During `nlp.update`, components can be passed a boolean set_annotations
to indicate whether they should assign annotations to the `Doc`. This
needs to be called if downstream components expect to use the
annotations during training, e.g. if we wanted to use tagger features in
the parser.
Components can specify their assignments and requirements, so we can
figure out which components have these inter-dependencies. After
figuring this out, we can guess whether to pass set_annotations=True.
We could also call set_annotations=True always, or even just have this
as the only behaviour. The downside of this is that it would require the
`Doc` objects to be created afresh to avoid problematic modifications.
One approach would be to make a fresh copy of the `Doc` objects within
`nlp.update()`, so that we can write to the objects without any
problems. If we do that, we can drop this logic and also drop the
`set_annotations` mechanism. I would be fine with that approach,
although it runs the risk of introducing some performance overhead, and
we'll have to take care to copy all extension attributes etc.
* Tidy up train-from-config a bit
* Fix accidentally quadratic perf in TokenAnnotation.brackets
When we're reading in the gold data, we had a nested loop where
we looped over the brackets for each token, looking for brackets
that start on that word. This is accidentally quadratic, because
we have one bracket per word (for the POS tags). So we had
an O(N**2) behaviour here that ended up being pretty slow.
To solve this I'm indexing the brackets by their starting word
on the TokenAnnotations object, and having a property to provide
the previous view.
* Fixes
* setting KB in the EL constructor, similar to how the model is passed on
* removing wikipedia example files - moved to projects
* throw an error when nlp.update is called with 2 positional arguments
* rewriting the config logic in create pipe to accomodate for other objects (e.g. KB) in the config
* update config files with new parameters
* avoid training pipeline components that don't have a model (like sentencizer)
* various small fixes + UX improvements
* small fixes
* set thinc to 8.0.0a9 everywhere
* remove outdated comment
* Fix most_similar for vectors with unused rows
Address issues related to the unused rows in the vector table and
`most_similar`:
* Update `most_similar()` to search only through rows that are in use
according to `key2row`.
* Raise an error when `most_similar(n=n)` is larger than the number of
vectors in the table.
* Set and restore `_unset` correctly when vectors are added or
deserialized so that new vectors are added in the correct row.
* Set data and keys to the same length in `Vocab.prune_vectors()` to
avoid spurious entries in `key2row`.
* Fix regression test using `most_similar`
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Add warning for misaligned character offset spans
* Resolve conflict
* Filter warnings in example scripts
Filter warnings in example scripts to show warnings once, in particular
warnings about misaligned entities.
Co-authored-by: Ines Montani <ines@ines.io>
Update Polish tokenizer for UD_Polish-PDB, which is a relatively major
change from the existing tokenizer. Unused exceptions files and
conflicting test cases removed.
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Reduce stored lexemes data, move feats to lookups
* Move non-derivable lexemes features (`norm / cluster / prob`) to
`spacy-lookups-data` as lookups
* Get/set `norm` in both lookups and `LexemeC`, serialize in lookups
* Remove `cluster` and `prob` from `LexemesC`, get/set/serialize in
lookups only
* Remove serialization of lexemes data as `vocab/lexemes.bin`
* Remove `SerializedLexemeC`
* Remove `Lexeme.to_bytes/from_bytes`
* Modify normalization exception loading:
* Always create `Vocab.lookups` table `lexeme_norm` for
normalization exceptions
* Load base exceptions from `lang.norm_exceptions`, but load
language-specific exceptions from lookups
* Set `lex_attr_getter[NORM]` including new lookups table in
`BaseDefaults.create_vocab()` and when deserializing `Vocab`
* Remove all cached lexemes when deserializing vocab to override
existing normalizations with the new normalizations (as a replacement
for the previous step that replaced all lexemes data with the
deserialized data)
* Skip English normalization test
Skip English normalization test because the data is now in
`spacy-lookups-data`.
* Remove norm exceptions
Moved to spacy-lookups-data.
* Move norm exceptions test to spacy-lookups-data
* Load extra lookups from spacy-lookups-data lazily
Load extra lookups (currently for cluster and prob) lazily from the
entry point `lg_extra` as `Vocab.lookups_extra`.
* Skip creating lexeme cache on load
To improve model loading times, do not create the full lexeme cache when
loading. The lexemes will be created on demand when processing.
* Identify numeric values in Lexeme.set_attrs()
With the removal of a special case for `PROB`, also identify `float` to
avoid trying to convert it with the `StringStore`.
