# cython: infer_types=True # cython: profile=True # coding: utf8 from __future__ import unicode_literals import numpy import srsly import random from collections import OrderedDict from thinc.api import chain from thinc.v2v import Affine, Maxout, Softmax from thinc.misc import LayerNorm from thinc.neural.util import to_categorical from thinc.neural.util import get_array_module from .functions import merge_subtokens 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 ..syntax import nonproj from ..attrs import POS, ID from ..parts_of_speech import X from ..kb import KnowledgeBase from .._ml import Tok2Vec, build_tagger_model, cosine, get_cossim_loss from .._ml import build_text_classifier, build_simple_cnn_text_classifier from .._ml import build_bow_text_classifier, build_nel_encoder from .._ml import link_vectors_to_models, zero_init, flatten from .._ml import masked_language_model, create_default_optimizer from ..errors import Errors, TempErrors 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 Model(cls, *shape, **kwargs): """Initialize a model for the pipe.""" raise NotImplementedError def __init__(self, vocab, model=True, **cfg): """Create a new pipe instance.""" raise NotImplementedError def __call__(self, 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. """ self.require_model() predictions = self.predict([doc]) if isinstance(predictions, tuple) and len(predictions) == 2: scores, tensors = predictions self.set_annotations([doc], scores, tensors=tensors) else: self.set_annotations([doc], predictions) return doc def require_model(self): """Raise an error if the component's model is not initialized.""" if getattr(self, "model", None) in (None, True, False): raise ValueError(Errors.E109.format(name=self.name)) def pipe(self, stream, batch_size=128, n_threads=-1): """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): docs = list(docs) predictions = self.predict(docs) if isinstance(predictions, tuple) and len(tuple) == 2: scores, tensors = predictions self.set_annotations(docs, scores, tensors=tensors) else: 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. """ self.require_model() raise NotImplementedError def set_annotations(self, docs, scores, tensors=None): """Modify a batch of documents, using pre-computed scores.""" raise NotImplementedError def update(self, docs, golds, drop=0.0, sgd=None, losses=None): """Learn from a batch of documents and gold-standard information, updating the pipe's model. Delegates to predict() and get_loss(). """ pass def rehearse(self, docs, sgd=None, losses=None, **config): pass def get_loss(self, docs, golds, scores): """Find the loss and gradient of loss for the batch of documents 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 pre-trained 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(self.model.ops, **self.cfg.get("optimizer", {})) def begin_training( self, get_gold_tuples=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.""" if self.model is True: self.model = self.Model(**self.cfg) if hasattr(self, "vocab"): link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd 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(), **kwargs): """Serialize the pipe to a bytestring. exclude (list): String names of serialization fields to exclude. RETURNS (bytes): The serialized object. """ serialize = OrderedDict() serialize["cfg"] = lambda: srsly.json_dumps(self.cfg) if self.model not in (True, False, None): serialize["model"] = self.model.to_bytes if hasattr(self, "vocab"): serialize["vocab"] = self.vocab.to_bytes exclude = util.get_serialization_exclude(serialize, exclude, kwargs) return util.to_bytes(serialize, exclude) def from_bytes(self, bytes_data, exclude=tuple(), **kwargs): """Load the pipe from a bytestring.""" def load_model(b): # TODO: Remove this once we don't have to handle previous models if self.cfg.get("pretrained_dims") and "pretrained_vectors" not in self.cfg: self.cfg["pretrained_vectors"] = self.vocab.vectors.name if self.model is True: self.model = self.Model(**self.cfg) try: self.model.from_bytes(b) except AttributeError: raise ValueError(Errors.E149) deserialize = OrderedDict() deserialize["cfg"] = lambda b: self.cfg.update(srsly.json_loads(b)) if hasattr(self, "vocab"): deserialize["vocab"] = lambda b: self.vocab.from_bytes(b) deserialize["model"] = load_model exclude = util.get_serialization_exclude(deserialize, exclude, kwargs) util.from_bytes(bytes_data, deserialize, exclude) return self def to_disk(self, path, exclude=tuple(), **kwargs): """Serialize the pipe to disk.""" serialize = OrderedDict() serialize["cfg"] = lambda p: srsly.write_json(p, self.cfg) serialize["vocab"] = lambda p: self.vocab.to_disk(p) if self.model not in (None, True, False): serialize["model"] = lambda p: p.open("wb").write(self.model.to_bytes()) exclude = util.get_serialization_exclude(serialize, exclude, kwargs) util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple(), **kwargs): """Load the pipe from disk.""" def load_model(p): # TODO: Remove this once we don't have to handle previous models if self.cfg.get("pretrained_dims") and "pretrained_vectors" not in self.cfg: self.cfg["pretrained_vectors"] = self.vocab.vectors.name if self.model is True: self.model = self.Model(**self.cfg) try: self.model.from_bytes(p.open("rb").read()) except AttributeError: raise ValueError(Errors.E149) deserialize = OrderedDict() deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p)) deserialize["vocab"] = lambda p: self.vocab.from_disk(p) deserialize["model"] = load_model exclude = util.get_serialization_exclude(deserialize, exclude, kwargs) util.from_disk(path, deserialize, exclude) return self class Tensorizer(Pipe): """Pre-train position-sensitive vectors for tokens.""" name = "tensorizer" @classmethod def Model(cls, output_size=300, **cfg): """Create a new statistical model for the class. width (int): Output size of the model. embed_size (int): Number of vectors in the embedding table. **cfg: Config parameters. RETURNS (Model): A `thinc.neural.Model` or similar instance. """ input_size = util.env_opt("token_vector_width", cfg.get("input_size", 96)) return zero_init(Affine(output_size, input_size, drop_factor=0.0)) def __init__(self, vocab, model=True, **cfg): """Construct a new statistical model. Weights are not allocated on initialisation. vocab (Vocab): A `Vocab` instance. The model must share the same `Vocab` instance with the `Doc` objects it will process. model (Model): A `Model` instance or `True` to allocate one later. **cfg: Config parameters. EXAMPLE: >>> from spacy.pipeline import TokenVectorEncoder >>> tok2vec = TokenVectorEncoder(nlp.vocab) >>> tok2vec.model = tok2vec.Model(128, 5000) """ self.vocab = vocab self.model = model self.input_models = [] self.cfg = dict(cfg) self.cfg.setdefault("cnn_maxout_pieces", 3) def __call__(self, doc): """Add context-sensitive vectors to a `Doc`, e.g. from a CNN or LSTM model. Vectors are set to the `Doc.tensor` attribute. docs (Doc or iterable): One or more documents to add vectors to. RETURNS (dict or None): Intermediate computations. """ tokvecses = self.predict([doc]) self.set_annotations([doc], tokvecses) return doc def pipe(self, stream, batch_size=128, n_threads=-1): """Process `Doc` objects as a stream. stream (iterator): A sequence of `Doc` objects to process. batch_size (int): Number of `Doc` objects to group. YIELDS (iterator): A sequence of `Doc` objects, in order of input. """ for docs in util.minibatch(stream, size=batch_size): docs = list(docs) tensors = self.predict(docs) self.set_annotations(docs, tensors) yield from docs def predict(self, docs): """Return a single tensor for a batch of documents. docs (iterable): A sequence of `Doc` objects. RETURNS (object): Vector representations for each token in the docs. """ self.require_model() inputs = self.model.ops.flatten([doc.tensor for doc in docs]) outputs = self.model(inputs) return self.model.ops.unflatten(outputs, [len(d) for d in docs]) def set_annotations(self, docs, tensors): """Set the tensor attribute for a batch of documents. docs (iterable): A sequence of `Doc` objects. tensors (object): Vector representation for each token in the docs. """ for doc, tensor in zip(docs, tensors): if tensor.shape[0] != len(doc): raise ValueError(Errors.E076.format(rows=tensor.shape[0], words=len(doc))) doc.tensor = tensor def update(self, docs, golds, state=None, drop=0.0, sgd=None, losses=None): """Update the model. docs (iterable): A batch of `Doc` objects. golds (iterable): A batch of `GoldParse` objects. drop (float): The