# cython: infer_types=True, profile=True import numpy import srsly import random from thinc.api import CosineDistance, to_categorical, get_array_module from thinc.api import set_dropout_rate, SequenceCategoricalCrossentropy import warnings from ..tokens.doc cimport Doc from ..syntax.nn_parser cimport Parser from ..syntax.ner cimport BiluoPushDown from ..syntax.arc_eager cimport ArcEager from ..morphology cimport Morphology from ..vocab cimport Vocab from .defaults import default_tagger, default_parser, default_ner, default_textcat from .defaults import default_nel, default_senter from .functions import merge_subtokens from ..language import Language, component from ..syntax import nonproj from ..gold.example import Example from ..attrs import POS, ID from ..util import link_vectors_to_models, create_default_optimizer from ..parts_of_speech import X from ..kb import KnowledgeBase from ..errors import Errors, TempErrors, Warnings from .. import util def _load_cfg(path): if path.exists(): return srsly.read_json(path) else: return {} class Pipe(object): """This class is not instantiated directly. Components inherit from it, and it defines the interface that components should follow to function as components in a spaCy analysis pipeline. """ name = None @classmethod def from_nlp(cls, nlp, model, **cfg): return cls(nlp.vocab, model, **cfg) def __init__(self, vocab, model, **cfg): """Create a new pipe instance.""" raise NotImplementedError def __call__(self, Doc doc): """Apply the pipe to one document. The document is modified in-place, and returned. Both __call__ and pipe should delegate to the `predict()` and `set_annotations()` methods. """ scores = self.predict([doc]) self.set_annotations([doc], scores) return doc def pipe(self, stream, batch_size=128): """Apply the pipe to a stream of documents. Both __call__ and pipe should delegate to the `predict()` and `set_annotations()` methods. """ for docs in util.minibatch(stream, size=batch_size): scores = self.predict(docs) self.set_annotations(docs, scores) yield from docs def predict(self, docs): """Apply the pipeline's model to a batch of docs, without modifying them. """ raise NotImplementedError def set_annotations(self, docs, scores): """Modify a batch of documents, using pre-computed scores.""" raise NotImplementedError def rehearse(self, examples, sgd=None, losses=None, **config): pass def get_loss(self, examples, scores): """Find the loss and gradient of loss for the batch of examples (with embedded docs) and their predicted scores.""" raise NotImplementedError def add_label(self, label): """Add an output label, to be predicted by the model. It's possible to extend pretrained models with new labels, but care should be taken to avoid the "catastrophic forgetting" problem. """ raise NotImplementedError def create_optimizer(self): return create_default_optimizer() def begin_training( self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs ): """Initialize the pipe for training, using data exampes if available. If no model has been initialized yet, the model is added.""" self.model.initialize() if hasattr(self, "vocab"): link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd def set_output(self, nO): if self.model.has_dim("nO") is not False: self.model.set_dim("nO", nO) if self.model.has_ref("output_layer"): self.model.get_ref("output_layer").set_dim("nO", nO) def get_gradients(self): """Get non-zero gradients of the model's parameters, as a dictionary keyed by the parameter ID. The values are (weights, gradients) tuples. """ gradients = {} queue = [self.model] seen = set() for node in queue: if node.id in seen: continue seen.add(node.id) if hasattr(node, "_mem") and node._mem.gradient.any(): gradients[node.id] = [node._mem.weights, node._mem.gradient] if hasattr(node, "_layers"): queue.extend(node._layers) return gradients def use_params(self, params): """Modify the pipe's model, to use the given parameter values.""" with self.model.use_params(params): yield def to_bytes(self, exclude=tuple()): """Serialize the pipe to a bytestring. exclude (list): String names of serialization fields to exclude. RETURNS (bytes): The serialized object. """ serialize = {} serialize["cfg"] = lambda: srsly.json_dumps(self.cfg) serialize["model"] = self.model.to_bytes if hasattr(self, "vocab"): serialize["vocab"] = self.vocab.to_bytes return util.to_bytes(serialize, exclude) def from_bytes(self, bytes_data, exclude=tuple()): """Load the pipe from a bytestring.""" def load_model(b): try: self.model.from_bytes(b) except AttributeError: raise ValueError(Errors.E149) deserialize = {} if hasattr(self, "vocab"): deserialize["vocab"] = lambda b: self.vocab.from_bytes(b) deserialize["cfg"] = lambda b: self.cfg.update(srsly.json_loads(b)) deserialize["model"] = load_model util.from_bytes(bytes_data, deserialize, exclude) return self def to_disk(self, path, exclude=tuple()): """Serialize the pipe to disk.""" serialize = {} serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg) serialize["vocab"] = lambda p: self.vocab.to_disk(p) serialize["model"] = lambda p: