entity_linker.py

import random
from itertools import islice
from pathlib import Path
from typing import Any, Callable, Dict, Iterable, List, Optional, Union

import srsly
from thinc.api import Config, CosineDistance, Model, Optimizer, set_dropout_rate
from thinc.types import Floats2d

from .. import util
from ..errors import Errors
from ..kb import Candidate, KnowledgeBase
from ..language import Language
from ..ml import empty_kb
from ..scorer import Scorer
from ..tokens import Doc, Span
from ..training import Example, validate_examples, validate_get_examples
from ..util import SimpleFrozenList, registry
from ..vocab import Vocab
from .legacy.entity_linker import EntityLinker_v1
from .pipe import deserialize_config
from .trainable_pipe import TrainablePipe

# See #9050
BACKWARD_OVERWRITE = True

default_model_config = """
[model]
@architectures = "spacy.EntityLinker.v2"

[model.tok2vec]
@architectures = "spacy.HashEmbedCNN.v2"
pretrained_vectors = null
width = 96
depth = 2
embed_size = 2000
window_size = 1
maxout_pieces = 3
subword_features = true
"""
DEFAULT_NEL_MODEL = Config().from_str(default_model_config)["model"]


@Language.factory(
    "entity_linker",
    requires=["doc.ents", "doc.sents", "token.ent_iob", "token.ent_type"],
    assigns=["token.ent_kb_id"],
    default_config={
        "model": DEFAULT_NEL_MODEL,
        "labels_discard": [],
        "n_sents": 0,
        "incl_prior": True,
        "incl_context": True,
        "entity_vector_length": 64,
        "get_candidates": {"@misc": "spacy.CandidateGenerator.v1"},
        "get_candidates_batch": {"@misc": "spacy.CandidateBatchGenerator.v1"},
        "generate_empty_kb": {"@misc": "spacy.EmptyKB.v2"},
        "overwrite": True,
        "scorer": {"@scorers": "spacy.entity_linker_scorer.v1"},
        "use_gold_ents": True,
        "candidates_batch_size": 1,
        "threshold": None,
    },
    default_score_weights={
        "nel_micro_f": 1.0,
        "nel_micro_r": None,
        "nel_micro_p": None,
    },
)
def make_entity_linker(
    nlp: Language,
    name: str,
    model: Model,
    *,
    labels_discard: Iterable[str],
    n_sents: int,
    incl_prior: bool,
    incl_context: bool,
    entity_vector_length: int,
    get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
    get_candidates_batch: Callable[
        [KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
    ],
    generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
    overwrite: bool,
    scorer: Optional[Callable],
    use_gold_ents: bool,
    candidates_batch_size: int,
    threshold: Optional[float] = None,
):
    """Construct an EntityLinker component.

    model (Model[List[Doc], Floats2d]): A model that learns document vector
        representations. Given a batch of Doc objects, it should return a single
        array, with one row per item in the batch.
    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.
    get_candidates_batch (
        Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]], Iterable[Candidate]]
        ): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
    generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
    scorer (Optional[Callable]): The scoring method.
    use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
        component must provide entity annotations.
    candidates_batch_size (int): Size of batches for entity candidate generation.
    threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the threshold,
        prediction is discarded. If None, predictions are not filtered by any threshold.
    """

    if not model.attrs.get("include_span_maker", False):
        # The only difference in arguments here is that use_gold_ents and threshold aren't 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,
        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,
        get_candidates_batch=get_candidates_batch,
        generate_empty_kb=generate_empty_kb,
        overwrite=overwrite,
        scorer=scorer,
        use_gold_ents=use_gold_ents,
        candidates_batch_size=candidates_batch_size,
        threshold=threshold,
    )


def entity_linker_score(examples, **kwargs):
    return Scorer.score_links(examples, negative_labels=[EntityLinker.NIL], **kwargs)