dropout rate. sgd (callable): An optimizer. RETURNS (dict): Results from the update. """ self.require_model() if isinstance(docs, Doc): docs = [docs] inputs = [] bp_inputs = [] for tok2vec in self.input_models: tensor, bp_tensor = tok2vec.begin_update(docs, drop=drop) inputs.append(tensor) bp_inputs.append(bp_tensor) inputs = self.model.ops.xp.hstack(inputs) scores, bp_scores = self.model.begin_update(inputs, drop=drop) loss, d_scores = self.get_loss(docs, golds, scores) d_inputs = bp_scores(d_scores, sgd=sgd) d_inputs = self.model.ops.xp.split(d_inputs, len(self.input_models), axis=1) for d_input, bp_input in zip(d_inputs, bp_inputs): bp_input(d_input, sgd=sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += loss return loss def get_loss(self, docs, golds, prediction): ids = self.model.ops.flatten([doc.to_array(ID).ravel() for doc in docs]) target = self.vocab.vectors.data[ids] d_scores = (prediction - target) / prediction.shape[0] loss = (d_scores ** 2).sum() return loss, d_scores def begin_training(self, gold_tuples=lambda: [], pipeline=None, sgd=None, **kwargs): """Allocate models, pre-process training data and acquire an optimizer. gold_tuples (iterable): Gold-standard training data. pipeline (list): The pipeline the model is part of. """ if pipeline is not None: for name, model in pipeline: if getattr(model, "tok2vec", None): self.input_models.append(model.tok2vec) if self.model is True: self.model = self.Model(**self.cfg) link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd class Tagger(Pipe): """Pipeline component for part-of-speech tagging. DOCS: https://spacy.io/api/tagger """ name = "tagger" def __init__(self, vocab, model=True, **cfg): self.vocab = vocab self.model = model self._rehearsal_model = None self.cfg = OrderedDict(sorted(cfg.items())) self.cfg.setdefault("cnn_maxout_pieces", 2) @property def labels(self): return tuple(self.vocab.morphology.tag_names) @property def tok2vec(self): if self.model in (None, True, False): return None else: return chain(self.model.tok2vec, flatten) def __call__(self, doc): tags, tokvecs = self.predict([doc]) self.set_annotations([doc], tags, tensors=tokvecs) return doc def pipe(self, stream, batch_size=128, n_threads=-1): for docs in util.minibatch(stream, size=batch_size): docs = list(docs) tag_ids, tokvecs = self.predict(docs) self.set_annotations(docs, tag_ids, tensors=tokvecs) yield from docs def predict(self, docs): self.require_model() 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.allocate((0, n_labels)) for doc in docs] tokvecs = self.model.ops.allocate((0, self.model.tok2vec.nO)) return guesses, tokvecs tokvecs = self.model.tok2vec(docs) scores = self.model.softmax(tokvecs) 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, tokvecs def set_annotations(self, docs, batch_tag_ids, tensors=None): 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 if tensors is not None and len(tensors): if isinstance(doc.tensor, numpy.ndarray) \ and not isinstance(tensors[i], numpy.ndarray): doc.extend_tensor(tensors[i].get()) else: doc.extend_tensor(tensors[i]) doc.is_tagged = True def update(self, docs, golds, drop=0., sgd=None, losses=None): self.require_model() if losses is not None and self.name not in losses: losses[self.name] = 0. tag_scores, bp_tag_scores = self.model.begin_update(docs, drop=drop) loss, d_tag_scores = self.get_loss(docs, golds, tag_scores) bp_tag_scores(d_tag_scores, sgd=sgd) if losses is not None: losses[self.name] += loss def rehearse(self, docs, drop=0., sgd=None, losses=None): """Perform a 'rehearsal' update, where we try to match the output of an initial model. """ if self._rehearsal_model is None: return guesses, backprop = self.model.begin_update(docs, drop=drop) target = self._rehearsal_model(docs) gradient = guesses - target backprop(gradient, sgd=sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += (gradient**2).sum() def get_loss(self, docs, golds, scores): scores = self.model.ops.flatten(scores) tag_index = {tag: i for i, tag in enumerate(self.labels)} cdef int idx = 0 correct = numpy.zeros((scores.shape[0],), dtype="i") guesses = scores.argmax(axis=1) known_labels = numpy.ones((scores.shape[0], 1), dtype="f") for gold in golds: for tag in gold.tags: if tag is None: correct[idx] = guesses[idx] elif