self.model.to_disk(p) util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple()): """Load the pipe from disk.""" def load_model(p): try: self.model.from_bytes(p.open("rb").read()) except AttributeError: raise ValueError(Errors.E149) deserialize = {} deserialize["vocab"] = lambda p: self.vocab.from_disk(p) deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p)) deserialize["model"] = load_model util.from_disk(path, deserialize, exclude) return self @component("tagger", assigns=["token.tag", "token.pos", "token.lemma"], default_model=default_tagger) class Tagger(Pipe): """Pipeline component for part-of-speech tagging. DOCS: https://spacy.io/api/tagger """ def __init__(self, vocab, model, **cfg): self.vocab = vocab self.model = model self._rehearsal_model = None self.cfg = dict(sorted(cfg.items())) @property def labels(self): return tuple(self.vocab.morphology.tag_names) def __call__(self, doc): tags = self.predict([doc]) self.set_annotations([doc], tags) return doc def pipe(self, stream, batch_size=128): for docs in util.minibatch(stream, size=batch_size): tag_ids = self.predict(docs) self.set_annotations(docs, tag_ids) yield from docs def predict(self, docs): if not any(len(doc) for doc in docs): # Handle cases where there are no tokens in any docs. n_labels = len(self.labels) guesses = [self.model.ops.alloc((0, n_labels)) for doc in docs] assert len(guesses) == len(docs) return guesses scores = self.model.predict(docs) assert len(scores) == len(docs), (len(scores), len(docs)) guesses = self._scores2guesses(scores) assert len(guesses) == len(docs) return guesses def _scores2guesses(self, scores): guesses = [] for doc_scores in scores: doc_guesses = doc_scores.argmax(axis=1) if not isinstance(doc_guesses, numpy.ndarray): doc_guesses = doc_guesses.get() guesses.append(doc_guesses) return guesses def set_annotations(self, docs, batch_tag_ids): if isinstance(docs, Doc): docs = [docs] cdef Doc doc cdef int idx = 0 cdef Vocab vocab = self.vocab assign_morphology = self.cfg.get("set_morphology", True) for i, doc in enumerate(docs): doc_tag_ids = batch_tag_ids[i] if hasattr(doc_tag_ids, "get"): doc_tag_ids = doc_tag_ids.get() for j, tag_id in enumerate(doc_tag_ids): # Don't clobber preset POS tags if doc.c[j].tag == 0: if doc.c[j].pos == 0 and assign_morphology: # Don't clobber preset lemmas lemma = doc.c[j].lemma vocab.morphology.assign_tag_id(&doc.c[j], tag_id) if lemma != 0 and lemma != doc.c[j].lex.orth: doc.c[j].lemma = lemma else: doc.c[j].tag = self.vocab.strings[self.labels[tag_id]] idx += 1 doc.is_tagged = True def update(self, examples, *, drop=0., sgd=None, losses=None, set_annotations=False): if losses is None: losses = {} losses.setdefault(self.name, 0.0) try: if not any(len(eg.predicted) if eg.predicted else 0 for eg in examples): # Handle cases where there are no tokens in any docs. return except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="Tagger", method="update", types=types)) set_dropout_rate(self.model, drop) tag_scores, bp_tag_scores = self.model.begin_update( [eg.predicted for eg in examples]) for sc in tag_scores: if self.model.ops.xp.isnan(sc.sum()): raise ValueError("nan value in scores") loss, d_tag_scores = self.get_loss(examples, tag_scores) bp_tag_scores(d_tag_scores) if sgd not in (None, False): self.model.finish_update(sgd) losses[self.name] += loss if set_annotations: docs = [eg.predicted for eg in examples] self.set_annotations(docs, self._scores2guesses(tag_scores)) return losses def rehearse(self, examples, drop=0., sgd=None, losses=None): """Perform a 'rehearsal' update, where we try to match the output of an initial model. """ try: docs = [eg.predicted for eg in examples] except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="Tagger", method="rehearse", types=types)) if self._rehearsal_model is None: return if not any(len(doc) for doc in docs): # Handle cases where there are no tokens in any docs. return set_dropout_rate(self.model, drop) guesses, backprop = self.model.begin_update(docs) target = self._rehearsal_model(examples) gradient = guesses - target backprop(gradient) self.model.finish_update(sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += (gradient**2).sum() def get_loss(self, examples, scores): loss_func = SequenceCategoricalCrossentropy(names=self.labels, normalize=False) truths = [eg.get_aligned("tag", as_string=True) for eg in examples] d_scores, loss = loss_func(scores, truths) if self.model.ops.xp.isnan(loss): raise ValueError("nan value when computing loss") return float(loss), d_scores def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): lemma_tables = ["lemma_rules", "lemma_index", "lemma_exc", "lemma_lookup"] if not any(table in self.vocab.lookups for table in lemma_tables): warnings.warn(Warnings.W022) if len(self.vocab.lookups.get_table("lexeme_norm", {})) == 0: warnings.warn(Warnings.W033.format(model="part-of-speech tagger")) orig_tag_map = dict(self.vocab.morphology.tag_map) new_tag_map = {} for example in get_examples(): try: y = example.y except AttributeError: raise TypeError(Errors.E978.format(name="Tagger", method="begin_training", types=type(example))) for