* Skip lexeme cache init in from_bytes
* Unskip and update lookups tests for python3.6+
* Update vocab pickle to include lookups_extra
* Update vocab serialization tests
Check strings rather than lexemes since lexemes aren't initialized
automatically, account for addition of "_SP".
* Re-skip lookups test because of python3.5
* Skip PROB/float values in Lexeme.set_attrs
* Convert is_oov from lexeme flag to lex in vectors
Instead of storing `is_oov` as a lexeme flag, `is_oov` reports whether
the lexeme has a vector.
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* make disable_pipes deprecated in favour of the new toggle_pipes
* rewrite disable_pipes statements
* update documentation
* remove bin/wiki_entity_linking folder
* one more fix
* remove deprecated link to documentation
* few more doc fixes
* add note about name change to the docs
* restore original disable_pipes
* small fixes
* fix typo
* fix error number to W096
* rename to select_pipes
* also make changes to the documentation
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* 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>
* Limiting noun_chunks for specific langauges
* Limiting noun_chunks for specific languages
Contributor Agreement
* Addressing review comments
* Removed unused fixtures and imports
* Add fa_tokenizer in test suite
* Use fa_tokenizer in test
* Undo extraneous reformatting
Co-authored-by: adrianeboyd <adrianeboyd@gmail.com>
Check that row is within bounds for the vector data array when adding a
vector.
Don't add vectors with rank OOV_RANK in `init-model` (change is due to
shift from OOV as 0 to OOV as OOV_RANK).
Remove `TAG` value from Danish and Swedish tokenizer exceptions because
it may not be included in a tag map (and these settings are problematic
as tokenizer exceptions anyway).
Instead of treating `'d` in contractions like `I'd` as `would` in all
cases in the tokenizer exceptions, leave the tagging and lemmatization
up to later components.
To fix the slow tokenizer URL (#4374) and allow `token_match` to take
priority over prefixes and suffixes by default, introduce a new
tokenizer option for a token match pattern that's applied after prefixes
and suffixes but before infixes.
* Initialize lower flag explicitly
* Handle whitespace words from GoldParse correctly when creating raw
text with orth variants
* Return the text with original casing if anything goes wrong
* `debug-data`: determine coverage of provided vectors
* `evaluate`: support `blank:lg` model to make it possible to just evaluate
tokenization
* `init-model`: add option to truncate vectors to N most frequent vectors
from word2vec file
* `train`:
* if training on GPU, only run evaluation/timing on CPU in the first
iteration
* if training is aborted, exit with a non-0 exit status
* simplify creation of KB by skipping dim reduction
* small fixes to train EL example script
* add KB creation and NEL training example scripts to example section
* update descriptions of example scripts in the documentation
* moving wiki_entity_linking folder from bin to projects
* remove test for wiki NEL functionality that is being moved
Reconstruction of the original PR #4697 by @MiniLau.
Removes unused `SENT_END` symbol and `IS_SENT_END` from `Matcher` schema
because the Matcher is only going to be able to support `IS_SENT_START`.
Improve GoldParse NER alignment by including all cases where the start
and end of the NER span can be aligned, regardless of internal
tokenization differences.
To do this, convert BILUO tags to character offsets, check start/end
alignment with `doc.char_span()`, and assign the BILUO tags for the
aligned spans. Alignment for `O/-` tags is handled through the
one-to-one and multi alignments.
Previously, pipelines with shared tok2vec weights would call the
tok2vec backprop callback multiple times, once for each pipeline
component. This caused errors for PyTorch, and was inefficient.
Instead, accumulate the gradient for all but one component, and just
call the callback once.
Modify jieba install message to instruct the user to use
`ChineseDefaults.use_jieba = False` so that it's possible to load
pkuseg-only models without jieba installed.
