Update SimpleNER (#5878)

* Fix `get_loss` to use NER annotation
* Add labels as part of cfg
* Add simple overfitting test
This commit is contained in:
Adriane Boyd 2020-08-05 14:43:29 +02:00 committed by GitHub
parent b88c5c701a
commit af125875cf
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2 changed files with 55 additions and 416 deletions

View File

@ -4,12 +4,12 @@ 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 ..tokens import Doc
from ..language import Language
from ..vocab import Vocab
from ..scorer import Scorer
from .. import util
from .pipe import Pipe
@ -37,7 +37,6 @@ DEFAULT_SIMPLE_NER_MODEL = Config().from_str(default_model_config)["model"]
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]
@ -60,7 +59,9 @@ class SimpleNER(Pipe):
self.vocab = vocab
self.model = model
self.name = name
self.labels = labels
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
)
@ -70,9 +71,20 @@ class SimpleNER(Pipe):
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.labels.append(label)
self.cfg["labels"].append(label)
self.vocab.strings.add(label)
def get_tag_names(self) -> List[str]:
if self.is_biluo:
@ -133,7 +145,7 @@ class SimpleNER(Pipe):
def get_loss(self, examples: List[Example], scores) -> Tuple[List[Floats2d], float]:
truths = []
for eg in examples:
tags = eg.get_aligned("TAG", as_string=True)
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)

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@ -1,418 +1,45 @@
import pytest
from collections import namedtuple
from thinc.api import NumpyOps
from spacy.ml._biluo import BILUO, _get_transition_table
from spacy.lang.en import English
from spacy.gold import Example
from spacy import util
from ..util import make_tempdir
@pytest.fixture(
params=[
["PER", "ORG", "LOC", "MISC"],
["GPE", "PERSON", "NUMBER", "CURRENCY", "EVENT"],
TRAIN_DATA = [
("Who is Shaka Khan?", {"entities": [(7, 17, "PERSON")]}),
("I like London and Berlin.", {"entities": [(7, 13, "LOC"), (18, 24, "LOC")]}),
]
)
def labels(request):
return request.param
@pytest.fixture
def ops():
return NumpyOps()
def test_overfitting_IO():
# Simple test to try and quickly overfit the SimpleNER component - ensuring the ML models work correctly
nlp = English()
ner = nlp.add_pipe("simple_ner")
train_examples = []
for text, annotations in TRAIN_DATA:
train_examples.append(Example.from_dict(nlp.make_doc(text), annotations))
for ent in annotations.get("entities"):
ner.add_label(ent[2])
optimizer = nlp.begin_training()
for i in range(50):
losses = {}
nlp.update(train_examples, sgd=optimizer, losses=losses)
assert losses["ner"] < 0.0001
def _get_actions(labels):
action_names = (
[f"B{label}" for label in labels]
+ [f"I{label}" for label in labels]
+ [f"L{label}" for label in labels]
+ [f"U{label}" for label in labels]
+ ["O"]
)
A = namedtuple("actions", action_names)
return A(**{name: i for i, name in enumerate(action_names)})
# test the trained model
test_text = "I like London."
