spaCy/spacy/pipeline/simple_ner.py
Ines Montani 950832f087
Tidy up pipes (#5906)
* Tidy up pipes

* Fix init, defaults and raise custom errors

* Update docs

* Update docs [ci skip]

* Apply suggestions from code review

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>

* Tidy up error handling and validation, fix consistency

* Simplify get_examples check

* Remove unused import [ci skip]

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-08-11 23:29:31 +02:00

212 lines
7.0 KiB
Python

from typing import List, Iterable, Optional, Dict, Tuple, Callable, Set
from thinc.types import Floats2d
from thinc.api import SequenceCategoricalCrossentropy, set_dropout_rate, Model
from thinc.api import Optimizer, Config
from thinc.util import to_numpy
from ..errors import Errors
from ..gold import Example, spans_from_biluo_tags, iob_to_biluo, biluo_to_iob
from ..gold import validate_examples
from ..tokens import Doc
from ..language import Language
from ..vocab import Vocab
from ..scorer import Scorer
from .pipe import Pipe
default_model_config = """
[model]
@architectures = "spacy.BILUOTagger.v1"
[model.tok2vec]
@architectures = "spacy.HashEmbedCNN.v1"
pretrained_vectors = null
width = 128
depth = 4
embed_size = 7000
window_size = 1
maxout_pieces = 3
subword_features = true
"""
DEFAULT_SIMPLE_NER_MODEL = Config().from_str(default_model_config)["model"]
@Language.factory(
"simple_ner",
assigns=["doc.ents"],
default_config={"labels": [], "model": DEFAULT_SIMPLE_NER_MODEL},
scores=["ents_p", "ents_r", "ents_f", "ents_per_type"],
default_score_weights={"ents_f": 1.0, "ents_p": 0.0, "ents_r": 0.0},
)
def make_simple_ner(
nlp: Language, name: str, model: Model, labels: Iterable[str]
) -> "SimpleNER":
return SimpleNER(nlp.vocab, model, name, labels=labels)
class SimpleNER(Pipe):
"""Named entity recognition with a tagging model. The model should include
validity constraints to ensure that only valid tag sequences are returned."""
def __init__(
self,
vocab: Vocab,
model: Model,
name: str = "simple_ner",
*,
labels: Iterable[str],
) -> None:
self.vocab = vocab
self.model = model
self.name = name
self.cfg = {"labels": []}
for label in labels:
self.add_label(label)
self.loss_func = SequenceCategoricalCrossentropy(
names=self.get_tag_names(), normalize=True, missing_value=None
)
assert self.model is not None
@property
def is_biluo(self) -> bool:
return self.model.name.startswith("biluo")
@property
def labels(self) -> Tuple[str]:
return tuple(self.cfg["labels"])
def add_label(self, label: str) -> None:
"""Add a new label to the pipe.
label (str): The label to add.
DOCS: https://spacy.io/api/simplener#add_label
"""
if not isinstance(label, str):
raise ValueError(Errors.E187)
if label not in self.labels:
self.cfg["labels"].append(label)
self.vocab.strings.add(label)
def get_tag_names(self) -> List[str]:
if self.is_biluo:
return (
[f"B-{label}" for label in self.labels]
+ [f"I-{label}" for label in self.labels]
+ [f"L-{label}" for label in self.labels]
+ [f"U-{label}" for label in self.labels]
+ ["O"]
)
else:
return (
[f"B-{label}" for label in self.labels]
+ [f"I-{label}" for label in self.labels]
+ ["O"]
)
def predict(self, docs: List[Doc]) -> List[Floats2d]:
scores = self.model.predict(docs)
return scores
def set_annotations(self, docs: List[Doc], scores: List[Floats2d]) -> None:
"""Set entities on a batch of documents from a batch of scores."""
tag_names = self.get_tag_names()
for i, doc in enumerate(docs):
actions = to_numpy(scores[i].argmax(axis=1))
tags = [tag_names[actions[j]] for j in range(len(doc))]
if not self.is_biluo:
tags = iob_to_biluo(tags)
doc.ents = spans_from_biluo_tags(doc, tags)
def update(
self,
examples: List[Example],
*,
set_annotations: bool = False,
drop: float = 0.0,
sgd: Optional[Optimizer] = None,
losses: Optional[Dict[str, float]] = None,
) -> Dict[str, float]:
if losses is None:
losses = {}
losses.setdefault("ner", 0.0)
validate_examples(examples, "SimpleNER.update")
if not any(_has_ner(eg) for eg in examples):
return losses
docs = [eg.predicted for eg in examples]
set_dropout_rate(self.model, drop)
scores, bp_scores = self.model.begin_update(docs)
loss, d_scores = self.get_loss(examples, scores)
bp_scores(d_scores)
if set_annotations:
self.set_annotations(docs, scores)
if sgd is not None:
self.model.finish_update(sgd)
losses["ner"] += loss
return losses
def get_loss(self, examples: List[Example], scores) -> Tuple[List[Floats2d], float]:
validate_examples(examples, "SimpleNER.get_loss")
truths = []
for eg in examples:
tags = eg.get_aligned_ner()
gold_tags = [(tag if tag != "-" else None) for tag in tags]
if not self.is_biluo:
gold_tags = biluo_to_iob(gold_tags)
truths.append(gold_tags)
for i in range(len(scores)):
if len(scores[i]) != len(truths[i]):
raise ValueError(
f"Mismatched output and gold sizes.\n"
f"Output: {len(scores[i])}, gold: {len(truths[i])}."
f"Input: {len(examples[i].doc)}"
)
d_scores, loss = self.loss_func(scores, truths)
return loss, d_scores
def begin_training(
self,
get_examples: Callable[[], Iterable[Example]],
pipeline: Optional[List[Tuple[str, Callable[[Doc], Doc]]]] = None,
sgd: Optional[Optimizer] = None,
):
all_labels = set()
if not hasattr(get_examples, "__call__"):
err = Errors.E930.format(name="SimpleNER", obj=type(get_examples))
raise ValueError(err)
for example in get_examples():
all_labels.update(_get_labels(example))
for label in sorted(all_labels):
self.add_label(label)
labels = self.labels
n_actions = self.model.attrs["get_num_actions"](len(labels))
self.model.set_dim("nO", n_actions)
self.model.initialize()
if pipeline is not None:
self.init_multitask_objectives(get_examples, pipeline, sgd=sgd, **self.cfg)
self.loss_func = SequenceCategoricalCrossentropy(
names=self.get_tag_names(), normalize=True, missing_value=None
)
return sgd
def init_multitask_objectives(self, *args, **kwargs):
pass
def score(self, examples, **kwargs):
validate_examples(examples, "SimpleNER.score")
return Scorer.score_spans(examples, "ents", **kwargs)
def _has_ner(example: Example) -> bool:
for ner_tag in example.get_aligned_ner():
if ner_tag != "-" and ner_tag is not None:
return True
else:
return False
def _get_labels(example: Example) -> Set[str]:
labels = set()
for ner_tag in example.get_aligned("ENT_TYPE", as_string=True):
if ner_tag != "O" and ner_tag != "-":
labels.add(ner_tag)
return labels