Commit Graph

411 Commits

Author SHA1 Message Date
svlandeg
02d87a8b2b fix showing dep arcs in streamlit script 2020-03-19 10:30:20 +01:00
Sofie Van Landeghem
5847be6022
Tok2Vec: extract-embed-encode (#5102)
* 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)
2020-03-08 13:23:18 +01:00
Sofie Van Landeghem
06f0a8daa0
Default settings to configurations (#4995)
* 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
2020-02-27 18:42:27 +01:00
Ines Montani
de11ea753a Merge branch 'master' into develop 2020-02-18 14:47:23 +01:00
Christos Aridas
ff8e71f46d
Update streamlit app (#5017)
* Update streamlit app [ci skip]

* Add all labels by default

* Tidy up and auto-format

Co-authored-by: Ines Montani <ines@ines.io>
2020-02-15 15:49:09 +01:00
Sofie Van Landeghem
569cc98982
Update spaCy for thinc 8.0.0 (#4920)
* Add load_from_config function

* Add train_from_config script

* Merge configs and expose via spacy.config

* Fix script

* Suggest create_evaluation_callback

* Hard-code for NER

* Fix errors

* Register command

* Add TODO

* Update train-from-config todos

* Fix imports

* Allow delayed setting of parser model nr_class

* Get train-from-config working

* Tidy up and fix scores and printing

* Hide traceback if cancelled

* Fix weighted score formatting

* Fix score formatting

* Make output_path optional

* Add Tok2Vec component

* Tidy up and add tok2vec_tensors

* Add option to copy docs in nlp.update

* Copy docs in nlp.update

* Adjust nlp.update() for set_annotations

* Don't shuffle pipes in nlp.update, decruft

* Support set_annotations arg in component update

* Support set_annotations in parser update

* Add get_gradients method

* Add get_gradients to parser

* Update errors.py

* Fix problems caused by merge

* Add _link_components method in nlp

* Add concept of 'listeners' and ControlledModel

* Support optional attributes arg in ControlledModel

* Try having tok2vec component in pipeline

* Fix tok2vec component

* Fix config

* Fix tok2vec

* Update for Example

* Update for Example

* Update config

* Add eg2doc util

* Update and add schemas/types

* Update schemas

* Fix nlp.update

* Fix tagger

* Remove hacks from train-from-config

* Remove hard-coded config str

* Calculate loss in tok2vec component

* Tidy up and use function signatures instead of models

* Support union types for registry models

* Minor cleaning in Language.update

* Make ControlledModel specifically Tok2VecListener

* Fix train_from_config

* Fix tok2vec

* Tidy up

* Add function for bilstm tok2vec

* Fix type

* Fix syntax

* Fix pytorch optimizer

* Add example configs

* Update for thinc describe changes

* Update for Thinc changes

* Update for dropout/sgd changes

* Update for dropout/sgd changes

* Unhack gradient update

* Work on refactoring _ml

* Remove _ml.py module

* WIP upgrade cli scripts for thinc

* Move some _ml stuff to util

* Import link_vectors from util

* Update train_from_config

* Import from util

* Import from util

* Temporarily add ml.component_models module

* Move ml methods

* Move typedefs

* Update load vectors

* Update gitignore

* Move imports

* Add PrecomputableAffine

* Fix imports

* Fix imports

* Fix imports

* Fix missing imports

* Update CLI scripts

* Update spacy.language

* Add stubs for building the models

* Update model definition

* Update create_default_optimizer

* Fix import

* Fix comment

* Update imports in tests

* Update imports in spacy.cli

* Fix import

* fix obsolete thinc imports

* update srsly pin

* from thinc to ml_datasets for example data such as imdb

* update ml_datasets pin

* using STATE.vectors

* small fix

* fix Sentencizer.pipe

* black formatting

* rename Affine to Linear as in thinc

* set validate explicitely to True

* rename with_square_sequences to with_list2padded

* rename with_flatten to with_list2array

* chaining layernorm

* small fixes

* revert Optimizer import

* build_nel_encoder with new thinc style

* fixes using model's get and set methods

* Tok2Vec in component models, various fixes

* fix up legacy tok2vec code

* add model initialize calls

* add in build_tagger_model

* small fixes

* setting model dims

* fixes for ParserModel

* various small fixes

* initialize thinc Models

* fixes

* consistent naming of window_size

* fixes, removing set_dropout

* work around Iterable issue

* remove legacy tok2vec

* util fix

* fix forward function of tok2vec listener

* more fixes

* trying to fix PrecomputableAffine (not succesful yet)