token in y: tag = token.tag_ if tag in orig_tag_map: new_tag_map[tag] = orig_tag_map[tag] else: new_tag_map[tag] = {POS: X} cdef Vocab vocab = self.vocab if new_tag_map: if "_SP" in orig_tag_map: new_tag_map["_SP"] = orig_tag_map["_SP"] vocab.morphology = Morphology(vocab.strings, new_tag_map, vocab.morphology.lemmatizer, exc=vocab.morphology.exc) self.set_output(len(self.labels)) doc_sample = [Doc(self.vocab, words=["hello", "world"])] if pipeline is not None: for name, component in pipeline: if component is self: break if hasattr(component, "pipe"): doc_sample = list(component.pipe(doc_sample)) else: doc_sample = [component(doc) for doc in doc_sample] self.model.initialize(X=doc_sample) # Get batch of example docs, example outputs to call begin_training(). # This lets the model infer shapes. link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd def add_label(self, label, values=None): if not isinstance(label, str): raise ValueError(Errors.E187) if label in self.labels: return 0 if self.model.has_dim("nO"): # Here's how the model resizing will work, once the # neuron-to-tag mapping is no longer controlled by # the Morphology class, which sorts the tag names. # The sorting makes adding labels difficult. # smaller = self.model._layers[-1] # larger = Softmax(len(self.labels)+1, smaller.nI) # copy_array(larger.W[:smaller.nO], smaller.W) # copy_array(larger.b[:smaller.nO], smaller.b) # self.model._layers[-1] = larger raise ValueError(TempErrors.T003) tag_map = dict(self.vocab.morphology.tag_map) if values is None: values = {POS: "X"} tag_map[label] = values self.vocab.morphology = Morphology( self.vocab.strings, tag_map=tag_map, lemmatizer=self.vocab.morphology.lemmatizer, exc=self.vocab.morphology.exc) return 1 def use_params(self, params): with self.model.use_params(params): yield def to_bytes(self, exclude=tuple()): serialize = {} serialize["model"] = self.model.to_bytes serialize["vocab"] = self.vocab.to_bytes serialize["cfg"] = lambda: srsly.json_dumps(self.cfg) tag_map = dict(sorted(self.vocab.morphology.tag_map.items())) serialize["tag_map"] = lambda: srsly.msgpack_dumps(tag_map) return util.to_bytes(serialize, exclude) def from_bytes(self, bytes_data, exclude=tuple()): def load_model(b): try: self.model.from_bytes(b) except AttributeError: raise ValueError(Errors.E149) def load_tag_map(b): tag_map = srsly.msgpack_loads(b) self.vocab.morphology = Morphology( self.vocab.strings, tag_map=tag_map, lemmatizer=self.vocab.morphology.lemmatizer, exc=self.vocab.morphology.exc) deserialize = { "vocab": lambda b: self.vocab.from_bytes(b), "tag_map": load_tag_map, "cfg": lambda b: self.cfg.update(srsly.json_loads(b)), "model": lambda b: load_model(b), } util.from_bytes(bytes_data, deserialize, exclude) return self def to_disk(self, path, exclude=tuple()): tag_map = dict(sorted(self.vocab.morphology.tag_map.items())) serialize = { "vocab": lambda p: self.vocab.to_disk(p), "tag_map": lambda p: srsly.write_msgpack(p, tag_map), "model": lambda p: self.model.to_disk(p), "cfg": lambda p: srsly.write_json(p, self.cfg), } util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple()): def load_model(p): with p.open("rb") as file_: try: self.model.from_bytes(file_.read()) except AttributeError: raise ValueError(Errors.E149) def load_tag_map(p): tag_map = srsly.read_msgpack(p) self.vocab.morphology = Morphology( self.vocab.strings, tag_map=tag_map, lemmatizer=self.vocab.morphology.lemmatizer, exc=self.vocab.morphology.exc) deserialize = { "vocab": lambda p: self.vocab.from_disk(p), "cfg": lambda p: self.cfg.update(_load_cfg(p)), "tag_map": load_tag_map, "model": load_model, } util.from_disk(path, deserialize, exclude) return self @component("senter", assigns=["token.is_sent_start"], default_model=default_senter) class SentenceRecognizer(Tagger): """Pipeline component for sentence segmentation. DOCS: https://spacy.io/api/sentencerecognizer """ def __init__(self, vocab, model, **cfg): self.vocab = vocab self.model = model self._rehearsal_model = None self.cfg = dict(sorted(cfg.items())) @property def labels(self): # labels are numbered by index internally, so this matches GoldParse # and Example where the sentence-initial tag is 1 and other positions # are 0 return tuple(["I", "S"]) def set_annotations(self, docs, batch_tag_ids): if isinstance(docs, Doc): docs = [docs] cdef Doc doc for i, doc in enumerate(docs): doc_tag_ids = batch_tag_ids[i] if hasattr(doc_tag_ids, "get"): doc_tag_ids = doc_tag_ids.get() for j, tag_id in enumerate(doc_tag_ids): # Don't clobber existing sentence boundaries if doc.c[j].sent_start == 0: if tag_id == 1: doc.c[j].sent_start = 1 else: doc.c[j].sent_start = -1 def get_loss(self, examples, scores): labels = self.labels loss_func = SequenceCategoricalCrossentropy(names=labels, normalize=False) truths = [] for eg in examples: eg_truth = [] for x in eg.get_aligned("sent_start"): if x == None: eg_truth.append(None) elif x == 1: eg_truth.append(labels[1]) else: # anything other than 1: 0, -1, -1 as uint64 eg_truth.append(labels[0]) truths.append(eg_truth) d_scores, loss = loss_func(scores, truths) if