spaCy/spacy/tests/pipeline/test_spancat.py

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Add SpanCategorizer component (#6747) * Draft spancat model * Add spancat model * Add test for extract_spans * Add extract_spans layer * Upd extract_spans * Add spancat model * Add test for spancat model * Upd spancat model * Update spancat component * Upd spancat * Update spancat model * Add quick spancat test * Import SpanCategorizer * Fix SpanCategorizer component * Import SpanGroup * Fix span extraction * Fix import * Fix import * Upd model * Update spancat models * Add scoring, update defaults * Update and add docs * Fix type * Update spacy/ml/extract_spans.py * Auto-format and fix import * Fix comment * Fix type * Fix type * Update website/docs/api/spancategorizer.md * Fix comment Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Better defense Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix labels list Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/extract_spans.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/pipeline/spancat.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Set annotations during update * Set annotations in spancat * fix imports in test * Update spacy/pipeline/spancat.py * replace MaxoutLogistic with LinearLogistic * fix config * various small fixes * remove set_annotations parameter in update * use our beloved tupley format with recent support for doc.spans * bugfix to allow renaming the default span_key (scores weren't showing up) * use different key in docs example * change defaults to better-working parameters from project (WIP) * register spacy.extract_spans.v1 for legacy purposes * Upd dev version so can build wheel * layers instead of architectures for smaller building blocks * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Include additional scores from overrides in combined score weights * Parameterize spans key in scoring Parameterize the `SpanCategorizer` `spans_key` for scoring purposes so that it's possible to evaluate multiple `spancat` components in the same pipeline. * Use the (intentionally very short) default spans key `sc` in the `SpanCategorizer` * Adjust the default score weights to include the default key * Adjust the scorer to use `spans_{spans_key}` as the prefix for the returned score * Revert addition of `attr_name` argument to `score_spans` and adjust the key in the `getter` instead. Note that for `spancat` components with a custom `span_key`, the score weights currently need to be modified manually in `[training.score_weights]` for them to be available during training. To suppress the default score weights `spans_sc_p/r/f` during training, set them to `null` in `[training.score_weights]`. * Update website/docs/api/scorer.md * Fix scorer for spans key containing underscore * Increment version * Add Spans to Evaluate CLI (#8439) * Add Spans to Evaluate CLI * Change to spans_key * Add spans per_type output Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Fix spancat GPU issues (#8455) * Fix GPU issues * Require thinc >=8.0.6 * Switch to glorot_uniform_init * Fix and test ngram suggester * Include final ngram in doc for all sizes * Fix ngrams for docs of the same length as ngram size * Handle batches of docs that result in no ngrams * Add tests Co-authored-by: Ines Montani <ines@ines.io> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Nirant <NirantK@users.noreply.github.com>
2021-06-24 13:35:27 +03:00
from numpy.testing import assert_equal
from spacy.language import Language
from spacy.training import Example
from spacy.util import fix_random_seed, registry
SPAN_KEY = "labeled_spans"
TRAIN_DATA = [
("Who is Shaka Khan?", {"spans": {SPAN_KEY: [(7, 17, "PERSON")]}}),
(
"I like London and Berlin.",
{"spans": {SPAN_KEY: [(7, 13, "LOC"), (18, 24, "LOC")]}},
),
]
def make_get_examples(nlp):
train_examples = []
for t in TRAIN_DATA:
eg = Example.from_dict(nlp.make_doc(t[0]), t[1])
train_examples.append(eg)
def get_examples():
return train_examples
return get_examples
def test_simple_train():
fix_random_seed(0)
nlp = Language()
spancat = nlp.add_pipe("spancat", config={"spans_key": SPAN_KEY})
get_examples = make_get_examples(nlp)
nlp.initialize(get_examples)
sgd = nlp.create_optimizer()
assert len(spancat.labels) != 0
for i in range(40):
losses = {}
nlp.update(list(get_examples()), losses=losses, drop=0.1, sgd=sgd)
doc = nlp("I like London and Berlin.")