* alloc instead of allocate

* add morphologizer

* rename residual

* rename fixes

* Fix predict function

* Update parser and parser model

* fixing few more tests

* Fix precomputable affine

* Update component model

* Update parser model

* Move backprop padding to own function, for test

* Update test

* Fix p. affine

* Update NEL

* build_bow_text_classifier and extract_ngrams

* Fix parser init

* Fix test add label

* add build_simple_cnn_text_classifier

* Fix parser init

* Set gpu off by default in example

* Fix tok2vec listener

* Fix parser model

* Small fixes

* small fix for PyTorchLSTM parameters

* revert my_compounding hack (iterable fixed now)

* fix biLSTM

* Fix uniqued

* PyTorchRNNWrapper fix

* small fixes

* use helper function to calculate cosine loss

* small fixes for build_simple_cnn_text_classifier

* putting dropout default at 0.0 to ensure the layer gets built

* using thinc util's set_dropout_rate

* moving layer normalization inside of maxout definition to optimize dropout

* temp debugging in NEL

* fixed NEL model by using init defaults !

* fixing after set_dropout_rate refactor

* proper fix

* fix test_update_doc after refactoring optimizers in thinc

* Add CharacterEmbed layer

* Construct tagger Model

* Add missing import

* Remove unused stuff

* Work on textcat

* fix test (again :)) after optimizer refactor

* fixes to allow reading Tagger from_disk without overwriting dimensions

* don't build the tok2vec prematuraly

* fix CharachterEmbed init

* CharacterEmbed fixes

* Fix CharacterEmbed architecture

* fix imports

* renames from latest thinc update

* one more rename

* add initialize calls where appropriate

* fix parser initialization

* Update Thinc version

* Fix errors, auto-format and tidy up imports

* Fix validation

* fix if bias is cupy array

* revert for now

* ensure it's a numpy array before running bp in ParserStepModel

* no reason to call require_gpu twice

* use CupyOps.to_numpy instead of cupy directly

* fix initialize of ParserModel

* remove unnecessary import

* fixes for CosineDistance

* fix device renaming

* use refactored loss functions (Thinc PR 251)

* overfitting test for tagger

* experimental settings for the tagger: avoid zero-init and subword normalization

* clean up tagger overfitting test

* use previous default value for nP

* remove toy config

* bringing layernorm back (had a bug - fixed in thinc)

* revert setting nP explicitly

* remove setting default in constructor

* restore values as they used to be

* add overfitting test for NER

* add overfitting test for dep parser

* add overfitting test for textcat

* fixing init for linear (previously affine)

* larger eps window for textcat

* ensure doc is not None

* Require newer thinc

* Make float check vaguer

* Slop the textcat overfit test more

* Fix textcat test

* Fix exclusive classes for textcat

* fix after renaming of alloc methods

* fixing renames and mandatory arguments (staticvectors WIP)

* upgrade to thinc==8.0.0.dev3

* refer to vocab.vectors directly instead of its name

* rename alpha to learn_rate

* adding hashembed and staticvectors dropout

* upgrade to thinc 8.0.0.dev4

* add name back to avoid warning W020

* thinc dev4

* update srsly

* using thinc 8.0.0a0 !