self.model.ops.xp.isnan(loss): raise ValueError("nan value when computing loss") return float(loss), d_scores def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): self.set_output(len(self.labels)) self.model.initialize() link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd def add_label(self, label, values=None): raise NotImplementedError def to_bytes(self, exclude=tuple()): serialize = {} serialize["model"] = self.model.to_bytes serialize["vocab"] = self.vocab.to_bytes serialize["cfg"] = lambda: srsly.json_dumps(self.cfg) return util.to_bytes(serialize, exclude) def from_bytes(self, bytes_data, exclude=tuple()): def load_model(b): try: self.model.from_bytes(b) except AttributeError: raise ValueError(Errors.E149) deserialize = { "vocab": lambda b: self.vocab.from_bytes(b), "cfg": lambda b: self.cfg.update(srsly.json_loads(b)), "model": lambda b: load_model(b), } util.from_bytes(bytes_data, deserialize, exclude) return self def to_disk(self, path, exclude=tuple()): serialize = { "vocab": lambda p: self.vocab.to_disk(p), "model": lambda p: p.open("wb").write(self.model.to_bytes()), "cfg": lambda p: srsly.write_json(p, self.cfg), } util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple()): def load_model(p): with p.open("rb") as file_: try: self.model.from_bytes(file_.read()) except AttributeError: raise ValueError(Errors.E149) deserialize = { "vocab": lambda p: self.vocab.from_disk(p), "cfg": lambda p: self.cfg.update(_load_cfg(p)), "model": load_model, } util.from_disk(path, deserialize, exclude) return self @component("nn_labeller") class MultitaskObjective(Tagger): """Experimental: Assist training of a parser or tagger, by training a side-objective. """ def __init__(self, vocab, model, **cfg): self.vocab = vocab self.model = model target = cfg["target"] # default: 'dep_tag_offset' if target == "dep": self.make_label = self.make_dep elif target == "tag": self.make_label = self.make_tag elif target == "ent": self.make_label = self.make_ent elif target == "dep_tag_offset": self.make_label = self.make_dep_tag_offset elif target == "ent_tag": self.make_label = self.make_ent_tag elif target == "sent_start": self.make_label = self.make_sent_start elif hasattr(target, "__call__"): self.make_label = target else: raise ValueError(Errors.E016) self.cfg = dict(cfg) @property def labels(self): return self.cfg.setdefault("labels", {}) @labels.setter def labels(self, value): self.cfg["labels"] = value def set_annotations(self, docs, dep_ids): pass def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): gold_examples = nonproj.preprocess_training_data(get_examples()) # for raw_text, doc_annot in gold_tuples: for example in gold_examples: for token in example.y: label = self.make_label(token) if label is not None and label not in self.labels: self.labels[label] = len(self.labels) self.model.initialize() link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd def predict(self, docs): tokvecs = self.model.get_ref("tok2vec")(docs) scores = self.model.get_ref("softmax")(tokvecs) return tokvecs, scores def get_loss(self, examples, scores): cdef int idx = 0 correct = numpy.zeros((scores.shape[0],), dtype="i") guesses = scores.argmax(axis=1) docs = [eg.predicted for eg in examples] for i, eg in enumerate(examples): # Handles alignment for tokenization differences doc_annots = eg.get_aligned() # TODO for j in range(len(eg.predicted)): tok_annots = {key: values[j] for key, values in tok_annots.items()} label = self.make_label(j, tok_annots) if label is None or label not in self.labels: correct[idx] = guesses[idx] else: correct[idx] = self.labels[label] idx += 1 correct = self.model.ops.xp.array(correct, dtype="i") d_scores = scores - to_categorical(correct, n_classes=scores.shape[1]) loss = (d_scores**2).sum() return float(loss), d_scores @staticmethod def make_dep(token): return token.dep_ @staticmethod def make_tag(token): return token.tag_ @staticmethod def make_ent(token): if token.ent_iob_ == "O": return "O" else: return token.ent_iob_ + "-" + token.ent_type_ @staticmethod def make_dep_tag_offset(token): dep = token.dep_ tag = token.tag_ offset = token.head.i - token.i offset = min(offset, 2) offset = max(offset, -2) return f"{dep}-{tag}:{offset}" @staticmethod def make_ent_tag(token): if token.ent_iob_ == "O": ent = "O" else: ent = token.ent_iob_ + "-" + token.ent_type_ tag = token.tag_ return f"{tag}-{ent}" @staticmethod def make_sent_start(token): """A multi-task objective for representing sentence boundaries, using BILU scheme. (O is impossible) """ if token.is_sent_start and token.is_sent_end: return "U-SENT" elif token.is_sent_start: return "B-SENT" else: return "I-SENT" class ClozeMultitask(Pipe): def __init__(self, vocab, model, **cfg): self.vocab = vocab self.model = model self.cfg = cfg self.distance = CosineDistance(ignore_zeros=True, normalize=False) # TODO: in config def set_annotations(self, docs, dep_ids): pass def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): link_vectors_to_models(self.vocab) self.model.initialize() X = self.model.ops.alloc((5, self.model.get_ref("tok2vec").get_dim("nO"))) self.model.output_layer.begin_training(X) if