from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple from thinc.api import Config, Model, Optimizer, set_dropout_rate from thinc.types import Floats2d from ..errors import Errors from ..language import Language from ..scorer import Scorer from ..tokens import Doc, Span from ..training import Example from ..util import registry from .spancat import DEFAULT_SPANS_KEY from .trainable_pipe import TrainablePipe span_finder_default_config = """ [model] @architectures = "spacy.SpanFinder.v1" [model.scorer] @layers = "spacy.LinearLogistic.v1" nO = 2 [model.tok2vec] @architectures = "spacy.Tok2Vec.v2" [model.tok2vec.embed] @architectures = "spacy.MultiHashEmbed.v2" width = 96 rows = [5000, 1000, 2500, 1000] attrs = ["NORM", "PREFIX", "SUFFIX", "SHAPE"] include_static_vectors = false [model.tok2vec.encode] @architectures = "spacy.MaxoutWindowEncoder.v2" width = ${model.tok2vec.embed.width} window_size = 1 maxout_pieces = 3 depth = 4 """ DEFAULT_SPAN_FINDER_MODEL = Config().from_str(span_finder_default_config)["model"] @Language.factory( "span_finder", assigns=["doc.spans"], default_config={ "threshold": 0.5, "model": DEFAULT_SPAN_FINDER_MODEL, "spans_key": DEFAULT_SPANS_KEY, "max_length": 25, "min_length": None, "scorer": {"@scorers": "spacy.span_finder_scorer.v1"}, }, default_score_weights={ f"spans_{DEFAULT_SPANS_KEY}_f": 1.0, f"spans_{DEFAULT_SPANS_KEY}_p": 0.0, f"spans_{DEFAULT_SPANS_KEY}_r": 0.0, }, ) def make_span_finder( nlp: Language, name: str, model: Model[Iterable[Doc], Floats2d], spans_key: str, threshold: float, max_length: Optional[int], min_length: Optional[int], scorer: Optional[Callable], ) -> "SpanFinder": """Create a SpanFinder component. The component predicts whether a token is the start or the end of a potential span. model (Model[List[Doc], Floats2d]): A model instance that is given a list of documents and predicts a probability for each token. spans_key (str): Key of the doc.spans dict to save the spans under. During initialization and training, the component will look for spans on the reference document under the same key. threshold (float): Minimum probability to consider a prediction positive. max_length (Optional[int]): Maximum length of the produced spans, defaults to None meaning unlimited length. min_length (Optional[int]): Minimum length of the produced spans, defaults to None meaning shortest span length is 1. scorer (Optional[Callable]): The scoring method. Defaults to Scorer.score_spans for the Doc.spans[spans_key] with overlapping spans allowed. """ return SpanFinder( nlp, model=model, threshold=threshold, name=name, scorer=scorer, max_length=max_length, min_length=min_length, spans_key=spans_key, ) @registry.scorers("spacy.span_finder_scorer.v1") def make_span_finder_scorer(): return span_finder_score def span_finder_score(examples: Iterable[Example], **kwargs) -> Dict[str, Any]: kwargs = dict(kwargs) attr_prefix = "spans_" key = kwargs["spans_key"] kwargs.setdefault("attr", f"{attr_prefix}{key}") kwargs.setdefault( "getter", lambda doc, key: doc.spans.get(key[len(attr_prefix) :], []) ) kwargs.setdefault("has_annotation", lambda doc: key in doc.spans) kwargs.setdefault("allow_overlap", True) kwargs.setdefault("labeled", False) scores = Scorer.score_spans(examples, **kwargs) scores.pop(f"{kwargs['attr']}_per_type", None) return scores def _char_indices(span: Span) -> Tuple[int, int]: start = span[0].idx end = span[-1].idx + len(span[-1]) return start, end class SpanFinder(TrainablePipe): """Pipeline that learns span boundaries. DOCS: https://spacy.io/api/spanfinder """ def __init__( self, nlp: Language, model: Model[Iterable[Doc], Floats2d], name: str = "span_finder", *, spans_key: str = DEFAULT_SPANS_KEY, threshold: float = 0.5, max_length: Optional[int] = None, min_length: Optional[int] = None, scorer: Optional[Callable] = span_finder_score, ) -> None: """Initialize the span finder. 