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
Co-authored-by: Ines Montani <ines@ines.io>
2020-01-29 17:06:46 +01:00
Sofie Van Landeghem
fbfc418745 run normal textcat train script with transformers (#4834)
* keep trf tok2vec and wordpiecer components during update

* also support transformer models for other example scripts
2020-01-16 02:01:23 +01:00
Sofie Van Landeghem
c70ccd543d Friendly error warning for NEL example script (#4881)
* make model positional arg and raise error if no vectors

* small doc fixes
2020-01-14 01:51:14 +01:00
Ines Montani
158b98a3ef Merge branch 'master' into develop 2019-12-21 18:55:03 +01:00
Sofie Van Landeghem
12158c1e3a Restore tqdm imports (#4804)
* set 4.38.0 to minimal version with color bug fix

* set imports back to proper place

* add upper range for tqdm
2019-12-16 13:12:19 +01:00
Sofie Van Landeghem
5355b0038f Update EL example (#4789)
* update EL example script after sentence-central refactor

* version bump

* set incl_prior to False for quick demo purposes

* clean up
2019-12-11 18:19:42 +01:00
adrianeboyd
faaa832518 Generalize handling of tokenizer special cases (#4259)
* Generalize handling of tokenizer special cases

Handle tokenizer special cases more generally by using the Matcher
internally to match special cases after the affix/token_match
tokenization is complete.

Instead of only matching special cases while processing balanced or
nearly balanced prefixes and suffixes, this recognizes special cases in
a wider range of contexts:

* Allows arbitrary numbers of prefixes/affixes around special cases
* Allows special cases separated by infixes

Existing tests/settings that couldn't be preserved as before:

* The emoticon '")' is no longer a supported special case
* The emoticon ':)' in "example:)" is a false positive again

When merged with #4258 (or the relevant cache bugfix), the affix and
token_match properties should be modified to flush and reload all
special cases to use the updated internal tokenization with the Matcher.

* Remove accidentally added test case

* Really remove accidentally added test

* Reload special cases when necessary

Reload special cases when affixes or token_match are modified. Skip
reloading during initialization.

* Update error code number

* Fix offset and whitespace in Matcher special cases

* Fix offset bugs when merging and splitting tokens
* Set final whitespace on final token in inserted special case

* Improve cache flushing in tokenizer

* Separate cache and specials memory (temporarily)
* Flush cache when adding special cases
* Repeated `self._cache = PreshMap()` and `self._specials = PreshMap()`
are necessary due to this bug:
https://github.com/explosion/preshed/issues/21

* Remove reinitialized PreshMaps on cache flush

* Update UD bin scripts

* Update imports for `bin/`
* Add all currently supported languages
* Update subtok merger for new Matcher validation
* Modify blinded check to look at tokens instead of lemmas (for corpora
with tokens but not lemmas like Telugu)

* Use special Matcher only for cases with affixes

* Reinsert specials cache checks during normal tokenization for special
cases as much as possible
  * Additionally include specials cache checks while splitting on infixes
  * Since the special Matcher needs consistent affix-only tokenization
    for the special cases themselves, introduce the argument
    `with_special_cases` in order to do tokenization with or without
    specials cache checks
* After normal tokenization, postprocess with special cases Matcher for
special cases containing affixes

* Replace PhraseMatcher with Aho-Corasick

Replace PhraseMatcher with the Aho-Corasick algorithm over numpy arrays
of the hash values for the relevant attribute. The implementation is
based on FlashText.

The speed should be similar to the previous PhraseMatcher. It is now
possible to easily remove match IDs and matches don't go missing with
large keyword lists / vocabularies.

Fixes #4308.

* Restore support for pickling

* Fix internal keyword add/remove for numpy arrays

* Add test for #4248, clean up test

* Improve efficiency of special cases handling

* Use PhraseMatcher instead of Matcher
* Improve efficiency of merging/splitting special cases in document
  * Process merge/splits in one pass without repeated token shifting
  * Merge in place if no splits

* Update error message number

* Remove UD script modifications

Only used for timing/testing, should be a separate PR

* Remove final traces of UD script modifications

* Update UD bin scripts

* Update imports for `bin/`
* Add all currently supported languages
* Update subtok merger for new Matcher validation
* Modify blinded check to look at tokens instead of lemmas (for corpora
with tokens but not lemmas like Telugu)

* Add missing loop for match ID set in search loop

* Remove cruft in matching loop for partial matches

There was a bit of unnecessary code left over from FlashText in the
matching loop to handle partial token matches, which we don't have with
PhraseMatcher.

