Store activations in `Doc`s when `save_activations` is enabled (#11002)
* Store activations in Doc when `store_activations` is enabled
This change adds the new `activations` attribute to `Doc`. This
attribute can be used by trainable pipes to store their activations,
probabilities, and guesses for downstream users.
As an example, this change modifies the `tagger` and `senter` pipes to
add an `store_activations` option. When this option is enabled, the
probabilities and guesses are stored in `set_annotations`.
* Change type of `store_activations` to `Union[bool, List[str]]`
When the value is:
- A bool: all activations are stored when set to `True`.
- A List[str]: the activations named in the list are stored
* Formatting fixes in Tagger
* Support store_activations in spancat and morphologizer
* Make Doc.activations type visible to MyPy
* textcat/textcat_multilabel: add store_activations option
* trainable_lemmatizer/entity_linker: add store_activations option
* parser/ner: do not currently support returning activations
* Extend tagger and senter tests
So that they, like the other tests, also check that we get no
activations if no activations were requested.
* Document `Doc.activations` and `store_activations` in the relevant pipes
* Start errors/warnings at higher numbers to avoid merge conflicts
Between the master and v4 branches.
* Add `store_activations` to docstrings.
* Replace store_activations setter by set_store_activations method
Setters that take a different type than what the getter returns are still
problematic for MyPy. Replace the setter by a method, so that type inference
works everywhere.
* Use dict comprehension suggested by @svlandeg
* Revert "Use dict comprehension suggested by @svlandeg"
This reverts commit 6e7b958f7060397965176c69649e5414f1f24988.
* EntityLinker: add type annotations to _add_activations
* _store_activations: make kwarg-only, remove doc_scores_lens arg
* set_annotations: add type annotations
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* TextCat.predict: return dict
* Make the `TrainablePipe.store_activations` property a bool
This means that we can also bring back `store_activations` setter.
* Remove `TrainablePipe.activations`
We do not need to enumerate the activations anymore since `store_activations` is
`bool`.
* Add type annotations for activations in predict/set_annotations
* Rename `TrainablePipe.store_activations` to `save_activations`
* Error E1400 is not used anymore
This error was used when activations were still `Union[bool, List[str]]`.
* Change wording in API docs after store -> save change
* docs: tag (save_)activations as new in spaCy 4.0
* Fix copied line in morphologizer activations test
* Don't train in any test_save_activations test
* Rename activations
- "probs" -> "probabilities"
- "guesses" -> "label_ids", except in the edit tree lemmatizer, where
"guesses" -> "tree_ids".
* Remove unused W400 warning.
This warning was used when we still allowed the user to specify
which activations to save.
* Formatting fixes
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Replace "kb_ids" by a constant
* spancat: replace a cast by an assertion
* Fix EOF spacing
* Fix comments in test_save_activations tests
* Do not set RNG seed in activation saving tests
* Revert "spancat: replace a cast by an assertion"
This reverts commit 0bd5730d16432443a2b247316928d4f789ad8741.
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-13 10:51:12 +03:00
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from typing import cast
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2023-06-26 12:41:03 +03:00
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2020-03-06 16:45:02 +03:00
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import pytest
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2020-10-13 22:07:13 +03:00
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from numpy.testing import assert_equal
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2020-03-06 16:45:02 +03:00
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from spacy import util
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2023-06-26 12:41:03 +03:00
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from spacy.attrs import SENT_START
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2020-03-06 16:45:02 +03:00
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from spacy.lang.en import English
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from spacy.language import Language
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Store activations in `Doc`s when `save_activations` is enabled (#11002)
* Store activations in Doc when `store_activations` is enabled
This change adds the new `activations` attribute to `Doc`. This
attribute can be used by trainable pipes to store their activations,
probabilities, and guesses for downstream users.
As an example, this change modifies the `tagger` and `senter` pipes to
add an `store_activations` option. When this option is enabled, the
probabilities and guesses are stored in `set_annotations`.
* Change type of `store_activations` to `Union[bool, List[str]]`
When the value is:
- A bool: all activations are stored when set to `True`.
- A List[str]: the activations named in the list are stored
* Formatting fixes in Tagger
* Support store_activations in spancat and morphologizer
* Make Doc.activations type visible to MyPy
* textcat/textcat_multilabel: add store_activations option
* trainable_lemmatizer/entity_linker: add store_activations option
* parser/ner: do not currently support returning activations
* Extend tagger and senter tests
So that they, like the other tests, also check that we get no
activations if no activations were requested.
* Document `Doc.activations` and `store_activations` in the relevant pipes
* Start errors/warnings at higher numbers to avoid merge conflicts
Between the master and v4 branches.
* Add `store_activations` to docstrings.
* Replace store_activations setter by set_store_activations method
Setters that take a different type than what the getter returns are still
problematic for MyPy. Replace the setter by a method, so that type inference
works everywhere.
* Use dict comprehension suggested by @svlandeg
* Revert "Use dict comprehension suggested by @svlandeg"
This reverts commit 6e7b958f7060397965176c69649e5414f1f24988.