@registry.scorers("spacy.entity_linker_scorer.v1")
def make_entity_linker_scorer():
    return entity_linker_score


class EntityLinker(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]],
        get_candidates_batch: Callable[
            [KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
        ],
        generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
        overwrite: bool = BACKWARD_OVERWRITE,
        scorer: Optional[Callable] = entity_linker_score,
        use_gold_ents: bool,
        candidates_batch_size: int,
        threshold: Optional[float] = None,
    ) -> 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.
        get_candidates_batch (
            Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]],
            Iterable[Candidate]]
            ): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
        generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
        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.
        candidates_batch_size (int): Size of batches for entity candidate generation.
        threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the
            threshold, prediction is discarded. If None, predictions are not filtered by any threshold.
        DOCS: https://spacy.io/api/entitylinker#init
        """

        if threshold is not None and not (0 <= threshold <= 1):
            raise ValueError(
                Errors.E1043.format(
                    range_start=0,
                    range_end=1,
                    value=threshold,
                )
            )

        self.vocab = vocab
        self.model = model
        self.name = name
        self.labels_discard = list(labels_discard)
        # how many neighbour sentences to take into account
        self.n_sents = n_sents
        self.incl_prior = incl_prior
        self.incl_context = incl_context
        self.get_candidates = get_candidates
        self.get_candidates_batch = get_candidates_batch
        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

        if candidates_batch_size < 1:
            raise ValueError(Errors.E1044)

    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)  # type: ignore

    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 hasattr(self.kb, "is_empty") and self.kb.is_empty():
            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.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 eg in islice(get_examples(), 10):
            doc = eg.x
            if self.use_gold_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)
        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],
        *,
        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.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

        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
        )
        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.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.get_matching_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.asarray2f(entity_encodings, dtype="float32")
        selected_encodings = sentence_encodings[keep_ents]

        # if there are no matches, short circuit
        if not keep_ents:
            out = self.model.ops.alloc2f(*sentence_encodings.shape)
            return 0, out

        if selected_encodings.shape != entity_encodings.shape:
            err = Errors.E147.format(
                method="get_loss", msg="gold entities do not match up"
            )
            raise RuntimeError(err)
        gradients = self.distance.get_grad(selected_encodings, entity_encodings)
        # 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)
        loss = loss / len(entity_encodings)
        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.
        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] = []
        xp = self.model.ops.xp
        if not docs:
            return final_kb_ids
        if isinstance(docs, Doc):
            docs = [docs]
        for i, doc in enumerate(docs):
            if len(doc) == 0:
                continue
            sentences = [s for s in doc.sents]

            # Loop over entities in batches.
            for ent_idx in range(0, len(doc.ents), self.candidates_batch_size):
                ent_batch = doc.ents[ent_idx : ent_idx + self.candidates_batch_size]

                # Look up candidate entities.
                valid_ent_idx = [
                    idx
                    for idx in range(len(ent_batch))
                    if ent_batch[idx].label_ not in self.labels_discard
                ]

                batch_candidates = list(
                    self.get_candidates_batch(
                        self.kb, [ent_batch[idx] for idx in valid_ent_idx]
                    )
                    if self.candidates_batch_size > 1
                    else [
                        self.get_candidates(self.kb, ent_batch[idx])
                        for idx in valid_ent_idx
                    ]
                )

                # Looping through each entity in batch (TODO: rewrite)
                for j, ent in enumerate(ent_batch):
                    assert hasattr(ent, "sents")
                    sents = list(ent.sents)
                    sent_indices = (
                        sentences.index(sents[0]),
                        sentences.index(sents[-1]),
                    )
                    assert sent_indices[1] >= sent_indices[0] >= 0

                    if self.incl_context:
                        # get n_neighbour sentences, clipped to the length of the document
                        start_sentence = max(0, sent_indices[0] - self.n_sents)
                        end_sentence = min(
                            len(sentences) - 1, sent_indices[1] + 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)
                        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(batch_candidates[j])
                        if not candidates:
                            # no prediction possible for this entity - setting to NIL
                            final_kb_ids.append(self.NIL)
                        elif len(candidates) == 1 and self.threshold is None:
                            # shortcut for efficiency reasons: take the 1 candidate
                            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)
                            final_kb_ids.append(
                                candidates[scores.argmax().item()].entity_
                                if self.threshold is None
                                or scores.max() >= self.threshold
                                else EntityLinker.NIL
                            )

        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":
        """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