* Replace dict trie with MapStruct trie

* Fix how match ID hash is stored/added

* Update fix for match ID vocab

* Switch from map_get_unless_missing to map_get

* Switch from numpy array to Token.get_struct_attr

Access token attributes directly in Doc instead of making a copy of the
relevant values in a numpy array.

Add unsatisfactory warning for hash collision with reserved terminal
hash key. (Ideally it would change the reserved terminal hash and redo
the whole trie, but for now, I'm hoping there won't be collisions.)

* Restructure imports to export find_matches

* Implement full remove()

Remove unnecessary trie paths and free unused maps.

Parallel to Matcher, raise KeyError when attempting to remove a match ID
that has not been added.

* Switch to PhraseMatcher.find_matches

* Switch to local cdef functions for span filtering

* Switch special case reload threshold to variable

Refer to variable instead of hard-coded threshold

* Move more of special case retokenize to cdef nogil

Move as much of the special case retokenization to nogil as possible.

* Rewrap sort as stdsort for OS X

* Rewrap stdsort with specific types

* Switch to qsort

* Fix merge

* Improve cmp functions

* Fix realloc

* Fix realloc again

* Initialize span struct while retokenizing

* Temporarily skip retokenizing

* Revert "Move more of special case retokenize to cdef nogil"

This reverts commit 0b7e52c797.

* Revert "Switch to qsort"

This reverts commit a98d71a942.

* Fix specials check while caching

* Modify URL test with emoticons

The multiple suffix tests result in the emoticon `:>`, which is now
retokenized into one token as a special case after the suffixes are
split off.

* Refactor _apply_special_cases()

* Use cdef ints for span info used in multiple spots

* Modify _filter_special_spans() to prefer earlier

Parallel to #4414, modify _filter_special_spans() so that the earlier
span is preferred for overlapping spans of the same length.

* Replace MatchStruct with Entity

Replace MatchStruct with Entity since the existing Entity struct is
nearly identical.

* Replace Entity with more general SpanC

* Replace MatchStruct with SpanC

* Add error in debug-data if no dev docs are available (see #4575)

* Update azure-pipelines.yml

* Revert "Update azure-pipelines.yml"

This reverts commit ed1060cf59.

* Use latest wasabi

* Reorganise install_requires

* add dframcy to universe.json (#4580)

* Update universe.json [ci skip]

* Fix multiprocessing for as_tuples=True (#4582)

* Fix conllu script (#4579)

* force extensions to avoid clash between example scripts

* fix arg order and default file encoding

* add example config for conllu script

* newline

* move extension definitions to main function

* few more encodings fixes

* Add load_from_docbin example [ci skip]

TODO: upload the file somewhere

* Update README.md

* Add warnings about 3.8 (resolves #4593) [ci skip]

* Fixed typo: Added space between "recognize" and "various" (#4600)

* Fix DocBin.merge() example (#4599)

* Replace function registries with catalogue (#4584)

* Replace functions registries with catalogue

* Update __init__.py

* Fix test

* Revert unrelated flag [ci skip]

* Bugfix/dep matcher issue 4590 (#4601)

* add contributor agreement for prilopes

* add test for issue #4590

* fix on_match params for DependencyMacther (#4590)

* Minor updates to language example sentences (#4608)

* Add punctuation to Spanish example sentences

* Combine multilanguage examples for lang xx

* Add punctuation to nb examples

* Always realloc to a larger size

Avoid potential (unlikely) edge case and cymem error seen in #4604.