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. threshold (float): Minimum probability to consider a prediction positive. scorer (Optional[Callable]): The scoring method. spans_key (str): Key of the doc.spans dict to save the spans under. During initialization and training, the component will look for spans on the reference document under the same key. max_length (Optional[int]): Maximum length of the produced spans, defaults to None meaning unlimited length. min_length (Optional[int]): Minimum length of the produced spans, defaults to None meaning shortest span length is 1. DOCS: https://spacy.io/api/spanfinder#init """ self.vocab = nlp.vocab if (max_length is not None and max_length < 1) or ( min_length is not None and min_length < 1 ): raise ValueError( Errors.E1053.format(min_length=min_length, max_length=max_length) ) self.model = model self.name = name self.scorer = scorer self.cfg: Dict[str, Any] = { "min_length": min_length, "max_length": max_length, "threshold": threshold, "spans_key": spans_key, } def predict(self, docs: Iterable[Doc]): """Apply the pipeline's model to a batch of docs, without modifying them. docs (Iterable[Doc]): The documents to predict. RETURNS: The models prediction for each document. DOCS: https://spacy.io/api/spanfinder#predict """ scores = self.model.predict(docs) return scores def set_annotations(self, docs: Iterable[Doc], scores: Floats2d) -> None: """Modify a batch of Doc objects, using pre-computed scores. docs (Iterable[Doc]): The documents to modify. scores: The scores to set, produced by SpanFinder predict method. DOCS: https://spacy.io/api/spanfinder#set_annotations """ offset = 0 for i, doc in enumerate(docs): doc.spans[self.cfg["spans_key"]] = [] starts = [] ends = [] doc_scores = scores[offset : offset + len(doc)] for token, token_score in zip(doc, doc_scores): if token_score[0] >= self.cfg["threshold"]: starts.append(token.i) if token_score[1] >= self.cfg["threshold"]: ends.append(token.i) for start in starts: for end in ends: span_length = end + 1 - start if span_length < 1: continue if ( self.cfg["min_length"] is None or self.cfg["min_length"] <= span_length ) and ( self.cfg["max_length"] is None or span_length <= self.cfg["max_length"] ): doc.spans[self.cfg["spans_key"]].append(doc[start : end + 1]) offset += len(doc) 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 (Optional[thinc.api.Optimizer]): The optimizer. losses (Optional[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/spanfinder#update """ if losses is None: losses = {} losses.setdefault(self.name, 0.0) predicted = [eg.predicted for eg in examples] set_dropout_rate(self.model, drop) scores, backprop_scores = self.model.begin_update(predicted) loss, d_scores = self.get_loss(examples, scores) backprop_scores(d_scores) if sgd is not None: self.finish_update(sgd) losses[self.name] += loss return losses def get_loss(self, examples, scores) -> Tuple[float, Floats2d]: """Find the loss and gradient of loss for the batch of documents and their predicted scores. examples (Iterable[Examples]): The batch of examples. scores: Scores representing the model's predictions. RETURNS (Tuple[float, Floats2d]): The loss and the gradient. DOCS: https://spacy.io/api/spanfinder#get_loss """ truths, masks = self._get_aligned_truth_scores(examples, self.model.ops) d_scores = scores - self.model.ops.asarray2f(truths) d_scores *= masks loss = float((d_scores**2).sum()) return loss, d_scores def _get_aligned_truth_scores(self, examples, ops) -> Tuple[Floats2d, Floats2d]: """Align scores of the predictions to the references for calculating the loss. """ truths = [] masks = [] for eg in examples: if eg.x.text != eg.y.text: raise ValueError(Errors.E1054.format(component="span_finder")) n_tokens = len(eg.predicted) truth = ops.xp.zeros((n_tokens, 2), dtype="float32") mask = ops.xp.ones((n_tokens, 2), dtype="float32") if self.cfg["spans_key"] in eg.reference.spans: for span in eg.reference.spans[self.cfg["spans_key"]]: ref_start_char, ref_end_char = _char_indices(span) pred_span = eg.predicted.char_span( ref_start_char, ref_end_char, alignment_mode="expand" ) pred_start_char, pred_end_char = _char_indices(pred_span) start_match = pred_start_char == ref_start_char end_match = pred_end_char == ref_end_char if start_match: truth[pred_span[0].i, 0] = 1 else: mask[pred_span[0].i, 0] = 0 if end_match: truth[pred_span[-1].i, 1] = 1 else: mask[pred_span[-1].i, 1] = 0 truths.append(truth) masks.append(mask) truths = ops.xp.concatenate(truths, axis=0) masks = ops.xp.concatenate(masks, axis=0) return truths, masks def initialize( self, get_examples: Callable[[], Iterable[Example]], *, nlp: Optional[Language] = None, ) -> 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 (Optional[Language]): The current nlp object the component is part of. DOCS: https://spacy.io/api/spanfinder#initialize """ subbatch: List[Example] = [] for eg in get_examples(): if len(subbatch) < 10: subbatch.append(eg) if subbatch: docs = [eg.reference for eg in subbatch] Y, _ = self._get_aligned_truth_scores(subbatch, self.model.ops) self.model.initialize(X=docs, Y=Y) else: self.model.initialize()