doc = nlp(test_text)
ents = doc.ents
assert len(ents) == 1
assert ents[0].text == "London"
assert ents[0].label_ == "LOC"
def test_init_biluo_layer(labels):
model = BILUO()
model.set_dim("nO", model.attrs["get_num_actions"](len(labels)))
model.initialize()
assert model.get_dim("nO") == len(labels) * 4 + 1
def test_transition_table(ops):
labels = ["per", "loc", "org"]
table = _get_transition_table(len(labels))
a = _get_actions(labels)
assert table.shape == (2, len(a), len(a))
# Not last token, prev action was B
assert table[0, a.Bper, a.Bper] == 0
assert table[0, a.Bper, a.Bloc] == 0
assert table[0, a.Bper, a.Borg] == 0
assert table[0, a.Bper, a.Iper] == 1
assert table[0, a.Bper, a.Iloc] == 0
assert table[0, a.Bper, a.Iorg] == 0
assert table[0, a.Bper, a.Lper] == 1
assert table[0, a.Bper, a.Lloc] == 0
assert table[0, a.Bper, a.Lorg] == 0
assert table[0, a.Bper, a.Uper] == 0
assert table[0, a.Bper, a.Uloc] == 0
assert table[0, a.Bper, a.Uorg] == 0
assert table[0, a.Bper, a.O] == 0
assert table[0, a.Bloc, a.Bper] == 0
assert table[0, a.Bloc, a.Bloc] == 0
assert table[0, a.Bloc, a.Borg] == 0
assert table[0, a.Bloc, a.Iper] == 0
assert table[0, a.Bloc, a.Iloc] == 1
assert table[0, a.Bloc, a.Iorg] == 0
assert table[0, a.Bloc, a.Lper] == 0
assert table[0, a.Bloc, a.Lloc] == 1
assert table[0, a.Bloc, a.Lorg] == 0
assert table[0, a.Bloc, a.Uper] == 0
assert table[0, a.Bloc, a.Uloc] == 0
assert table[0, a.Bloc, a.Uorg] == 0
assert table[0, a.Bloc, a.O] == 0
assert table[0, a.Borg, a.Bper] == 0
assert table[0, a.Borg, a.Bloc] == 0
assert table[0, a.Borg, a.Borg] == 0
assert table[0, a.Borg, a.Iper] == 0
assert table[0, a.Borg, a.Iloc] == 0
assert table[0, a.Borg, a.Iorg] == 1
assert table[0, a.Borg, a.Lper] == 0
assert table[0, a.Borg, a.Lloc] == 0
assert table[0, a.Borg, a.Lorg] == 1
assert table[0, a.Borg, a.Uper] == 0
assert table[0, a.Borg, a.Uloc] == 0
assert table[0, a.Borg, a.Uorg] == 0
assert table[0, a.Borg, a.O] == 0
# Not last token, prev action was I
assert table[0, a.Iper, a.Bper] == 0
assert table[0, a.Iper, a.Bloc] == 0
assert table[0, a.Iper, a.Borg] == 0
assert table[0, a.Iper, a.Iper] == 1
assert table[0, a.Iper, a.Iloc] == 0
assert table[0, a.Iper, a.Iorg] == 0
assert table[0, a.Iper, a.Lper] == 1
assert table[0, a.Iper, a.Lloc] == 0
assert table[0, a.Iper, a.Lorg] == 0
assert table[0, a.Iper, a.Uper] == 0
assert table[0, a.Iper, a.Uloc] == 0
assert table[0, a.Iper, a.Uorg] == 0
assert table[0, a.Iper, a.O] == 0
assert table[0, a.Iloc, a.Bper] == 0
assert table[0, a.Iloc, a.Bloc] == 0
assert table[0, a.Iloc, a.Borg] == 0
assert table[0, a.Iloc, a.Iper] == 0
assert table[0, a.Iloc, a.Iloc] == 1
assert table[0, a.Iloc, a.Iorg] == 0