* Add error in debug-data if no dev docs are available (see #4575)

* Update debug-data for GoldCorpus / Example

* Ignore None label in misaligned NER data
2019-11-13 21:24:35 +01:00
Sofie Van Landeghem
e48a09df4e Example class for training data (#4543)
* OrigAnnot class instead of gold.orig_annot list of zipped tuples

* from_orig to replace from_annot_tuples

* rename to RawAnnot

* some unit tests for GoldParse creation and internal format

* removing orig_annot and switching to lists instead of tuple

* rewriting tuples to use RawAnnot (+ debug statements, WIP)

* fix pop() changing the data

* small fixes

* pop-append fixes

* return RawAnnot for existing GoldParse to have uniform interface

* clean up imports

* fix merge_sents

* add unit test for 4402 with new structure (not working yet)

* introduce DocAnnot

* typo fixes

* add unit test for merge_sents

* rename from_orig to from_raw

* fixing unit tests

* fix nn parser

* read_annots to produce text, doc_annot pairs

* _make_golds fix

* rename golds_to_gold_annots

* small fixes

* fix encoding

* have golds_to_gold_annots use DocAnnot

* missed a spot

* merge_sents as function in DocAnnot

* allow specifying only part of the token-level annotations

* refactor with Example class + underlying dicts

* pipeline components to work with Example objects (wip)

* input checking

* fix yielding

* fix calls to update

* small fixes

* fix scorer unit test with new format

* fix kwargs order

* fixes for ud and conllu scripts

* fix reading data for conllu script

* add in proper errors (not fixed numbering yet to avoid merge conflicts)

* fixing few more small bugs

* fix EL script
2019-11-11 17:35:27 +01:00
Ines Montani
83381018d3 Add load_from_docbin example [ci skip]
TODO: upload the file somewhere
2019-11-05 11:52:43 +01:00
Sofie Van Landeghem
4ec7623288 Fix conllu script (#4579)
* force extensions to avoid clash between example scripts

* fix arg order and default file encoding

* add example config for conllu script

* newline

* move extension definitions to main function

* few more encodings fixes
2019-11-04 20:31:26 +01:00
Matthew Honnibal
f8d740bfb1
Fix --gold-preproc train cli command (#4392)
* Fix get labels for textcat

* Fix char_embed for gpu

* Revert "Fix char_embed for gpu"

This reverts commit 055b9a9e85.

* Fix passing of cats in gold.pyx

* Revert "Match pop with append for training format (#4516)"

This reverts commit 8e7414dace.

* Fix popping gold parses

* Fix handling of cats in gold tuples

* Fix name

* Fix ner_multitask_objective script

* Add test for 4402
2019-10-27 21:58:50 +01:00
Sofie Van Landeghem
8e7414dace Match pop with append for training format (#4516)
* trying to fix script - not succesful yet

* match pop() with extend() to avoid changing the data

* few more pop-extend fixes

* reinsert deleted print statement

* fix print statement

* add last tested version

* append instead of extend

* add in few comments

* quick fix for 4402 + unit test

* fixing number of docs (not counting cats)

* more fixes

* fix len

* print tmp file instead of using data from examples dir

* print tmp file instead of using data from examples dir (2)
2019-10-27 16:01:32 +01:00
Ines Montani
5e59c9b3ee Fix unicode strings in examples [ci skip] 2019-10-18 18:47:59 +02:00
Sofie Van Landeghem
2d249a9502 KB extensions and better parsing of WikiData (#4375)
* fix overflow error on windows

* more documentation & logging fixes

* md fix

* 3 different limit parameters to play with execution time

* bug fixes directory locations

* small fixes

* exclude dev test articles from prior probabilities stats

* small fixes

* filtering wikidata entities, removing numeric and meta items

* adding aliases from wikidata also to the KB

* fix adding WD aliases

* adding also new aliases to previously added entities

* fixing comma's

* small doc fixes

* adding subclassof filtering

* append alias functionality in KB

* prevent appending the same entity-alias pair

* fix for appending WD aliases

* remove date filter

* remove unnecessary import

* small corrections and reformatting

* remove WD aliases for now (too slow)