* EntityLinker: add type annotations to _add_activations
* _store_activations: make kwarg-only, remove doc_scores_lens arg
* set_annotations: add type annotations
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* TextCat.predict: return dict
* Make the `TrainablePipe.store_activations` property a bool
This means that we can also bring back `store_activations` setter.
* Remove `TrainablePipe.activations`
We do not need to enumerate the activations anymore since `store_activations` is
`bool`.
* Add type annotations for activations in predict/set_annotations
* Rename `TrainablePipe.store_activations` to `save_activations`
* Error E1400 is not used anymore
This error was used when activations were still `Union[bool, List[str]]`.
* Change wording in API docs after store -> save change
* docs: tag (save_)activations as new in spaCy 4.0
* Fix copied line in morphologizer activations test
* Don't train in any test_save_activations test
* Rename activations
- "probs" -> "probabilities"
- "guesses" -> "label_ids", except in the edit tree lemmatizer, where
"guesses" -> "tree_ids".
* Remove unused W400 warning.
This warning was used when we still allowed the user to specify
which activations to save.
* Formatting fixes
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Replace "kb_ids" by a constant
* spancat: replace a cast by an assertion
* Fix EOF spacing
* Fix comments in test_save_activations tests
* Do not set RNG seed in activation saving tests
* Revert "spancat: replace a cast by an assertion"
This reverts commit 0bd5730d16432443a2b247316928d4f789ad8741.
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-13 10:51:12 +03:00
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from spacy.pipeline import TrainablePipe
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2020-03-06 16:45:02 +03:00
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from spacy.tests.util import make_tempdir
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2023-06-26 12:41:03 +03:00
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from spacy.training import Example
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2020-03-06 16:45:02 +03:00
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2023-01-16 12:25:53 +03:00
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def test_is_distillable():
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nlp = English()
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senter = nlp.add_pipe("senter")
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assert senter.is_distillable
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2020-03-06 16:45:02 +03:00
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def test_label_types():
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nlp = Language()
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2020-07-22 14:42:59 +03:00
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senter = nlp.add_pipe("senter")
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2020-03-06 16:45:02 +03:00
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with pytest.raises(NotImplementedError):
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senter.add_label("A")
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2020-05-21 21:17:14 +03:00
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2020-03-06 16:45:02 +03:00
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SENT_STARTS = [0] * 14
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SENT_STARTS[0] = 1
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SENT_STARTS[5] = 1
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SENT_STARTS[9] = 1
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TRAIN_DATA = [
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2020-05-21 21:17:14 +03:00
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(
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"I like green eggs. Eat blue ham. I like purple eggs.",
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{"sent_starts": SENT_STARTS},
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),
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(
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"She likes purple eggs. They hate ham. You like yellow eggs.",
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{"sent_starts": SENT_STARTS},
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),
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]
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2020-09-13 11:55:36 +03:00
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2020-09-28 22:35:09 +03:00
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def test_initialize_examples():
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2020-09-08 23:44:25 +03:00
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nlp = Language()
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nlp.add_pipe("senter")
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2020-09-08 23:44:25 +03:00
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train_examples = []
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for t in TRAIN_DATA:
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train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
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# you shouldn't really call this more than once, but for testing it should be fine
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nlp.initialize()
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nlp.initialize(get_examples=lambda: train_examples)
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2020-10-08 22:33:49 +03:00
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with pytest.raises(TypeError):
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nlp.initialize(get_examples=lambda: None)
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2020-10-08 22:33:49 +03:00
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with pytest.raises(TypeError):
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nlp.initialize(get_examples=train_examples)
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2020-03-06 16:45:02 +03:00
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def test_overfitting_IO():
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# Simple test to try and quickly overfit the senter - ensuring the ML models work correctly
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nlp = English()
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train_examples = []
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for t in TRAIN_DATA:
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train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
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2020-07-09 02:41:58 +03:00
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# add some cases where SENT_START == -1
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train_examples[0].reference[10].is_sent_start = False
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train_examples[1].reference[1].is_sent_start = False
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train_examples[1].reference[11].is_sent_start = False
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2020-07-22 14:42:59 +03:00
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nlp.add_pipe("senter")
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optimizer = nlp.initialize()
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for i in range(200):
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losses = {}
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nlp.update(train_examples, sgd=optimizer, losses=losses)
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2020-04-03 14:02:46 +03:00
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assert losses["senter"] < 0.001
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# test the trained model
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test_text = TRAIN_DATA[0][0]
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doc = nlp(test_text)
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gold_sent_starts = [0] * 14
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gold_sent_starts[0] = 1
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gold_sent_starts[5] = 1
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gold_sent_starts[9] = 1
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assert [int(t.is_sent_start) for t in doc] == gold_sent_starts
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2020-03-06 16:45:02 +03:00
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# Also test the results are still the same after IO
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with make_tempdir() as tmp_dir:
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nlp.to_disk(tmp_dir)
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nlp2 = util.load_model_from_path(tmp_dir)
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doc2 = nlp2(test_text)
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2020-03-08 15:23:18 +03:00
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assert [int(t.is_sent_start) for t in doc2] == gold_sent_starts
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2020-10-13 22:07:13 +03:00
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# Make sure that running pipe twice, or comparing to call, always amounts to the same predictions
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texts = [
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"Just a sentence.",
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"Then one more sentence about London.",
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"Here is another one.",
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"I like London.",
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]
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batch_deps_1 = [doc.to_array([SENT_START]) for doc in nlp.pipe(texts)]
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batch_deps_2 = [doc.to_array([SENT_START]) for doc in nlp.pipe(texts)]
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no_batch_deps = [
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doc.to_array([SENT_START]) for doc in [nlp(text) for text in texts]
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]
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assert_equal(batch_deps_1, batch_deps_2)
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assert_equal(batch_deps_1, no_batch_deps)
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2022-02-05 19:59:24 +03:00
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# test internal pipe labels vs. Language.pipe_labels with hidden labels
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assert nlp.get_pipe("senter").labels == ("I", "S")
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assert "senter" not in nlp.pipe_labels
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Store activations in `Doc`s when `save_activations` is enabled (#11002)
* Store activations in Doc when `store_activations` is enabled
This change adds the new `activations` attribute to `Doc`. This
attribute can be used by trainable pipes to store their activations,
probabilities, and guesses for downstream users.