tag in tag_index: correct[idx] = tag_index[tag] else: correct[idx] = 0 known_labels[idx] = 0. idx += 1 correct = self.model.ops.xp.array(correct, dtype="i") d_scores = scores - to_categorical(correct, nb_classes=scores.shape[1]) d_scores *= self.model.ops.asarray(known_labels) loss = (d_scores**2).sum() d_scores = self.model.ops.unflatten(d_scores, [len(d) for d in docs]) return float(loss), d_scores def begin_training(self, get_gold_tuples=lambda: [], pipeline=None, sgd=None, **kwargs): orig_tag_map = dict(self.vocab.morphology.tag_map) new_tag_map = OrderedDict() for raw_text, annots_brackets in get_gold_tuples(): _ = annots_brackets.pop() for annots, brackets in annots_brackets: ids, words, tags, heads, deps, ents = annots for tag in tags: 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: vocab.morphology = Morphology(vocab.strings, new_tag_map, vocab.morphology.lemmatizer, exc=vocab.morphology.exc) self.cfg["pretrained_vectors"] = kwargs.get("pretrained_vectors") if self.model is True: for hp in ["token_vector_width", "conv_depth"]: if hp in kwargs: self.cfg[hp] = kwargs[hp] self.model = self.Model(self.vocab.morphology.n_tags, **self.cfg) link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd @classmethod def Model(cls, n_tags, **cfg): if cfg.get("pretrained_dims") and not cfg.get("pretrained_vectors"): raise ValueError(TempErrors.T008) return build_tagger_model(n_tags, **cfg) def add_label(self, label, values=None): if label in self.labels: return 0 if self.model not in (True, False, None): # 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(), **kwargs): serialize = OrderedDict() if self.model not in (None, True, False): serialize["model"] = self.model.to_bytes serialize["vocab"] = self.vocab.to_bytes serialize["cfg"] = lambda: srsly.json_dumps(self.cfg) tag_map = OrderedDict(sorted(self.vocab.morphology.tag_map.items())) serialize["tag_map"] = lambda: srsly.msgpack_dumps(tag_map) exclude = util.get_serialization_exclude(serialize, exclude, kwargs) return util.to_bytes(serialize, exclude) def from_bytes(self, bytes_data, exclude=tuple(), **kwargs): def load_model(b): # TODO: Remove this once we don't have to handle previous models if self.cfg.get("pretrained_dims") and "pretrained_vectors" not in self.cfg: self.cfg["pretrained_vectors"] = self.vocab.vectors.name if self.model is True: token_vector_width = util.env_opt( "token_vector_width", self.cfg.get("token_vector_width", 96)) self.model = self.Model(self.vocab.morphology.n_tags, **self.cfg) 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 = OrderedDict(( ("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)), )) exclude = util.get_serialization_exclude(deserialize, exclude, kwargs) util.from_bytes(bytes_data, deserialize, exclude) return self def to_disk(self, path, exclude=tuple(), **kwargs): tag_map = OrderedDict(sorted(self.vocab.morphology.tag_map.items())) serialize = OrderedDict(( ("vocab", lambda p: self.vocab.to_disk(p)), ("tag_map", lambda p: srsly.write_msgpack(p, tag_map)), ("model", lambda p: p.open("wb").write(self.model.to_bytes())), ("cfg", lambda p: srsly.write_json(p, self.cfg)) )) exclude = util.get_serialization_exclude(serialize, exclude, kwargs) util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple(), **kwargs): def load_model(p): # TODO: Remove this once we don't have to handle previous models if self.cfg.get("pretrained_dims") and "pretrained_vectors" not in self.cfg: self.cfg["pretrained_vectors"] = self.vocab.vectors.name if self.model is True: self.model = self.Model(self.vocab.morphology.n_tags, **self.cfg) 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 = OrderedDict(( ("cfg", lambda p: self.cfg.update(_load_cfg(p))), ("vocab", lambda p: self.vocab.from_disk(p)), ("tag_map", load_tag_map), ("model", load_model), )) exclude = util.get_serialization_exclude(deserialize, exclude, kwargs) util.from_disk(path, deserialize, exclude) return self class MultitaskObjective(Tagger): """Experimental: Assist training of a parser or tagger, by training a side-objective. """ name = "nn_labeller" def __init__(self, vocab, model=True, target='dep_tag_offset', **cfg): self.vocab = vocab self.model = model 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) self.cfg.setdefault("cnn_maxout_pieces", 