spaCy/spacy/pipeline
Lj Miranda 53687b5bca Add spancat_singlelabel pipeline for multiclass and non-overlapping span labelling tasks (#11365)
* [wip] Update

* [wip] Update

* Add initial port

* [wip] Update

* Fix all imports

* Add spancat_exclusive to pipeline

* [WIP] Update

* [ci skip] Add breakpoint for debugging

* Use spacy.SpanCategorizer.v1 as default archi

* Update spacy/pipeline/spancat_exclusive.py

Co-authored-by: kadarakos <kadar.akos@gmail.com>

* [ci skip] Small updates

* Use Softmax v2 directly from thinc

* Cache the label map

* Fix mypy errors

However, I ignored line 370 because it opened up a bunch of type errors
that might be trickier to solve and might lead to a more complicated
codebase.

* avoid multiplication with 1.0

Co-authored-by: kadarakos <kadar.akos@gmail.com>

* Update spacy/pipeline/spancat_exclusive.py

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Update component versions to v2

* Add scorer to docstring

* Add _n_labels property to SpanCategorizer

Instead of using len(self.labels) in initialize() I am using a private
property self._n_labels. This achieves implementation parity and allows
me to delete the whole initialize() method for spancat_exclusive (since
it's now the same with spancat).

* Inherit from SpanCat instead of TrainablePipe

This commit changes the inheritance structure of Exclusive_Spancat,
now it's inheriting from SpanCategorizer than TrainablePipe. This
allows me to remove duplicate methods that are already present in
the parent function.

* Revert documentation link to spancat

* Fix init call for exclusive spancat

* Update spacy/pipeline/spancat_exclusive.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Import Suggester from spancat

* Include zero_init.v1 for spancat

* Implement _allow_extra_label to use _n_labels

To ensure that spancat / spancat_exclusive cannot be resized after
initialization, I inherited the _allow_extra_label() method from
spacy/pipeline/trainable_pipe.pyx and used self._n_labels instead
of len(self.labels) for checking.

I think that changing it locally is a better solution rather than
forcing each class that inherits TrainablePipe to use the self._n_labels
attribute.

Also note that I turned-off black formatting in this block of code
because it reads better without the overhang.

* Extend existing tests to spancat_exclusive

In this commit, I extended the existing tests for spancat to include
spancat_exclusive. I parametrized the test functions with 'name'
(similar var name with textcat and textcat_multilabel) for each
applicable test.

TODO: Add overfitting tests for spancat_exclusive

* Update documentation for spancat

* Turn on formatting for allow_extra_label

* Remove initializers in default config

* Use DEFAULT_EXCL_SPANCAT_MODEL

I also renamed spancat_exclusive_default_config into
spancat_excl_default_config because black does some not pretty
formatting changes.

* Update documentation

Update grammar and usage

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Clarify docstring for Exclusive_SpanCategorizer

* Remove mypy ignore and typecast labels to list

* Fix documentation API

* Use a single variable for tests

* Update defaults for number of rows

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Put back initializers in spancat config

Whenever I remove model.scorer.init_w and model.scorer.init_b,
I encounter an error in the test:

    SystemError: <method '__getitem__' of 'dict' objects> returned a result
    with an error set.

My Thinc version is 8.1.5, but I can't seem to check what's causing the
error.

* Update spancat_exclusive docstring

* Remove init_W and init_B parameters

This commit is expected to fail until the new Thinc release.

* Require thinc>=8.1.6 for serializable Softmax defaults

* Handle zero suggestions to make tests pass

I'm not sure if this is the most elegant solution. But what should
happen is that the _make_span_group function MUST return an empty
SpanGroup if there are no suggestions.

The error happens when the 'scores' variable is empty. We cannot
get the 'predicted' and other downstream vars.

* Better approach for handling zero suggestions

* Update website/docs/api/spancategorizer.md

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spancategorizer headers

* Apply suggestions from code review

Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>

* Add default value in negative_weight in docs

* Add default value in allow_overlap in docs

* Update how spancat_exclusive is constructed

In this commit, I added the following:
- Put the default values of negative_weight and allow_overlap
    in the default_config dictionary.
- Rename make_spancat -> make_exclusive_spancat

* Run prettier on spancategorizer.mdx

* Change exactly one -> at most one

* Add suggester documentation in Exclusive_SpanCategorizer

* Add suggester to spancat docstrings

* merge multilabel and singlelabel spancat

* rename spancat_exclusive to singlelable

* wire up different make_spangroups for single and multilabel

* black

* black

* add docstrings

* more docstring and fix negative_label

* don't rely on default arguments

* black

* remove spancat exclusive

* replace single_label with add_negative_label and adjust inference

* mypy

* logical bug in configuration check

* add spans.attrs[scores]