assert table[0, a.Iloc, a.Lper] == 0
assert table[0, a.Iloc, a.Lloc] == 1
assert table[0, a.Iloc, a.Lorg] == 0
assert table[0, a.Iloc, a.Uper] == 0
assert table[0, a.Iloc, a.Uloc] == 0
assert table[0, a.Iloc, a.Uorg] == 0
assert table[0, a.Iloc, a.O] == 0
assert table[0, a.Iorg, a.Bper] == 0
assert table[0, a.Iorg, a.Bloc] == 0
assert table[0, a.Iorg, a.Borg] == 0
assert table[0, a.Iorg, a.Iper] == 0
assert table[0, a.Iorg, a.Iloc] == 0
assert table[0, a.Iorg, a.Iorg] == 1
assert table[0, a.Iorg, a.Lper] == 0
assert table[0, a.Iorg, a.Lloc] == 0
assert table[0, a.Iorg, a.Lorg] == 1
assert table[0, a.Iorg, a.Uper] == 0
assert table[0, a.Iorg, a.Uloc] == 0
assert table[0, a.Iorg, a.Uorg] == 0
assert table[0, a.Iorg, a.O] == 0
# Not last token, prev action was L
assert table[0, a.Lper, a.Bper] == 1
assert table[0, a.Lper, a.Bloc] == 1
assert table[0, a.Lper, a.Borg] == 1
assert table[0, a.Lper, a.Iper] == 0
assert table[0, a.Lper, a.Iloc] == 0
assert table[0, a.Lper, a.Iorg] == 0
assert table[0, a.Lper, a.Lper] == 0
assert table[0, a.Lper, a.Lloc] == 0
assert table[0, a.Lper, a.Lorg] == 0
assert table[0, a.Lper, a.Uper] == 1
assert table[0, a.Lper, a.Uloc] == 1
assert table[0, a.Lper, a.Uorg] == 1
assert table[0, a.Lper, a.O] == 1
assert table[0, a.Lloc, a.Bper] == 1
assert table[0, a.Lloc, a.Bloc] == 1
assert table[0, a.Lloc, a.Borg] == 1
assert table[0, a.Lloc, a.Iper] == 0
assert table[0, a.Lloc, a.Iloc] == 0
assert table[0, a.Lloc, a.Iorg] == 0
assert table[0, a.Lloc, a.Lper] == 0
assert table[0, a.Lloc, a.Lloc] == 0
assert table[0, a.Lloc, a.Lorg] == 0
assert table[0, a.Lloc, a.Uper] == 1
assert table[0, a.Lloc, a.Uloc] == 1
assert table[0, a.Lloc, a.Uorg] == 1
assert table[0, a.Lloc, a.O] == 1
assert table[0, a.Lorg, a.Bper] == 1
assert table[0, a.Lorg, a.Bloc] == 1
assert table[0, a.Lorg, a.Borg] == 1
assert table[0, a.Lorg, a.Iper] == 0
assert table[0, a.Lorg, a.Iloc] == 0
assert table[0, a.Lorg, a.Iorg] == 0
assert table[0, a.Lorg, a.Lper] == 0
assert table[0, a.Lorg, a.Lloc] == 0
assert table[0, a.Lorg, a.Lorg] == 0
assert table[0, a.Lorg, a.Uper] == 1
assert table[0, a.Lorg, a.Uloc] == 1
assert table[0, a.Lorg, a.Uorg] == 1
assert table[0, a.Lorg, a.O] == 1
# Not last token, prev action was U
assert table[0, a.Uper, a.Bper] == 1
assert table[0, a.Uper, a.Bloc] == 1
assert table[0, a.Uper, a.Borg] == 1
assert table[0, a.Uper, a.Iper] == 0
assert table[0, a.Uper, a.Iloc] == 0
assert table[0, a.Uper, a.Iorg] == 0
assert table[0, a.Uper, a.Lper] == 0
assert table[0, a.Uper, a.Lloc] == 0
assert table[0, a.Uper, a.Lorg] == 0
assert table[0, a.Uper, a.Uper] == 1
assert table[0, a.Uper, a.Uloc] == 1
assert table[0, a.Uper, a.Uorg] == 1