sgd is None: sgd = self.create_optimizer() return sgd def predict(self, docs): tokvecs = self.model.get_ref("tok2vec")(docs) vectors = self.model.get_ref("output_layer")(tokvecs) return tokvecs, vectors def get_loss(self, examples, vectors, prediction): # The simplest way to implement this would be to vstack the # token.vector values, but that's a bit inefficient, especially on GPU. # Instead we fetch the index into the vectors table for each of our tokens, # and look them up all at once. This prevents data copying. ids = self.model.ops.flatten([eg.predicted.to_array(ID).ravel() for eg in examples]) target = vectors[ids] gradient = self.distance.get_grad(prediction, target) loss = self.distance.get_loss(prediction, target) return loss, gradient def update(self, examples, *, drop=0., set_annotations=False, sgd=None, losses=None): pass def rehearse(self, examples, drop=0., sgd=None, losses=None): if losses is not None and self.name not in losses: losses[self.name] = 0. set_dropout_rate(self.model, drop) try: predictions, bp_predictions = self.model.begin_update([eg.predicted for eg in examples]) except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="ClozeMultitask", method="rehearse", types=types)) loss, d_predictions = self.get_loss(examples, self.vocab.vectors.data, predictions) bp_predictions(d_predictions) if sgd is not None: self.model.finish_update(sgd) if losses is not None: losses[self.name] += loss @component("textcat", assigns=["doc.cats"], default_model=default_textcat) class TextCategorizer(Pipe): """Pipeline component for text classification. DOCS: https://spacy.io/api/textcategorizer """ def __init__(self, vocab, model, **cfg): self.vocab = vocab self.model = model self._rehearsal_model = None self.cfg = dict(cfg) @property def labels(self): return tuple(self.cfg.setdefault("labels", [])) def require_labels(self): """Raise an error if the component's model has no labels defined.""" if not self.labels: raise ValueError(Errors.E143.format(name=self.name)) @labels.setter def labels(self, value): self.cfg["labels"] = tuple(value) def pipe(self, stream, batch_size=128): for docs in util.minibatch(stream, size=batch_size): scores = self.predict(docs) self.set_annotations(docs, scores) yield from docs def predict(self, docs): tensors = [doc.tensor for doc in docs] if not any(len(doc) for doc in docs): # Handle cases where there are no tokens in any docs. xp = get_array_module(tensors) scores = xp.zeros((len(docs), len(self.labels))) return scores scores = self.model.predict(docs) scores = self.model.ops.asarray(scores) return scores def set_annotations(self, docs, scores): for i, doc in enumerate(docs): for j, label in enumerate(self.labels): doc.cats[label] = float(scores[i, j]) def update(self, examples, *, drop=0., set_annotations=False, sgd=None, losses=None): if losses is None: losses = {} losses.setdefault(self.name, 0.0) try: if not any(len(eg.predicted) if eg.predicted else 0 for eg in examples): # Handle cases where there are no tokens in any docs. return losses except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="TextCategorizer", method="update", types=types)) set_dropout_rate(self.model, drop) scores, bp_scores = self.model.begin_update( [eg.predicted for eg in examples] ) loss, d_scores = self.get_loss(examples, scores) bp_scores(d_scores) if sgd is not None: self.model.finish_update(sgd) losses[self.name] += loss if set_annotations: docs = [eg.predicted for eg in examples] self.set_annotations(docs, scores=scores) return losses def rehearse(self, examples, drop=0., sgd=None, losses=None): if self._rehearsal_model is None: return try: docs = [eg.predicted for eg in examples] except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="TextCategorizer", method="rehearse", types=types)) if not any(len(doc) for doc in docs): # Handle cases where there are no tokens in any docs. return set_dropout_rate(self.model, drop) scores, bp_scores = self.model.begin_update(docs) target = self._rehearsal_model(examples) gradient = scores - target bp_scores(gradient) if sgd is not None: self.model.finish_update(sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += (gradient**2).sum() def _examples_to_truth(self, examples): truths = numpy.zeros((len(examples), len(self.labels)), dtype="f") not_missing = numpy.ones((len(examples), len(self.labels)), dtype="f") for i, eg in enumerate(examples): for j, label in enumerate(self.labels): if label in eg.reference.cats: truths[i, j] = eg.reference.cats[label] else: not_missing[i, j] = 0. truths = self.model.ops.asarray(truths) return truths, not_missing def get_loss(self, examples, scores): truths, not_missing = self._examples_to_truth(examples) not_missing = self.model.ops.asarray(not_missing) d_scores = (scores-truths) / scores.shape[0] d_scores *= not_missing mean_square_error = (d_scores**2).sum(axis=1).mean() return float(mean_square_error), d_scores def add_label(self, label): if not isinstance(label, str): raise ValueError(Errors.E187) if label in self.labels: return 0 if self.model.has_dim("nO"): # This