* Add pkuseg and serialization support for Chinese
Add support for pkuseg alongside jieba
* Specify model through `Language` meta:
* split on characters (if no word segmentation packages are installed)
```
Chinese(meta={"tokenizer": {"config": {"use_jieba": False, "use_pkuseg": False}}})
```
* jieba (remains the default tokenizer if installed)
```
Chinese()
Chinese(meta={"tokenizer": {"config": {"use_jieba": True}}}) # explicit
```
* pkuseg
```
Chinese(meta={"tokenizer": {"config": {"pkuseg_model": "default", "use_jieba": False, "use_pkuseg": True}}})
```
* The new tokenizer setting `require_pkuseg` is used to override
`use_jieba` default, which is intended for models that provide a pkuseg
model:
```
nlp_pkuseg = Chinese(meta={"tokenizer": {"config": {"pkuseg_model": "default", "require_pkuseg": True}}})
nlp = Chinese() # has `use_jieba` as `True` by default
nlp.from_bytes(nlp_pkuseg.to_bytes()) # `require_pkuseg` overrides `use_jieba` when calling the tokenizer
```
Add support for serialization of tokenizer settings and pkuseg model, if
loaded
* Add sorting for `Language.to_bytes()` serialization of `Language.meta`
so that the (emptied, but still present) tokenizer metadata is in a
consistent position in the serialized data
Extend tests to cover all three tokenizer configurations and
serialization
* Fix from_disk and tests without jieba or pkuseg
* Load cfg first and only show error if `use_pkuseg`
* Fix blank/default initialization in serialization tests
* Explicitly initialize jieba's cache on init
* Add serialization for pkuseg pre/postprocessors
* Reformat pkuseg install message
* Matcher support for Span, as well as Doc #5056
* Removes an import unused
* Signed contributors agreement
* Code optimization and better test
* Add error message for bad Matcher call argument
* Fix merging
* Use max(uint64) for OOV lexeme rank
* Add test for default OOV rank
* Revert back to thinc==7.4.0
Requiring the updated version of thinc was unnecessary.
* Define OOV_RANK in one place
Define OOV_RANK in one place in `util`.
* Fix formatting [ci skip]
* Switch to external definitions of max(uint64)
Switch to external defintions of max(uint64) and confirm that they are
equal.
* Add Doc init from list of words and text
Add an option to initialize a `Doc` from a text and list of words where
the words may or may not include all whitespace tokens. If the text and
words are mismatched, raise an error.
* Fix error code
* Remove all whitespace before aligning words/text
* Move words/text init to util function
* Update error message
* Rename to get_words_and_spaces
* Fix formatting
* Fixed typo in cli warning
Fixed a typo in the warning for the provision of exactly two labels, which have not been designated as binary, to textcat.
* Create and signed contributor form
* Use inline flags in token_match patterns
Use inline flags in `token_match` patterns so that serializing does not
lose the flag information.
* Modify inline flag
* Modify inline flag
* Add pos and morph scoring to Scorer
Add pos, morph, and morph_per_type to `Scorer`. Report pos and morph
accuracy in `spacy evaluate`.
* Update morphologizer for v3
* switch to tagger-based morphologizer
* use `spacy.HashCharEmbedCNN` for morphologizer defaults
* add `Doc.is_morphed` flag
* Add morphologizer to train CLI
* Add basic morphologizer pipeline tests
* Add simple morphologizer training example
* Remove subword_features from CharEmbed models
Remove `subword_features` argument from `spacy.HashCharEmbedCNN.v1` and
`spacy.HashCharEmbedBiLSTM.v1` since in these cases `subword_features`
is always `False`.
* Rename setting in morphologizer example
Use `with_pos_tags` instead of `without_pos_tags`.
* Fix kwargs for spacy.HashCharEmbedBiLSTM.v1
* Remove defaults for spacy.HashCharEmbedBiLSTM.v1
Remove default `nM/nC` for `spacy.HashCharEmbedBiLSTM.v1`.
* Set random seed for textcat overfitting test
* bring back default build_text_classifier method
* remove _set_dims_ hack in favor of proper dim inference
* add tok2vec initialize to unit test
* small fixes
* add unit test for various textcat config settings
* logistic output layer does not have nO
* fix window_size setting
* proper fix
* fix W initialization
* Update textcat training example
* Use ml_datasets
* Convert training data to `Example` format
* Use `n_texts` to set proportionate dev size
* fix _init renaming on latest thinc
* avoid setting a non-existing dim
* update to thinc==8.0.0a2
* add BOW and CNN defaults for easy testing
* various experiments with train_textcat script, fix softmax activation in textcat bow
* allow textcat train script to work on other datasets as well
* have dataset as a parameter
* train textcat from config, with example config
* add config for training textcat
* formatting
* fix exclusive_classes
* fixing BOW for GPU
* bump thinc to 8.0.0a3 (not published yet so CI will fail)
* add in link_vectors_to_models which got deleted
Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
* Check whether doc is instantiated
When creating docs to pair with gold parses, modify test to check
whether a doc is unset rather than whether it contains tokens.
* Restore test of evaluate on an empty doc
* Set a minimal gold.orig for the scorer
Without a minimal gold.orig the scorer can't evaluate empty docs. This
is the v3 equivalent of #4925.