assert table[0, a.Uper, a.O] == 1
assert table[0, a.Uloc, a.Bper] == 1
assert table[0, a.Uloc, a.Bloc] == 1
assert table[0, a.Uloc, a.Borg] == 1
assert table[0, a.Uloc, a.Iper] == 0
assert table[0, a.Uloc, a.Iloc] == 0
assert table[0, a.Uloc, a.Iorg] == 0
assert table[0, a.Uloc, a.Lper] == 0
assert table[0, a.Uloc, a.Lloc] == 0
assert table[0, a.Uloc, a.Lorg] == 0
assert table[0, a.Uloc, a.Uper] == 1
assert table[0, a.Uloc, a.Uloc] == 1
assert table[0, a.Uloc, a.Uorg] == 1
assert table[0, a.Uloc, a.O] == 1
assert table[0, a.Uorg, a.Bper] == 1
assert table[0, a.Uorg, a.Bloc] == 1
assert table[0, a.Uorg, a.Borg] == 1
assert table[0, a.Uorg, a.Iper] == 0
assert table[0, a.Uorg, a.Iloc] == 0
assert table[0, a.Uorg, a.Iorg] == 0
assert table[0, a.Uorg, a.Lper] == 0
assert table[0, a.Uorg, a.Lloc] == 0
assert table[0, a.Uorg, a.Lorg] == 0
assert table[0, a.Uorg, a.Uper] == 1
assert table[0, a.Uorg, a.Uloc] == 1
assert table[0, a.Uorg, a.Uorg] == 1
assert table[0, a.Uorg, a.O] == 1
# Not last token, prev action was O
assert table[0, a.O, a.Bper] == 1
assert table[0, a.O, a.Bloc] == 1
assert table[0, a.O, a.Borg] == 1
assert table[0, a.O, a.Iper] == 0
assert table[0, a.O, a.Iloc] == 0
assert table[0, a.O, a.Iorg] == 0
assert table[0, a.O, a.Lper] == 0
assert table[0, a.O, a.Lloc] == 0
assert table[0, a.O, a.Lorg] == 0
assert table[0, a.O, a.Uper] == 1
assert table[0, a.O, a.Uloc] == 1
assert table[0, a.O, a.Uorg] == 1
assert table[0, a.O, a.O] == 1
# Last token, prev action was B
assert table[1, a.Bper, a.Bper] == 0
assert table[1, a.Bper, a.Bloc] == 0
assert table[1, a.Bper, a.Borg] == 0
assert table[1, a.Bper, a.Iper] == 0
assert table[1, a.Bper, a.Iloc] == 0
assert table[1, a.Bper, a.Iorg] == 0
assert table[1, a.Bper, a.Lper] == 1
assert table[1, a.Bper, a.Lloc] == 0
assert table[1, a.Bper, a.Lorg] == 0
assert table[1, a.Bper, a.Uper] == 0
assert table[1, a.Bper, a.Uloc] == 0
assert table[1, a.Bper, a.Uorg] == 0
assert table[1, a.Bper, a.O] == 0
assert table[1, a.Bloc, a.Bper] == 0
assert table[1, a.Bloc, a.Bloc] == 0
assert table[0, a.Bloc, a.Borg] == 0
assert table[1, a.Bloc, a.Iper] == 0
assert table[1, a.Bloc, a.Iloc] == 0
assert table[1, a.Bloc, a.Iorg] == 0
assert table[1, a.Bloc, a.Lper] == 0
assert table[1, a.Bloc, a.Lloc] == 1
assert table[1, a.Bloc, a.Lorg] == 0
assert table[1, a.Bloc, a.Uper] == 0
assert table[1, a.Bloc, a.Uloc] == 0
assert table[1, a.Bloc, a.Uorg] == 0
assert table[1, a.Bloc, a.O] == 0
assert table[1, a.Borg, a.Bper] == 0
assert table[1, a.Borg, a.Bloc] == 0
assert table[1, a.Borg, a.Borg] == 0
assert table[1, a.Borg, a.Iper] == 0
assert table[1, a.Borg, a.Iloc] == 0
assert table[1, a.Borg, a.Iorg] == 0
assert table[1, a.Borg, a.Lper] == 0