As an example, this change modifies the `tagger` and `senter` pipes to
add an `store_activations` option. When this option is enabled, the
probabilities and guesses are stored in `set_annotations`.
* Change type of `store_activations` to `Union[bool, List[str]]`
When the value is:
- A bool: all activations are stored when set to `True`.
- A List[str]: the activations named in the list are stored
* Formatting fixes in Tagger
* Support store_activations in spancat and morphologizer
* Make Doc.activations type visible to MyPy
* textcat/textcat_multilabel: add store_activations option
* trainable_lemmatizer/entity_linker: add store_activations option
* parser/ner: do not currently support returning activations
* Extend tagger and senter tests
So that they, like the other tests, also check that we get no
activations if no activations were requested.
* Document `Doc.activations` and `store_activations` in the relevant pipes
* Start errors/warnings at higher numbers to avoid merge conflicts
Between the master and v4 branches.
* Add `store_activations` to docstrings.
* Replace store_activations setter by set_store_activations method
Setters that take a different type than what the getter returns are still
problematic for MyPy. Replace the setter by a method, so that type inference
works everywhere.
* Use dict comprehension suggested by @svlandeg
* Revert "Use dict comprehension suggested by @svlandeg"
This reverts commit 6e7b958f7060397965176c69649e5414f1f24988.
* EntityLinker: add type annotations to _add_activations
* _store_activations: make kwarg-only, remove doc_scores_lens arg
* set_annotations: add type annotations
* Apply suggestions from code review
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* TextCat.predict: return dict
* Make the `TrainablePipe.store_activations` property a bool
This means that we can also bring back `store_activations` setter.
* Remove `TrainablePipe.activations`
We do not need to enumerate the activations anymore since `store_activations` is
`bool`.
* Add type annotations for activations in predict/set_annotations
* Rename `TrainablePipe.store_activations` to `save_activations`
* Error E1400 is not used anymore
This error was used when activations were still `Union[bool, List[str]]`.
* Change wording in API docs after store -> save change
* docs: tag (save_)activations as new in spaCy 4.0
* Fix copied line in morphologizer activations test
* Don't train in any test_save_activations test
* Rename activations
- "probs" -> "probabilities"
- "guesses" -> "label_ids", except in the edit tree lemmatizer, where
"guesses" -> "tree_ids".
* Remove unused W400 warning.
This warning was used when we still allowed the user to specify
which activations to save.
* Formatting fixes
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
* Replace "kb_ids" by a constant
* spancat: replace a cast by an assertion
* Fix EOF spacing
* Fix comments in test_save_activations tests
* Do not set RNG seed in activation saving tests
* Revert "spancat: replace a cast by an assertion"
This reverts commit 0bd5730d16432443a2b247316928d4f789ad8741.
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2022-09-13 10:51:12 +03:00
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def test_save_activations():
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# Test if activations are correctly added to Doc when requested.
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nlp = English()
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senter = cast(TrainablePipe, nlp.add_pipe("senter"))
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train_examples = []
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for t in TRAIN_DATA:
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train_examples.append(Example.from_dict(nlp.make_doc(t[0]), t[1]))
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nlp.initialize(get_examples=lambda: train_examples)
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nO = senter.model.get_dim("nO")
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doc = nlp("This is a test.")
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assert "senter" not in doc.activations
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senter.save_activations = True
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doc = nlp("This is a test.")
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assert "senter" in doc.activations
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assert set(doc.activations["senter"].keys()) == {"label_ids", "probabilities"}
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assert doc.activations["senter"]["probabilities"].shape == (5, nO)
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assert doc.activations["senter"]["label_ids"].shape == (5,)
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