assert doc.spans[spancat.key] == doc.spans[SPAN_KEY]
assert len(doc.spans[spancat.key]) == 2
assert doc.spans[spancat.key][0].text == "London"
scores = nlp.evaluate(get_examples())
assert f"spans_{SPAN_KEY}_f" in scores
assert scores[f"spans_{SPAN_KEY}_f"] == 1.0
def test_ngram_suggester(en_tokenizer):
# test different n-gram lengths
for size in [1, 2, 3]:
ngram_suggester = registry.misc.get("ngram_suggester.v1")(sizes=[size])
docs = [
en_tokenizer(text)
for text in [
"a",
"a b",
"a b c",
"a b c d",
"a b c d e",
"a " * 100,
]
]
ngrams = ngram_suggester(docs)
# span sizes are correct
for s in ngrams.data:
assert s[1] - s[0] == size
# spans are within docs
offset = 0
for i, doc in enumerate(docs):
spans = ngrams.dataXd[offset : offset + ngrams.lengths[i]]
spans_set = set()
for span in spans:
assert 0 <= span[0] < len(doc)
assert 0 < span[1] <= len(doc)
spans_set.add((span[0], span[1]))
# spans are unique
assert spans.shape[0] == len(spans_set)
offset += ngrams.lengths[i]
# the number of spans is correct
2021-06-28 12:48:00 +03:00
assert_equal(ngrams.lengths, [max(0, len(doc) - (size - 1)) for doc in docs])
Add SpanCategorizer component (#6747) * Draft spancat model * Add spancat model * Add test for extract_spans * Add extract_spans layer * Upd extract_spans * Add spancat model * Add test for spancat model * Upd spancat model * Update spancat component * Upd spancat * Update spancat model * Add quick spancat test * Import SpanCategorizer * Fix SpanCategorizer component * Import SpanGroup * Fix span extraction * Fix import * Fix import * Upd model * Update spancat models * Add scoring, update defaults * Update and add docs * Fix type * Update spacy/ml/extract_spans.py * Auto-format and fix import * Fix comment * Fix type * Fix type * Update website/docs/api/spancategorizer.md * Fix comment Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Better defense Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Fix labels list Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/ml/extract_spans.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Update spacy/pipeline/spancat.py Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> * Set annotations during update * Set annotations in spancat * fix imports in test * Update spacy/pipeline/spancat.py * replace MaxoutLogistic with LinearLogistic * fix config * various small fixes * remove set_annotations parameter in update * use our beloved tupley format with recent support for doc.spans * bugfix to allow renaming the default span_key (scores weren't showing up) * use different key in docs example * change defaults to better-working parameters from project (WIP) * register spacy.extract_spans.v1 for legacy purposes * Upd dev version so can build wheel * layers instead of architectures for smaller building blocks * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Update website/docs/api/spancategorizer.md Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Include additional scores from overrides in combined score weights * Parameterize spans key in scoring Parameterize the `SpanCategorizer` `spans_key` for scoring purposes so that it's possible to evaluate multiple `spancat` components in the same pipeline. * Use the (intentionally very short) default spans key `sc` in the `SpanCategorizer` * Adjust the default score weights to include the default key * Adjust the scorer to use `spans_{spans_key}` as the prefix for the returned score * Revert addition of `attr_name` argument to `score_spans` and adjust the key in the `getter` instead. Note that for `spancat` components with a custom `span_key`, the score weights currently need to be modified manually in `[training.score_weights]` for them to be available during training. To suppress the default score weights `spans_sc_p/r/f` during training, set them to `null` in `[training.score_weights]`. * Update website/docs/api/scorer.md * Fix scorer for spans key containing underscore * Increment version * Add Spans to Evaluate CLI (#8439) * Add Spans to Evaluate CLI * Change to spans_key * Add spans per_type output Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> * Fix spancat GPU issues (#8455) * Fix GPU issues * Require thinc >=8.0.6 * Switch to glorot_uniform_init * Fix and test ngram suggester * Include final ngram in doc for all sizes * Fix ngrams for docs of the same length as ngram size * Handle batches of docs that result in no ngrams * Add tests Co-authored-by: Ines Montani <ines@ines.io> Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com> Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com> Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com> Co-authored-by: Nirant <NirantK@users.noreply.github.com>
2021-06-24 13:35:27 +03:00
# test 1-3-gram suggestions
ngram_suggester = registry.misc.get("ngram_suggester.v1")(sizes=[1, 2, 3])
docs = [
en_tokenizer(text) for text in ["a", "a b", "a b c", "a b c d", "a b c d e"]
]
ngrams = ngram_suggester(docs)
assert_equal(ngrams.lengths, [1, 3, 6, 9, 12])
assert_equal(
ngrams.data,
[
# doc 0
[0, 1],
# doc 1
[0, 1],
[1, 2],
[0, 2],
# doc 2
[0, 1],
[1, 2],
[2, 3],
[0, 2],
[1, 3],
[0, 3],
# doc 3
[0, 1],
[1, 2],
[2, 3],
[3, 4],
[0, 2],
[1, 3],
[2, 4],
[0, 3],
[1, 4],
# doc 4
[0, 1],
[1, 2],
[2, 3],
[3, 4],
[4, 5],
[0, 2],
[1, 3],
[2, 4],
[3, 5],
[0, 3],
[1, 4],
[2, 5],
],
)
# test some empty docs
ngram_suggester = registry.misc.get("ngram_suggester.v1")(sizes=[1])
docs = [en_tokenizer(text) for text in ["", "a", ""]]
ngrams = ngram_suggester(docs)
assert_equal(ngrams.lengths, [len(doc) for doc in docs])
# test all empty docs
ngram_suggester = registry.misc.get("ngram_suggester.v1")(sizes=[1])
docs = [en_tokenizer(text) for text in ["", "", ""]]
ngrams = ngram_suggester(docs)
assert_equal(ngrams.lengths, [len(doc) for doc in docs])