assert table[1, a.Borg, a.Lloc] == 0
assert table[1, a.Borg, a.Lorg] == 1
assert table[1, a.Borg, a.Uper] == 0
assert table[1, a.Borg, a.Uloc] == 0
assert table[1, a.Borg, a.Uorg] == 0
assert table[1, a.Borg, a.O] == 0
# Last token, prev action was I
assert table[1, a.Iper, a.Bper] == 0
assert table[1, a.Iper, a.Bloc] == 0
assert table[1, a.Iper, a.Borg] == 0
assert table[1, a.Iper, a.Iper] == 0
assert table[1, a.Iper, a.Iloc] == 0
assert table[1, a.Iper, a.Iorg] == 0
assert table[1, a.Iper, a.Lper] == 1
assert table[1, a.Iper, a.Lloc] == 0
assert table[1, a.Iper, a.Lorg] == 0
assert table[1, a.Iper, a.Uper] == 0
assert table[1, a.Iper, a.Uloc] == 0
assert table[1, a.Iper, a.Uorg] == 0
assert table[1, a.Iper, a.O] == 0
assert table[1, a.Iloc, a.Bper] == 0
assert table[1, a.Iloc, a.Bloc] == 0
assert table[1, a.Iloc, a.Borg] == 0
assert table[1, a.Iloc, a.Iper] == 0
assert table[1, a.Iloc, a.Iloc] == 0
assert table[1, a.Iloc, a.Iorg] == 0
assert table[1, a.Iloc, a.Lper] == 0
assert table[1, a.Iloc, a.Lloc] == 1
assert table[1, a.Iloc, a.Lorg] == 0
assert table[1, a.Iloc, a.Uper] == 0
assert table[1, a.Iloc, a.Uloc] == 0
assert table[1, a.Iloc, a.Uorg] == 0
assert table[1, a.Iloc, a.O] == 0
assert table[1, a.Iorg, a.Bper] == 0
assert table[1, a.Iorg, a.Bloc] == 0
assert table[1, a.Iorg, a.Borg] == 0
assert table[1, a.Iorg, a.Iper] == 0
assert table[1, a.Iorg, a.Iloc] == 0
assert table[1, a.Iorg, a.Iorg] == 0
assert table[1, a.Iorg, a.Lper] == 0
assert table[1, a.Iorg, a.Lloc] == 0
assert table[1, a.Iorg, a.Lorg] == 1
assert table[1, a.Iorg, a.Uper] == 0
assert table[1, a.Iorg, a.Uloc] == 0
assert table[1, a.Iorg, a.Uorg] == 0
assert table[1, a.Iorg, a.O] == 0
# Last token, prev action was L
assert table[1, a.Lper, a.Bper] == 0
assert table[1, a.Lper, a.Bloc] == 0
assert table[1, a.Lper, a.Borg] == 0
assert table[1, a.Lper, a.Iper] == 0
assert table[1, a.Lper, a.Iloc] == 0
assert table[1, a.Lper, a.Iorg] == 0
assert table[1, a.Lper, a.Lper] == 0
assert table[1, a.Lper, a.Lloc] == 0
assert table[1, a.Lper, a.Lorg] == 0
assert table[1, a.Lper, a.Uper] == 1
assert table[1, a.Lper, a.Uloc] == 1
assert table[1, a.Lper, a.Uorg] == 1
assert table[1, a.Lper, a.O] == 1
assert table[1, a.Lloc, a.Bper] == 0
assert table[1, a.Lloc, a.Bloc] == 0
assert table[1, a.Lloc, a.Borg] == 0
assert table[1, a.Lloc, a.Iper] == 0
assert table[1, a.Lloc, a.Iloc] == 0
assert table[1, a.Lloc, a.Iorg] == 0
assert table[1, a.Lloc, a.Lper] == 0
assert table[1, a.Lloc, a.Lloc] == 0
assert table[1, a.Lloc, a.Lorg] == 0
assert table[1, a.Lloc, a.Uper] == 1
assert table[1, a.Lloc, a.Uloc] == 1
assert table[1, a.Lloc, a.Uorg] == 1
assert table[1, a.Lloc, a.O] == 1