functionality was available previously, but was broken. # The problem is that we resize the last layer, but the last layer # is actually just an ensemble. We're not resizing the child layers # - a huge problem. raise ValueError(Errors.E116) # smaller = self.model._layers[-1] # larger = Linear(len(self.labels)+1, smaller.nI) # copy_array(larger.W[:smaller.nO], smaller.W) # copy_array(larger.b[:smaller.nO], smaller.b) # self.model._layers[-1] = larger self.labels = tuple(list(self.labels) + [label]) return 1 def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): # TODO: begin_training is not guaranteed to see all data / labels ? examples = list(get_examples()) for example in examples: try: y = example.y except AttributeError: raise TypeError(Errors.E978.format(name="TextCategorizer", method="update", types=type(example))) for cat in y.cats: self.add_label(cat) self.require_labels() docs = [Doc(Vocab(), words=["hello"])] truths, _ = self._examples_to_truth(examples) self.set_output(len(self.labels)) link_vectors_to_models(self.vocab) self.model.initialize(X=docs, Y=truths) if sgd is None: sgd = self.create_optimizer() return sgd cdef class DependencyParser(Parser): """Pipeline component for dependency parsing. DOCS: https://spacy.io/api/dependencyparser """ # cdef classes can't have decorators, so we're defining this here name = "parser" factory = "parser" assigns = ["token.dep", "token.is_sent_start", "doc.sents"] requires = [] TransitionSystem = ArcEager @property def postprocesses(self): output = [nonproj.deprojectivize] if self.cfg.get("learn_tokens") is True: output.append(merge_subtokens) return tuple(output) def add_multitask_objective(self, mt_component): self._multitasks.append(mt_component) def init_multitask_objectives(self, get_examples, pipeline, sgd=None, **cfg): # TODO: transfer self.model.get_ref("tok2vec") to the multitask's model ? for labeller in self._multitasks: labeller.model.set_dim("nO", len(self.labels)) if labeller.model.has_ref("output_layer"): labeller.model.get_ref("output_layer").set_dim("nO", len(self.labels)) labeller.begin_training(get_examples, pipeline=pipeline, sgd=sgd) def __reduce__(self): return (DependencyParser, (self.vocab, self.model), (self.moves, self.cfg)) def __getstate__(self): return (self.moves, self.cfg) def __setstate__(self, state): moves, config = state self.moves = moves self.cfg = config @property def labels(self): labels = set() # Get the labels from the model by looking at the available moves for move in self.move_names: if "-" in move: label = move.split("-")[1] if "||" in label: label = label.split("||")[1] labels.add(label) return tuple(sorted(labels)) cdef class EntityRecognizer(Parser): """Pipeline component for named entity recognition. DOCS: https://spacy.io/api/entityrecognizer """ name = "ner" factory = "ner" assigns = ["doc.ents", "token.ent_iob", "token.ent_type"] requires = [] TransitionSystem = BiluoPushDown def add_multitask_objective(self, mt_component): self._multitasks.append(mt_component) def init_multitask_objectives(self, get_examples, pipeline, sgd=None, **cfg): # TODO: transfer self.model.get_ref("tok2vec") to the multitask's model ? for labeller in self._multitasks: labeller.model.set_dim("nO", len(self.labels)) if labeller.model.has_ref("output_layer"): labeller.model.get_ref("output_layer").set_dim("nO", len(self.labels)) labeller.begin_training(get_examples, pipeline=pipeline) def __reduce__(self): return (EntityRecognizer, (self.vocab, self.model), (self.moves, self.cfg)) def __getstate__(self): return self.moves, self.cfg def __setstate__(self, state): moves, config = state self.moves = moves self.cfg = config @property def labels(self): # Get the labels from the model by looking at the available moves, e.g. # B-PERSON, I-PERSON, L-PERSON, U-PERSON labels = set(move.split("-")[1] for move in self.move_names if move[0] in ("B", "I", "L", "U")) return tuple(sorted(labels)) @component( "entity_linker", requires=["doc.ents", "doc.sents", "token.ent_iob", "token.ent_type"], assigns=["token.ent_kb_id"], default_model=default_nel, ) class EntityLinker(Pipe): """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, model, **cfg): self.vocab = vocab self.model = model self.kb = None self.kb = cfg.get("kb", None) if self.kb is None: # create an empty KB that should be filled by calling from_disk self.kb = KnowledgeBase(vocab=vocab) else: del cfg["kb"] # we don't want to duplicate its serialization if not isinstance(self.kb, KnowledgeBase): raise ValueError(Errors.E990.format(type=type(self.kb))) self.cfg = dict(cfg) self.distance = CosineDistance(normalize=False) # how many neightbour sentences to take into account self.n_sents = cfg.get("n_sents", 0) def require_kb(self): # Raise an error if the knowledge base is not initialized. if len(self.kb) == 0: raise ValueError(Errors.E139.format(name=self.name)) def begin_training(self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs): self.require_kb() nO = self.kb.entity_vector_length self.set_output(nO) self.model.initialize() if sgd is None: sgd = self.create_optimizer() return