* single label make_spangroup test

* bugfix

* black

* tests for make_span_group with negative labels

* refactor make_span_group

* black

* Update spacy/tests/pipeline/test_spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* remove duplicate declaration

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* raise error instead of just print

* make label mapper private

* update docs

* run prettier

* Update website/docs/api/spancategorizer.mdx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update website/docs/api/spancategorizer.mdx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* don't keep recomputing self._label_map for each span

* typo in docs

* Intervals to private and document 'name' param

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update spacy/pipeline/spancat.py

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* add Tag to new features

* replace tags

* revert

* revert

* revert

* revert

* Update website/docs/api/spancategorizer.mdx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* Update website/docs/api/spancategorizer.mdx

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>

* prettier

* Fix merge

* Update website/docs/api/spancategorizer.mdx

* remove references to 'single_label'

* remove old paragraph

* Add spancat_singlelabel to config template

* Format

* Extend init config tests

---------

Co-authored-by: kadarakos <kadar.akos@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2023-03-09 10:33:16 +01:00
..
_edit_tree_internals Refactor error messages to remove hardcoded strings (#10729) 2022-05-02 13:38:46 +02:00
_parser_internals account for NER labels with a hyphen in the name (#10960) 2022-06-17 20:02:37 +01:00
legacy Refactor KB for easier customization (#11268) 2022-09-08 10:38:07 +02:00
__init__.py Add SpanRuler component (#9880) 2022-06-02 13:12:53 +02:00
attributeruler.py Merge remote-tracking branch 'upstream/master' into chore/update-develop-from-master-v3.2-1 2021-10-26 11:53:50 +02:00
dep_parser.pyx account for NER labels with a hyphen in the name (#10960) 2022-06-17 20:02:37 +01:00
edit_tree_lemmatizer.py Fix speed problem with top_k>1 on CPU in edit tree lemmatizer (#12017) 2023-01-20 19:34:11 +01:00
entity_linker.py Make generation of empty KnowledgeBase instances configurable in EntityLinker (#12320) 2023-03-01 17:33:31 +01:00
entityruler.py Enable fuzzy text matching in Matcher (#11359) 2023-01-10 10:36:17 +01:00
functions.py Add doc_cleaner component (#9659) 2021-11-23 15:33:33 +01:00
lemmatizer.py Merge remote-tracking branch 'upstream/master' into chore/update-develop-from-master-v3.2-1 2021-10-26 11:53:50 +02:00
morphologizer.pyx Tagger: use unnormalized probabilities for inference (#10197) 2022-03-15 14:15:31 +01:00
multitask.pyx Replace negative rows with 0 in StaticVectors (#7674) 2021-04-22 18:04:15 +10:00
ner.pyx account for NER labels with a hyphen in the name (#10960) 2022-06-17 20:02:37 +01:00
pipe.pxd TrainablePipe (#6213) 2020-10-08 21:33:49 +02:00
pipe.pyi Add Pipe.hide_labels to omit labels from pipeline meta (#10175) 2022-02-05 17:59:24 +01:00
pipe.pyx Fix config validation failures caused by NVTX pipeline wrappers (#11460) 2022-09-12 14:55:41 +02:00
sentencizer.pyx Add overwrite settings for more components (#9050) 2021-09-30 15:35:55 +02:00
senter.pyx Tagger: use unnormalized probabilities for inference (#10197) 2022-03-15 14:15:31 +01:00
span_ruler.py Enable fuzzy text matching in Matcher (#11359) 2023-01-10 10:36:17 +01:00
spancat.py Add spancat_singlelabel pipeline for multiclass and non-overlapping span labelling tasks (#11365) 2023-03-09 10:33:16 +01:00
tagger.pyx Tagger: use unnormalized probabilities for inference (#10197) 2022-03-15 14:15:31 +01:00
textcat_multilabel.py Improve score_cats for use with multiple textcat components (#11820) 2023-01-09 11:43:48 +01:00
textcat.py Rename modified textcat scorer to v2 (#11971) 2022-12-29 14:01:08 +01:00
tok2vec.py Prevent tok2vec to broadcast to listeners when predicting (#11385) 2022-09-12 15:36:48 +02:00
trainable_pipe.pxd Refactor scoring methods to use registered functions (#8766) 2021-08-10 15:13:39 +02:00
trainable_pipe.pyx Fix config validation failures caused by NVTX pipeline wrappers (#11460) 2022-09-12 14:55:41 +02:00
transition_parser.pxd Parser: use C saxpy/sgemm provided by the Ops implementation (#10773) 2022-05-27 11:20:52 +02:00
transition_parser.pyx precompute_hiddens/Parser: do not look up CPU ops (3.4) (#11069) 2022-07-05 10:53:42 +02:00