equal length",
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)
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)
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# cosine similarity
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sims = xp.dot(entity_encodings, sentence_encoding_t) / (
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sentence_norm * entity_norm
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)
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if sims.shape != prior_probs.shape:
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raise ValueError(Errors.E161)
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scores = prior_probs + sims - (prior_probs * sims)
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best_index = scores.argmax().item()
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best_candidate = candidates[best_index]
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final_kb_ids.append(best_candidate.entity_)
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if not (len(final_kb_ids) == entity_count):
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err = Errors.E147.format(
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method="predict", msg="result variables not of equal length"
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)
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raise RuntimeError(err)
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return final_kb_ids
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def set_annotations(self, docs: Iterable[Doc], kb_ids: List[str]) -> None:
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"""Modify a batch of documents, using pre-computed scores.
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docs (Iterable[Doc]): The documents to modify.
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kb_ids (List[str]): The IDs to set, produced by EntityLinker.predict.
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DOCS: https://spacy.io/api/entitylinker#set_annotations
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"""
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count_ents = len([ent for doc in docs for ent in doc.ents])
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if count_ents != len(kb_ids):
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raise ValueError(Errors.E148.format(ents=count_ents, ids=len(kb_ids)))
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i = 0
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overwrite = self.cfg["overwrite"]
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for doc in docs:
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for ent in doc.ents:
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kb_id = kb_ids[i]
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i += 1
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for token in ent:
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if token.ent_kb_id == 0 or overwrite:
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token.ent_kb_id_ = kb_id
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def to_bytes(self, *, exclude=tuple()):
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"""Serialize the pipe to a bytestring.
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exclude (Iterable[str]): String names of serialization fields to exclude.
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RETURNS (bytes): The serialized object.
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DOCS: https://spacy.io/api/entitylinker#to_bytes
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"""
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self._validate_serialization_attrs()
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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
|