sgd def update(self, examples, *, set_annotations=False, drop=0.0, sgd=None, losses=None): self.require_kb() if losses is None: losses = {} losses.setdefault(self.name, 0.0) if not examples: return losses sentence_docs = [] try: docs = [eg.predicted for eg in examples] except AttributeError: types = set([type(eg) for eg in examples]) raise TypeError(Errors.E978.format(name="EntityLinker", method="update", types=types)) if set_annotations: # This seems simpler than other ways to get that exact output -- but # it does run the model twice :( predictions = self.model.predict(docs) for eg in examples: sentences = [s for s in eg.predicted.sents] kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True) for ent in eg.predicted.ents: kb_id = kb_ids[ent.start] # KB ID of the first token is the same as the whole span 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) # 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 0.0 sentence_encodings, bp_context = self.model.begin_update(sentence_docs) loss, d_scores = self.get_similarity_loss( sentence_encodings=sentence_encodings, examples=examples ) bp_context(d_scores) if sgd is not None: self.model.finish_update(sgd) losses[self.name] += loss if set_annotations: self.set_annotations(docs, predictions) return losses def get_similarity_loss(self, examples, sentence_encodings): entity_encodings = [] for eg in examples: kb_ids = eg.get_aligned("ENT_KB_ID", as_string=True) for ent in eg.predicted.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: raise RuntimeError(Errors.E147.format(method="get_similarity_loss", msg="gold entities do not match up")) gradients = self.distance.get_grad(sentence_encodings, entity_encodings) loss = self.distance.get_loss(sentence_encodings, entity_encodings) loss = loss / len(entity_encodings) return loss, gradients def __call__(self, doc): kb_ids = self.predict([doc]) self.set_annotations([doc], kb_ids) return doc def pipe(self, stream, batch_size=128): for docs in util.minibatch(stream, size=batch_size): kb_ids = self.predict(docs) self.set_annotations(docs, kb_ids) yield from docs def predict(self, docs): """ Return the KB IDs for each entity in each doc, including NIL if there is no prediction """ self.require_kb() entity_count = 0 final_kb_ids = [] 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 sentence and each entity # This may go wrong if there are entities across sentences - which shouldn't happen normally. for sent_index, sent in enumerate(sentences): if sent.ents: # get n_neightbour 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) sentence_encoding = self.model.predict([sent_doc])[0] xp = get_array_module(sentence_encoding) sentence_encoding_t = sentence_encoding.T sentence_norm = xp.linalg.norm(sentence_encoding_t) for ent in sent.ents: entity_count += 1 to_discard = self.cfg.get("labels_discard", []) if to_discard and ent.label_ in to_discard: # ignoring this entity - setting to NIL final_kb_ids.append(self.NIL) else: candidates = self.kb.get_candidates(ent.text) 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) # this will set all prior probabilities to 0 if they should be excluded from the model prior_probs = xp.asarray([c.prior_prob for c in candidates]) if not self.cfg.get("incl_prior", True): prior_probs = xp.asarray([0.0 for c in candidates]) scores = prior_probs # add in similarity from the context if self.cfg.get("incl_context", True): 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): raise RuntimeError(Errors.E147.format(method="predict", msg="result variables not of equal length")) return final_kb_ids def set_annotations(self, docs, kb_ids): 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 for doc in docs: for ent in doc.ents: kb_id = kb_ids[i] i += 1 for token in ent: token.ent_kb_id_ = kb_id def to_disk(self, path, exclude=tuple()): serialize = {} self.cfg["entity_width"] = self.kb.entity_vector_length serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg) serialize["vocab"] = lambda p: self.vocab.to_disk(p) serialize["kb"] = lambda p: self.kb.dump(p) serialize["model"] = lambda p: self.model.to_disk(p) util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple()): def load_model(p): try: self.model.from_bytes(p.open("rb").read()) except AttributeError: raise ValueError(Errors.E149) def load_kb(p): self.kb = KnowledgeBase(vocab=self.vocab, entity_vector_length=self.cfg["entity_width"]) self.kb.load_bulk(p) deserialize = {} deserialize["vocab"] = lambda p: self.vocab.from_disk(p) deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p)) deserialize["kb"] = load_kb 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 @component("sentencizer", assigns=["token.is_sent_start", "doc.sents"]) class Sentencizer(Pipe): """Segment the Doc into sentences using a rule-based strategy. DOCS: https://spacy.io/api/sentencizer """ default_punct_chars = ['!', '.', '?', '։', '؟', '۔', '܀', '܁', '܂', '߹', '।', '॥', '၊', '။', '።', '፧', '፨', '᙮', '᜵', '᜶', '᠃', '᠉', '᥄', '᥅', '᪨', '᪩', '᪪', '᪫', '᭚', '᭛', '᭞', '᭟', '᰻', '᰼', '᱾', '᱿', '‼', '‽', '⁇', '⁈', '⁉', '⸮', '⸼', '꓿', '꘎', '꘏', '꛳', '꛷', '꡶', '꡷', '꣎', '꣏', '꤯', '꧈', '꧉', '꩝', '꩞', '꩟', '꫰', '꫱', '꯫', '﹒', '﹖', '﹗', '!', '.', '?', '𐩖', '𐩗', '𑁇', '𑁈', '𑂾', '𑂿', '𑃀', '𑃁', '𑅁', '𑅂', '𑅃', '𑇅', '𑇆', '𑇍', '𑇞', '𑇟', '𑈸', '𑈹', '𑈻', '𑈼', '𑊩', '𑑋', '𑑌', '𑗂', '𑗃', '𑗉', '𑗊', '𑗋', '𑗌', '𑗍', '𑗎', '𑗏', '𑗐', '𑗑', '𑗒', '𑗓', '𑗔', '𑗕', '𑗖', '𑗗', '𑙁', '𑙂', '𑜼', '𑜽', '𑜾', '𑩂', '𑩃', '𑪛', '𑪜', '𑱁', '𑱂', '𖩮', '𖩯', '𖫵', '𖬷', '𖬸', '𖭄', '𛲟', '𝪈', '。', '。'] def __init__(self, punct_chars=None, **kwargs): """Initialize the sentencizer. punct_chars (list): Punctuation characters to split on. Will be serialized with the nlp object. RETURNS (Sentencizer): The sentencizer component. DOCS: https://spacy.io/api/sentencizer#init """ if punct_chars: self.punct_chars = set(punct_chars) else: self.punct_chars = set(self.default_punct_chars) @classmethod def from_nlp(cls, nlp, model=None, **cfg): return cls(**cfg) def begin_training( self, get_examples=lambda: [], pipeline=None, sgd=None, **kwargs ): pass def __call__(self, doc): """Apply the sentencizer to a Doc and set Token.is_sent_start. example (Doc or Example): The document to process. RETURNS (Doc or Example): The processed Doc or Example. DOCS: https://spacy.io/api/sentencizer#call """ start = 0 seen_period = False for i, token in enumerate(doc): is_in_punct_chars = token.text in self.punct_chars token.is_sent_start = i == 0 if seen_period and not token.is_punct and not is_in_punct_chars: doc[start].is_sent_start = True start = token.i seen_period = False elif is_in_punct_chars: seen_period = True if start < len(doc): doc[start].is_sent_start = True return doc def pipe(self, stream, batch_size=128): for docs in util.minibatch(stream, size=batch_size): predictions = self.predict(docs) self.set_annotations(docs, predictions) yield from docs def predict(self, docs): """Apply the pipeline's model to a batch of docs, without modifying them. """ if not any(len(doc) for doc in docs): # Handle cases where there are no tokens in any docs. guesses = [[] for doc in docs] return guesses guesses = [] for doc in docs: doc_guesses = [False] * len(doc) if len(doc) > 0: start = 0 seen_period = False doc_guesses[0] = True for i, token in enumerate(doc): is_in_punct_chars = token.text in self.punct_chars if seen_period and not token.is_punct and not is_in_punct_chars: doc_guesses[start] = True start = token.i seen_period = False elif is_in_punct_chars: seen_period = True if start < len(doc): doc_guesses[start] = True guesses.append(doc_guesses) return guesses def set_annotations(self, docs, batch_tag_ids): if isinstance(docs, Doc): docs = [docs] cdef Doc doc cdef int idx = 0 for i, doc in enumerate(docs): doc_tag_ids = batch_tag_ids[i] for j, tag_id in enumerate(doc_tag_ids): # Don't clobber existing sentence boundaries if doc.c[j].sent_start == 0: if tag_id: doc.c[j].sent_start = 1 else: doc.c[j].sent_start = -1 def to_bytes(self, **kwargs): """Serialize the sentencizer to a bytestring. RETURNS (bytes): The serialized object. DOCS: https://spacy.io/api/sentencizer#to_bytes """ return srsly.msgpack_dumps({"punct_chars": list(self.punct_chars)}) def from_bytes(self, bytes_data, **kwargs): """Load the sentencizer from a bytestring. bytes_data (bytes): The data to load. returns (Sentencizer): The loaded object. DOCS: https://spacy.io/api/sentencizer#from_bytes """ cfg = srsly.msgpack_loads(bytes_data) self.punct_chars = set(cfg.get("punct_chars", self.default_punct_chars)) return self def to_disk(self, path, exclude=tuple(), **kwargs): """Serialize the sentencizer to disk. DOCS: https://spacy.io/api/sentencizer#to_disk """ path = util.ensure_path(path) path = path.with_suffix(".json") srsly.write_json(path, {"punct_chars": list(self.punct_chars)}) def from_disk(self, path, exclude=tuple(), **kwargs): """Load the sentencizer from disk. DOCS: https://spacy.io/api/sentencizer#from_disk """ path = util.ensure_path(path) path = path.with_suffix(".json") cfg = srsly.read_json(path) self.punct_chars = set(cfg.get("punct_chars", self.default_punct_chars)) return self # Cython classes can't be decorated, so we need to add the factories here Language.factories["parser"] = lambda nlp, model, **cfg: parser_factory(nlp, model, **cfg) Language.factories["ner"] = lambda nlp, model, **cfg: ner_factory(nlp, model, **cfg) def parser_factory(nlp, model, **cfg): default_config = {"learn_tokens": False, "min_action_freq": 30, "beam_width": 1, "beam_update_prob": 1.0} if model is None: model = default_parser() warnings.warn(Warnings.W098.format(name="parser")) for key, value in default_config.items(): if key not in cfg: cfg[key] = value return DependencyParser.from_nlp(nlp, model, **cfg) def ner_factory(nlp, model, **cfg): default_config = {"learn_tokens": False, "min_action_freq": 30, "beam_width": 1, "beam_update_prob": 1.0} if model is None: model = default_ner() warnings.warn(Warnings.W098.format(name="ner")) for key, value in default_config.items(): if key not in cfg: cfg[key] = value return EntityRecognizer.from_nlp(nlp, model, **cfg) __all__ = ["Tagger", "DependencyParser", "EntityRecognizer", "TextCategorizer", "EntityLinker", "Sentencizer", "SentenceRecognizer"]