Fix spancat training on nested entities (#9007)

* overfitting test on non-overlapping entities

* add failing overfitting test for overlapping entities

* failing test for list comprehension

* remove test that was put in separate PR

* bugfix

* cleanup

spacy/pipeline/spancat.py

@@ -398,7 +398,7 @@ class SpanCategorizer(TrainablePipe):
         pass
 
     def _get_aligned_spans(self, eg: Example):
-        return eg.get_aligned_spans_y2x(eg.reference.spans.get(self.key, []))
+        return eg.get_aligned_spans_y2x(eg.reference.spans.get(self.key, []), allow_overlap=True)
 
     def _make_span_group(
         self, doc: Doc, indices: Ints2d, scores: Floats2d, labels: List[str]

spacy/tests/pipeline/test_spancat.py

@@ -2,11 +2,14 @@ import pytest
 import numpy
 from numpy.testing import assert_array_equal, assert_almost_equal
 from thinc.api import get_current_ops
+
+from spacy import util
+from spacy.lang.en import English
 from spacy.language import Language
 from spacy.tokens.doc import SpanGroups
 from spacy.tokens import SpanGroup
 from spacy.training import Example
-from spacy.util import fix_random_seed, registry
+from spacy.util import fix_random_seed, registry, make_tempdir
 
 OPS = get_current_ops()
 
@@ -20,17 +23,21 @@ TRAIN_DATA = [
     ),
 ]
 
+TRAIN_DATA_OVERLAPPING = [
+    ("Who is Shaka Khan?", {"spans": {SPAN_KEY: [(7, 17, "PERSON")]}}),
+    (
+        "I like London and Berlin",
+        {"spans": {SPAN_KEY: [(7, 13, "LOC"), (18, 24, "LOC"), (7, 24, "DOUBLE_LOC")]}},
+    ),
+]
 
-def make_get_examples(nlp):
+
+def make_examples(nlp, data=TRAIN_DATA):
     train_examples = []
-    for t in TRAIN_DATA:
+    for t in 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
+    return train_examples
 
 
 def test_no_label():
@@ -57,9 +64,7 @@ def test_implicit_labels():
     nlp = Language()
     spancat = nlp.add_pipe("spancat", config={"spans_key": SPAN_KEY})
     assert len(spancat.labels) == 0
-    train_examples = []
-    for t in TRAIN_DATA:
-        train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
+    train_examples = make_examples(nlp)
     nlp.initialize(get_examples=lambda: train_examples)
     assert spancat.labels == ("PERSON", "LOC")
 
@@ -140,30 +145,6 @@ def test_make_spangroup(max_positive, nr_results):
     assert_almost_equal(0.9, spangroup.attrs["scores"][-1], 5)
 
 
-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 len(doc.spans[spancat.key].attrs["scores"]) == 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
-    # also test that the spancat works for just a single entity in a sentence
-    doc = nlp("London")
-    assert len(doc.spans[spancat.key]) == 1
-
-
 def test_ngram_suggester(en_tokenizer):
     # test different n-gram lengths
     for size in [1, 2, 3]:
@@ -282,3 +263,92 @@ def test_ngram_sizes(en_tokenizer):
     range_suggester = suggester_factory(min_size=2, max_size=4)
     ngrams_3 = range_suggester(docs)
     assert_array_equal(OPS.to_numpy(ngrams_3.lengths), [0, 1, 3, 6, 9])
+
+
+def test_overfitting_IO():
+    # Simple test to try and quickly overfit the spancat component - ensuring the ML models work correctly
+    fix_random_seed(0)
+    nlp = English()
+    spancat = nlp.add_pipe("spancat", config={"spans_key": SPAN_KEY})
+    train_examples = make_examples(nlp)
+    optimizer = nlp.initialize(get_examples=lambda: train_examples)
+    assert spancat.model.get_dim("nO") == 2
+    assert set(spancat.labels) == {"LOC", "PERSON"}
+
+    for i in range(50):
+        losses = {}
+        nlp.update(train_examples, sgd=optimizer, losses=losses)
+    assert losses["spancat"] < 0.01
+
+    # test the trained model
+    test_text = "I like London and Berlin"
+    doc = nlp(test_text)
+    assert doc.spans[spancat.key] == doc.spans[SPAN_KEY]
+    spans = doc.spans[SPAN_KEY]
+    assert len(spans) == 2
+    assert len(spans.attrs["scores"]) == 2
+    assert min(spans.attrs["scores"]) > 0.9
+    assert set([span.text for span in spans]) == {"London", "Berlin"}
+    assert set([span.label_ for span in spans]) == {"LOC"}
+
+    # 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)
+        spans2 = doc2.spans[SPAN_KEY]
+        assert len(spans2) == 2
+        assert len(spans2.attrs["scores"]) == 2
+        assert min(spans2.attrs["scores"]) > 0.9
+        assert set([span.text for span in spans2]) == {"London", "Berlin"}
+        assert set([span.label_ for span in spans2]) == {"LOC"}
+
+    # Test scoring
+    scores = nlp.evaluate(train_examples)
+    assert f"spans_{SPAN_KEY}_f" in scores
+    assert scores[f"spans_{SPAN_KEY}_p"] == 1.0
+    assert scores[f"spans_{SPAN_KEY}_r"] == 1.0
+    assert scores[f"spans_{SPAN_KEY}_f"] == 1.0
+
+    # also test that the spancat works for just a single entity in a sentence
+    doc = nlp("London")
+    assert len(doc.spans[spancat.key]) == 1
+
+
+def test_overfitting_IO_overlapping():
+    # Test for overfitting on overlapping entities
+    fix_random_seed(0)
+    nlp = English()
+    spancat = nlp.add_pipe("spancat", config={"spans_key": SPAN_KEY})
+
+    train_examples = make_examples(nlp, data=TRAIN_DATA_OVERLAPPING)
+    optimizer = nlp.initialize(get_examples=lambda: train_examples)
+    assert spancat.model.get_dim("nO") == 3
+    assert set(spancat.labels) == {"PERSON", "LOC", "DOUBLE_LOC"}
+
+    for i in range(50):
+        losses = {}
+        nlp.update(train_examples, sgd=optimizer, losses=losses)
+    assert losses["spancat"] < 0.01
+
+    # test the trained model
+    test_text = "I like London and Berlin"
+    doc = nlp(test_text)
+    spans = doc.spans[SPAN_KEY]
+    assert len(spans) == 3
+    assert len(spans.attrs["scores"]) == 3
+    assert min(spans.attrs["scores"]) > 0.9
+    assert set([span.text for span in spans]) == {"London", "Berlin", "London and Berlin"}
+    assert set([span.label_ for span in spans]) == {"LOC", "DOUBLE_LOC"}
+
+    # 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)
+        spans2 = doc2.spans[SPAN_KEY]
+        assert len(spans2) == 3
+        assert len(spans2.attrs["scores"]) == 3
+        assert min(spans2.attrs["scores"]) > 0.9
+        assert set([span.text for span in spans2]) == {"London", "Berlin", "London and Berlin"}
+        assert set([span.label_ for span in spans2]) == {"LOC", "DOUBLE_LOC"}