* Modify Vector.resize to work with cupy
Modify `Vectors.resize` to work with cupy. Modify behavior when resizing
to a different vector dimension so that individual vectors are truncated
or extended with zeros instead of having the original values filled into
the new shape without regard for the original axes.
* Update spacy/tests/vocab_vectors/test_vectors.py
Co-Authored-By: Matthew Honnibal <honnibal+gh@gmail.com>
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
* Omit per_type scores from model-best calculations
The addition of per_type scores to the included metrics (#4911) causes
errors when they're compared while determining the best model, so omit
them for this `max()` comparison.
* Add default speed data for interrupted train CLI
Add better speed meta defaults so that an interrupted iteration still
produces a best model.
Co-authored-by: Ines Montani <ines@ines.io>
UD_Danish-DDT has (as far as I can tell) hallucinated periods after
abbreviations, so the changes are an artifact of the corpus and not due
to anything meaningful about Danish tokenization.
* Revert changes to priority of `token_match` so that it has priority
over all other tokenizer patterns
* Add lookahead and potentially slow lookbehind back to the default URL
pattern
* Expand character classes in URL pattern to improve matching around
lookaheads and lookbehinds related to #4882
* Revert changes to Hungarian tokenizer
* Revert (xfail) several URL tests to their status before #4374
* Update `tokenizer.explain()` and docs accordingly
* avoid changing original config
* fix elif structure, batch with just int crashes otherwise
* tok2vec example with doc2feats, encode and embed architectures
* further clean up MultiHashEmbed
* further generalize Tok2Vec to work with extract-embed-encode parts
* avoid initializing the charembed layer with Docs (for now ?)
* small fixes for bilstm config (still does not run)
* rename to core layer
* move new configs
* walk model to set nI instead of using core ref
* fix senter overfitting test to be more similar to the training data (avoid flakey behaviour)
* merge_entities sets the vector in the vocab for the merged token
* add unit test
* import unicode_literals
* move code to _merge function
* only set vector if vocab has non-zero vectors
* Update sentence recognizer
* rename `sentrec` to `senter`
* use `spacy.HashEmbedCNN.v1` by default
* update to follow `Tagger` modifications
* remove component methods that can be inherited from `Tagger`
* add simple initialization and overfitting pipeline tests
* Update serialization test for senter
* Improve token head verification
Improve the verification for valid token heads when heads are set:
* in `Token.head`: heads come from the same document
* in `Doc.from_array()`: head indices are within the bounds of the
document
* Improve error message
* Fix model-final/model-best meta
* include speed and accuracy from final iteration
* combine with speeds from base model if necessary
* Include token_acc metric for all components
* fix grad_clip naming
* cleaning up pretrained_vectors out of cfg
* further refactoring Model init's
* move Model building out of pipes
* further refactor to require a model config when creating a pipe
* small fixes
* making cfg in nn_parser more consistent
* fixing nr_class for parser
* fixing nn_parser's nO
* fix printing of loss
* architectures in own file per type, consistent naming
* convenience methods default_tagger_config and default_tok2vec_config
* let create_pipe access default config if available for that component
* default_parser_config
* move defaults to separate folder
* allow reading nlp from package or dir with argument 'name'
* architecture spacy.VocabVectors.v1 to read static vectors from file
* cleanup
* default configs for nel, textcat, morphologizer, tensorizer
* fix imports
* fixing unit tests
* fixes and clean up
* fixing defaults, nO, fix unit tests
* restore parser IO
* fix IO
* 'fix' serialization test
* add *.cfg to manifest
* fix example configs with additional arguments
* replace Morpohologizer with Tagger
* add IO bit when testing overfitting of tagger (currently failing)
* fix IO - don't initialize when reading from disk
* expand overfitting tests to also check IO goes OK
* remove dropout from HashEmbed to fix Tagger performance
* add defaults for sentrec
* update thinc
* always pass a Model instance to a Pipe
* fix piped_added statement
* remove obsolete W029
* remove obsolete errors
* restore byte checking tests (work again)
* clean up test
* further test cleanup
* convert from config to Model in create_pipe
* bring back error when component is not initialized
* cleanup
* remove calls for nlp2.begin_training
* use thinc.api in imports
* allow setting charembed's nM and nC
* fix for hardcoded nM/nC + unit test
* formatting fixes
* trigger build
* add lemma option to displacy 'dep' visualiser
* more compact list comprehension
* add option to doc
* fix test and add lemmas to util.get_doc
* fix capital
* remove lemma from get_doc
* cleanup
