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a1c5b694be
spaCy/spacy/tests/pipeline/test_simple_ner.py
Matthew Honnibal 333b1a308b
Adapt parser and NER for transformers (#5449) 
* Draft layer for BILUO actions

* Fixes to biluo layer

* WIP on BILUO layer

* Add tests for BILUO layer

* Format

* Fix transitions

* Update test

* Link in the simple_ner

* Update BILUO tagger

* Update __init__

* Import simple_ner

* Update test

* Import

* Add files

* Add config

* Fix label passing for BILUO and tagger

* Fix label handling for simple_ner component

* Update simple NER test

* Update config

* Hack train script

* Update BILUO layer

* Fix SimpleNER component

* Update train_from_config

* Add biluo_to_iob helper

* Add IOB layer

* Add IOBTagger model

* Update biluo layer

* Update SimpleNER tagger

* Update BILUO

* Read random seed in train-from-config

* Update use of normal_init

* Fix normalization of gradient in SimpleNER

* Update IOBTagger

* Remove print

* Tweak masking in BILUO

* Add dropout in SimpleNER

* Update thinc

* Tidy up simple_ner

* Fix biluo model

* Unhack train-from-config

* Update setup.cfg and requirements

* Add tb_framework.py for parser model

* Try to avoid memory leak in BILUO

* Move ParserModel into spacy.ml, avoid need for subclass.

* Use updated parser model

* Remove incorrect call to model.initializre in PrecomputableAffine

* Update parser model

* Avoid divide by zero in tagger

* Add extra dropout layer in tagger

* Refine minibatch_by_words function to avoid oom

* Fix parser model after refactor

* Try to avoid div-by-zero in SimpleNER

* Fix infinite loop in minibatch_by_words

* Use SequenceCategoricalCrossentropy in Tagger

* Fix parser model when hidden layer

* Remove extra dropout from tagger

* Add extra nan check in tagger

* Fix thinc version

* Update tests and imports

* Fix test

* Update test

* Update tests

* Fix tests

* Fix test

Co-authored-by: Ines Montani <ines@ines.io>
2020-05-18 22:23:33 +02:00

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import pytest
from collections import namedtuple
from thinc.api import NumpyOps
from spacy.ml._biluo import BILUO, _get_transition_table
from spacy.pipeline.simple_ner import SimpleNER
import spacy
@pytest.fixture(params=[
["PER", "ORG", "LOC", "MISC"],
["GPE", "PERSON", "NUMBER", "CURRENCY", "EVENT"]
])
def labels(request):
return request.param
@pytest.fixture
def ops():
return NumpyOps()
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)})
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
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