2) @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, tensors=None): pass def begin_training(self, get_gold_tuples=lambda: [], pipeline=None, tok2vec=None, sgd=None, **kwargs): gold_tuples = nonproj.preprocess_training_data(get_gold_tuples()) for raw_text, annots_brackets in gold_tuples: for annots, brackets in annots_brackets: ids, words, tags, heads, deps, ents = annots for i in range(len(ids)): label = self.make_label(i, words, tags, heads, deps, ents) if label is not None and label not in self.labels: self.labels[label] = len(self.labels) if self.model is True: token_vector_width = util.env_opt("token_vector_width") self.model = self.Model(len(self.labels), tok2vec=tok2vec) link_vectors_to_models(self.vocab) if sgd is None: sgd = self.create_optimizer() return sgd @classmethod def Model(cls, n_tags, tok2vec=None, **cfg): token_vector_width = util.env_opt("token_vector_width", 96) softmax = Softmax(n_tags, token_vector_width*2) model = chain( tok2vec, LayerNorm(Maxout(token_vector_width*2, token_vector_width, pieces=3)), softmax ) model.tok2vec = tok2vec model.softmax = softmax return model def predict(self, docs): self.require_model() tokvecs = self.model.tok2vec(docs) scores = self.model.softmax(tokvecs) return tokvecs, scores def get_loss(self, docs, golds, scores): if len(docs) != len(golds): raise ValueError(Errors.E077.format(value="loss", n_docs=len(docs), n_golds=len(golds))) cdef int idx = 0 correct = numpy.zeros((scores.shape[0],), dtype="i") guesses = scores.argmax(axis=1) for i, gold in enumerate(golds): for j in range(len(docs[i])): # Handes alignment for tokenization differences label = self.make_label(j, gold.words, gold.tags, gold.heads, gold.labels, gold.ents) 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, nb_classes=scores.shape[1]) loss = (d_scores**2).sum() return float(loss), d_scores @staticmethod def make_dep(i, words, tags, heads, deps, ents): if deps[i] is None or heads[i] is None: return None return deps[i] @staticmethod def make_tag(i, words, tags, heads, deps, ents): return tags[i] @staticmethod def make_ent(i, words, tags, heads, deps, ents): if ents is None: return None return ents[i] @staticmethod def make_dep_tag_offset(i, words, tags, heads, deps, ents): if deps[i] is None or heads[i] is None: return None offset = heads[i] - i offset = min(offset, 2) offset = max(offset, -2) return "%s-%s:%d" % (deps[i], tags[i], offset) @staticmethod def make_ent_tag(i, words, tags, heads, deps, ents): if ents is None or ents[i] is None: return None else: return "%s-%s" % (tags[i], ents[i]) @staticmethod def make_sent_start(target, words, tags, heads, deps, ents, cache=True, _cache={}): """A multi-task objective for representing sentence boundaries, using BILU scheme. (O is impossible) The implementation of this method uses an internal cache that relies on the identity of the heads array, to avoid requiring a new piece of gold data. You can pass cache=False if you know the cache will do the wrong thing. """ assert len(words) == len(heads) assert target < len(words), (target, len(words)) if cache: if id(heads) in _cache: return _cache[id(heads)][target] else: for key in list(_cache.keys()): _cache.pop(key) sent_tags = ["I-SENT"] * len(words) _cache[id(heads)] = sent_tags else: sent_tags = ["I-SENT"] * len(words) def _find_root(child): seen = set([child]) while child is not None and heads[child] != child: seen.add(child) child = heads[child] return child sentences = {} for i in range(len(words)): root = _find_root(i) if root is None: sent_tags[i] = None else: sentences.setdefault(root, []).append(i) for root, span in sorted(sentences.items()): if len(span) == 1: sent_tags[span[0]] = "U-SENT" else: sent_tags[span[0]] = "B-SENT" sent_tags[span[-1]] = "L-SENT" return sent_tags[target] class ClozeMultitask(Pipe): @classmethod def Model(cls, vocab, tok2vec, **cfg): output_size = vocab.vectors.data.shape[1] output_layer = chain( LayerNorm(Maxout(output_size, tok2vec.nO, pieces=3)), zero_init(Affine(output_size, output_size, drop_factor=0.0)) ) model = chain(tok2vec, output_layer) model = masked_language_model(vocab, model) model.tok2vec = tok2vec model.output_layer = output_layer return model def __init__(self, vocab, model=True, **cfg): self.vocab = vocab self.model = model self.cfg = cfg def set_annotations(self, docs, dep_ids, tensors=None): pass def begin_training(self, get_gold_tuples=lambda: [], pipeline=None, tok2vec=None, sgd=None, **kwargs): link_vectors_to_models(self.vocab) if self.model is True: self.model = self.Model(self.vocab, tok2vec) X = self.model.ops.allocate((5, self.model.tok2vec.nO)) self.model.output_layer.begin_training(X) if sgd is None: sgd = self.create_optimizer() return sgd def predict(self, docs): self.require_model() tokvecs = self.model.tok2vec(docs) vectors = self.model.output_layer(tokvecs) return tokvecs, vectors def get_loss(self, docs, 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([doc.to_array(ID).ravel() for doc in docs]) target = vectors[ids] gradient = (prediction - target) / prediction.shape[0] loss = (gradient**2).sum() return float(loss), gradient def update(self, docs, golds, drop=0., sgd=None, losses=None): pass def rehearse(self, docs, drop=0., sgd=None, losses=None): self.require_model() if losses is not None and self.name not in losses: losses[self.name] = 0. predictions, bp_predictions = self.model.begin_update(docs, drop=drop) loss, d_predictions = self.get_loss(docs, self.vocab.vectors.data, predictions) bp_predictions(d_predictions, sgd=sgd) if losses is not None: losses[self.name] += loss class TextCategorizer(Pipe): """Pipeline component for text classification. DOCS: https://spacy.io/api/textcategorizer """ name = 'textcat' @classmethod def Model(cls, nr_class=1, **cfg): embed_size = util.env_opt("embed_size", 2000) if "token_vector_width" in cfg: token_vector_width = cfg["token_vector_width"] else: token_vector_width = util.env_opt("token_vector_width", 96) if cfg.get("architecture") == "simple_cnn": tok2vec = Tok2Vec(token_vector_width, embed_size, **cfg) return build_simple_cnn_text_classifier(tok2vec, nr_class, **cfg) elif cfg.get("architecture") == "bow": return build_bow_text_classifier(nr_class, **cfg) else: return build_text_classifier(nr_class, **cfg) @property def tok2vec(self): if self.model in (None, True, False): return None else: return self.model.tok2vec def __init__(self, vocab, model=True, **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, n_threads=-1): for docs in util.minibatch(stream, size=batch_size): docs = list(docs) scores, tensors = self.predict(docs) self.set_annotations(docs, scores, tensors=tensors) yield from docs def predict(self, docs): self.require_model() 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, tensors scores = self.model(docs) scores = self.model.ops.asarray(scores) return scores, tensors def set_annotations(self, docs, scores, tensors=None): for i, doc in enumerate(docs): for j, label in enumerate(self.labels): doc.cats[label] = float(scores[i, j]) def update(self, docs, golds, state=None, drop=0., sgd=None, losses=None): self.require_model() scores, bp_scores = self.model.begin_update(docs, drop=drop) loss, d_scores = self.get_loss(docs, golds, scores) bp_scores(d_scores, sgd=sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += loss def rehearse(self, docs, drop=0., sgd=None, losses=None): if self._rehearsal_model is None: return scores, bp_scores = self.model.begin_update(docs, drop=drop) target = self._rehearsal_model(docs) gradient = scores - target bp_scores(gradient, sgd=sgd) if losses is not None: losses.setdefault(self.name, 0.0) losses[self.name] += (gradient**2).sum() def get_loss(self, docs, golds, scores): truths = numpy.zeros((len(golds), len(self.labels)), dtype="f") not_missing = numpy.ones((len(golds), len(self.labels)), dtype="f") for i, gold in enumerate(golds): for j, label in enumerate(self.labels): if label in gold.cats: truths[i, j] = gold.cats[label] else: not_missing[i, j] = 0. truths = self.model.ops.asarray(truths) 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 label in self.labels: return 0 if self.model not in (None, True, False): # 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 = Affine(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_gold_tuples=lambda: [], pipeline=None, sgd=None, **kwargs): for raw_text, annots_brackets in get_gold_tuples(): cats = annots_brackets.pop() for cat in cats: self.add_label(cat) if self.model is True: self.cfg["pretrained_vectors"] = kwargs.get("pretrained_vectors") self.require_labels() self.model = self.Model(len(self.labels), **self.cfg) link_vectors_to_models(self.vocab) 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 """ name = "parser" 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, target): if target == "cloze": cloze = ClozeMultitask(self.vocab) self._multitasks.append(cloze) else: labeller = MultitaskObjective(self.vocab, target=target) self._multitasks.append(labeller) def init_multitask_objectives(self, get_gold_tuples, pipeline, sgd=None, **cfg): for labeller in self._multitasks: tok2vec = self.model.tok2vec labeller.begin_training(get_gold_tuples, pipeline=pipeline, tok2vec=tok2vec, sgd=sgd) def __reduce__(self): return (DependencyParser, (self.vocab, self.moves, self.model), None, None) @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" TransitionSystem = BiluoPushDown nr_feature = 6 def add_multitask_objective(self, target): if target == "cloze": cloze = ClozeMultitask(self.vocab) self._multitasks.append(cloze) else: labeller = MultitaskObjective(self.vocab, target=target) self._multitasks.append(labeller) def init_multitask_objectives(self, get_gold_tuples, pipeline, sgd=None, **cfg): for labeller in self._multitasks: tok2vec = self.model.tok2vec labeller.begin_training(get_gold_tuples, pipeline=pipeline, tok2vec=tok2vec) def __reduce__(self): return (EntityRecognizer, (self.vocab, self.moves, self.model), None, None) @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)) class EntityLinker(Pipe): """Pipeline component for named entity linking. DOCS: https://spacy.io/api/entitylinker """ name = 'entity_linker' NIL = "NIL" # string used to refer to a non-existing link @classmethod def Model(cls, **cfg): embed_width = cfg.get("embed_width", 300) hidden_width = cfg.get("hidden_width", 128) type_to_int = cfg.get("type_to_int", dict()) model = build_nel_encoder(embed_width=embed_width, hidden_width=hidden_width, ner_types=len(type_to_int), **cfg) return model def __init__(self, vocab, **cfg): self.vocab = vocab self.model = True self.kb = None self.cfg = dict(cfg) def set_kb(self, kb): self.kb = kb def require_model(self): # Raise an error if the component's model is not initialized. if getattr(self, "model", None) in (None, True, False): raise ValueError(Errors.E109.format(name=self.name)) def require_kb(self): # Raise an error if the knowledge base is not initialized. if getattr(self, "kb", None) in (None, True, False): raise ValueError(Errors.E139.format(name=self.name)) def begin_training(self, get_gold_tuples=lambda: [], pipeline=None, sgd=None, **kwargs): self.require_kb() self.cfg["entity_width"] = self.kb.entity_vector_length if self.model is True: self.model = self.Model(**self.cfg) if sgd is None: sgd = self.create_optimizer() return sgd def update(self, docs, golds, state=None, drop=0.0, sgd=None, losses=None): self.require_model() self.require_kb() if losses is not None: losses.setdefault(self.name, 0.0) if not docs or not golds: return 0 if len(docs) != len(golds): raise ValueError(Errors.E077.format(value="EL training", n_docs=len(docs), n_golds=len(golds))) if isinstance(docs, Doc): docs = [docs] golds = [golds] context_docs = [] for doc, gold in zip(docs, golds): ents_by_offset = dict() for ent in doc.ents: ents_by_offset["{}_{}".format(ent.start_char, ent.end_char)] = ent for entity, kb_dict in gold.links.items(): start, end = entity mention = doc.text[start:end] for kb_id, value in kb_dict.items(): # Currently only training on the positive instances if value: context_docs.append(doc) context_encodings, bp_context = self.model.begin_update(context_docs, drop=drop) loss, d_scores = self.get_similarity_loss(scores=context_encodings, golds=golds, docs=None) bp_context(d_scores, sgd=sgd) if losses is not None: losses[self.name] += loss return loss def get_similarity_loss(self, docs, golds, scores): entity_encodings = [] for gold in golds: for entity, kb_dict in gold.links.items(): for kb_id, value in kb_dict.items(): # this loss function assumes we're only using positive examples if value: entity_encoding = self.kb.get_vector(kb_id) entity_encodings.append(entity_encoding) entity_encodings = self.model.ops.asarray(entity_encodings, dtype="float32") if scores.shape != entity_encodings.shape: raise RuntimeError(Errors.E147.format(method="get_loss", msg="gold entities do not match up")) loss, gradients = get_cossim_loss(yh=scores, y=entity_encodings) loss = loss / len(entity_encodings) return loss, gradients def get_loss(self, docs, golds, scores): cats = [] for gold in golds: for entity, kb_dict in gold.links.items(): for kb_id, value in kb_dict.items(): cats.append([value]) cats = self.model.ops.asarray(cats, dtype="float32") if len(scores) != len(cats): raise RuntimeError(Errors.E147.format(method="get_loss", msg="gold entities do not match up")) d_scores = (scores - cats) loss = (d_scores ** 2).sum() loss = loss / len(cats) return loss, d_scores def __call__(self, doc): kb_ids, tensors = self.predict([doc]) self.set_annotations([doc], kb_ids, tensors=tensors) return doc def pipe(self, stream, batch_size=128, n_threads=-1): for docs in util.minibatch(stream, size=batch_size): docs = list(docs) kb_ids, tensors = self.predict(docs) self.set_annotations(docs, kb_ids, tensors=tensors) 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_model() self.require_kb() entity_count = 0 final_kb_ids = [] final_tensors = [] if not docs: return final_kb_ids, final_tensors if isinstance(docs, Doc): docs = [docs] context_encodings = self.model(docs) xp = get_array_module(context_encodings) for i, doc in enumerate(docs): if len(doc) > 0: # currently, the context is the same for each entity in a sentence (should be refined) context_encoding = context_encodings[i] context_enc_t = context_encoding.T norm_1 = xp.linalg.norm(context_enc_t) for ent in doc.ents: entity_count += 1 candidates = self.kb.get_candidates(ent.text) if not candidates: final_kb_ids.append(self.NIL) # no prediction possible for this entity final_tensors.append(context_encoding) 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]) norm_2 = 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, context_enc_t) / (norm_1 * norm_2) if sims.shape != prior_probs.shape: raise ValueError(Errors.E161) scores = prior_probs + sims - (prior_probs*sims) # TODO: thresholding best_index = scores.argmax() best_candidate = candidates[best_index] final_kb_ids.append(best_candidate.entity_) final_tensors.append(context_encoding) if not (len(final_tensors) == len(final_kb_ids) == entity_count): raise RuntimeError(Errors.E147.format(method="predict", msg="result variables not of equal length")) return final_kb_ids, final_tensors def set_annotations(self, docs, kb_ids, tensors=None): 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(), **kwargs): serialize = OrderedDict() 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) if self.model not in (None, True, False): serialize["model"] = lambda p: p.open("wb").write(self.model.to_bytes()) exclude = util.get_serialization_exclude(serialize, exclude, kwargs) util.to_disk(path, serialize, exclude) def from_disk(self, path, exclude=tuple(), **kwargs): def load_model(p): if self.model is True: self.model = self.Model(**self.cfg) try: self.model.from_bytes(p.open("rb").read()) except AttributeError: raise ValueError(Errors.E149) def load_kb(p): kb = KnowledgeBase(vocab=self.vocab, entity_vector_length=self.cfg["entity_width"]) kb.load_bulk(p) self.set_kb(kb) deserialize = OrderedDict() deserialize["cfg"] = lambda p: self.cfg.update(_load_cfg(p)) deserialize["vocab"] = lambda p: self.vocab.from_disk(p) deserialize["kb"] = load_kb deserialize["model"] = load_model exclude = util.get_serialization_exclude(deserialize, exclude, kwargs) util.from_disk(path, deserialize, exclude) return self def rehearse(self, docs, sgd=None, losses=None, **config): raise NotImplementedError def add_label(self, label): raise NotImplementedError class Sentencizer(object): """Segment the Doc into sentences using a rule-based strategy. DOCS: https://spacy.io/api/sentencizer """ name = "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) def __call__(self, doc): """Apply the sentencizer to a Doc and set Token.is_sent_start. doc (Doc): The document to process. RETURNS (Doc): The processed Doc. 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 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 __all__ = ["Tagger", "DependencyParser", "EntityRecognizer", "Tensorizer", "TextCategorizer", "EntityLinker", "Sentencizer"]