assert table[1, a.Lorg, a.Bper] == 0
assert table[1, a.Lorg, a.Bloc] == 0
assert table[1, a.Lorg, a.Borg] == 0
assert table[1, a.Lorg, a.Iper] == 0
assert table[1, a.Lorg, a.Iloc] == 0
assert table[1, a.Lorg, a.Iorg] == 0
assert table[1, a.Lorg, a.Lper] == 0
assert table[1, a.Lorg, a.Lloc] == 0
assert table[1, a.Lorg, a.Lorg] == 0
assert table[1, a.Lorg, a.Uper] == 1
assert table[1, a.Lorg, a.Uloc] == 1
assert table[1, a.Lorg, a.Uorg] == 1
assert table[1, a.Lorg, a.O] == 1
# Last token, prev action was U
assert table[1, a.Uper, a.Bper] == 0
assert table[1, a.Uper, a.Bloc] == 0
assert table[1, a.Uper, a.Borg] == 0
assert table[1, a.Uper, a.Iper] == 0
assert table[1, a.Uper, a.Iloc] == 0
assert table[1, a.Uper, a.Iorg] == 0
assert table[1, a.Uper, a.Lper] == 0
assert table[1, a.Uper, a.Lloc] == 0
assert table[1, a.Uper, a.Lorg] == 0
assert table[1, a.Uper, a.Uper] == 1
assert table[1, a.Uper, a.Uloc] == 1
assert table[1, a.Uper, a.Uorg] == 1
assert table[1, a.Uper, a.O] == 1
assert table[1, a.Uloc, a.Bper] == 0
assert table[1, a.Uloc, a.Bloc] == 0
assert table[1, a.Uloc, a.Borg] == 0
assert table[1, a.Uloc, a.Iper] == 0
assert table[1, a.Uloc, a.Iloc] == 0
assert table[1, a.Uloc, a.Iorg] == 0
assert table[1, a.Uloc, a.Lper] == 0
assert table[1, a.Uloc, a.Lloc] == 0
assert table[1, a.Uloc, a.Lorg] == 0
assert table[1, a.Uloc, a.Uper] == 1
assert table[1, a.Uloc, a.Uloc] == 1
assert table[1, a.Uloc, a.Uorg] == 1
assert table[1, a.Uloc, a.O] == 1
assert table[1, a.Uorg, a.Bper] == 0
assert table[1, a.Uorg, a.Bloc] == 0
assert table[1, a.Uorg, a.Borg] == 0
assert table[1, a.Uorg, a.Iper] == 0
assert table[1, a.Uorg, a.Iloc] == 0
assert table[1, a.Uorg, a.Iorg] == 0
assert table[1, a.Uorg, a.Lper] == 0
assert table[1, a.Uorg, a.Lloc] == 0
assert table[1, a.Uorg, a.Lorg] == 0
assert table[1, a.Uorg, a.Uper] == 1
assert table[1, a.Uorg, a.Uloc] == 1
assert table[1, a.Uorg, a.Uorg] == 1
assert table[1, a.Uorg, a.O] == 1
# Last token, prev action was O
assert table[1, a.O, a.Bper] == 0
assert table[1, a.O, a.Bloc] == 0
assert table[1, a.O, a.Borg] == 0
assert table[1, a.O, a.Iper] == 0
assert table[1, a.O, a.Iloc] == 0
assert table[1, a.O, a.Iorg] == 0
assert table[1, a.O, a.Lper] == 0
assert table[1, a.O, a.Lloc] == 0
assert table[1, a.O, a.Lorg] == 0
assert table[1, a.O, a.Uper] == 1
assert table[1, a.O, a.Uloc] == 1
assert table[1, a.O, a.Uorg] == 1
assert table[1, a.O, a.O] == 1
# Also test the results are still the same after IO
with make_tempdir() as tmp_dir:
nlp.to_disk(tmp_dir)
nlp2 = util.load_model_from_path(tmp_dir)
doc2 = nlp2(test_text)
ents2 = doc2.ents
assert len(ents2) == 1
assert ents2[0].text == "London"
assert ents2[0].label_ == "LOC"