* removing numeric entities from training and evaluation

* small fixes

* shortcut during prediction if there is only one candidate

* add counts and fscore logging, remove FP NER from evaluation

* fix entity_linker.predict to take docs instead of single sentences

* remove enumeration sentences from the WP dataset

* entity_linker.update to process full doc instead of single sentence

* spelling corrections and dump locations in readme

* NLP IO fix

* reading KB is unnecessary at the end of the pipeline

* small logging fix

* remove empty files
2019-10-14 12:28:53 +02:00
adrianeboyd
d2d2baaf76 Revert training example edit from #4327 (#4403)
I think the original annotation was correct and this change also
unfortunately introduced a cycle into the dependency tree.
2019-10-10 17:00:26 +02:00
adrianeboyd
6f54e59fe7 Fix util.filter_spans() to prefer first span in overlapping sam… (#4414)
* Update util.filter_spans() to prefer earlier spans

* Add filter_spans test for first same-length span

* Update entity relation example to refer to util.filter_spans()
2019-10-10 17:00:03 +02:00
Ines Montani
52b5912dbf Tidy up [ci skip] 2019-10-02 12:05:59 +02:00
adrianeboyd
d82241218a Make the default NER labels less model-specific [ci skip] (#4361) 2019-10-02 12:05:17 +02:00
Ines Montani
b6670bf0c2 Use consistent spelling 2019-10-02 10:37:39 +02:00
Ines Montani
867e93aae2 Add Streamlit example [ci skip] 2019-10-02 01:21:20 +02:00
EarlGreyT
1e9e2d8aa1 fix typo in first token (#4327)
* fix typo in first token

The head of 'in' is review which has an offset of 4 and not 44

* added contributor agreement
2019-09-27 14:49:36 +02:00
adrianeboyd
b5d999e510 Add textcat to train CLI (#4226)
* Add doc.cats to spacy.gold at the paragraph level

Support `doc.cats` as `"cats": [{"label": string, "value": number}]` in
the spacy JSON training format at the paragraph level.

* `spacy.gold.docs_to_json()` writes `docs.cats`

* `GoldCorpus` reads in cats in each `GoldParse`

* Update instances of gold_tuples to handle cats

Update iteration over gold_tuples / gold_parses to handle addition of
cats at the paragraph level.

* Add textcat to train CLI

* Add textcat options to train CLI
* Add textcat labels in `TextCategorizer.begin_training()`
* Add textcat evaluation to `Scorer`:
  * For binary exclusive classes with provided label: F1 for label
  * For 2+ exclusive classes: F1 macro average
  * For multilabel (not exclusive): ROC AUC macro average (currently
relying on sklearn)
* Provide user info on textcat evaluation settings, potential
incompatibilities
* Provide pipeline to Scorer in `Language.evaluate` for textcat config
* Customize train CLI output to include only metrics relevant to current
pipeline
* Add textcat evaluation to evaluate CLI

* Fix handling of unset arguments and config params

Fix handling of unset arguments and model confiug parameters in Scorer
initialization.

* Temporarily add sklearn requirement

* Remove sklearn version number

* Improve Scorer handling of models without textcats

* Fixing Scorer handling of models without textcats

* Update Scorer output for python 2.7

* Modify inf in Scorer for python 2.7

* Auto-format

Also make small adjustments to make auto-formatting with black easier and produce nicer results

* Move error message to Errors

* Update documentation

* Add cats to annotation JSON format [ci skip]

* Fix tpl flag and docs [ci skip]

* Switch to internal roc_auc_score

Switch to internal `roc_auc_score()` adapted from scikit-learn.

* Add AUCROCScore tests and improve errors/warnings

* Add tests for AUCROCScore and roc_auc_score
* Add missing error for only positive/negative values
* Remove unnecessary warnings and errors

* Make reduced roc_auc_score functions private

Because most of the checks and warnings have been stripped for the
internal functions and access is only intended through `ROCAUCScore`,
make the functions for roc_auc_score adapted from scikit-learn private.

* Check that data corresponds with multilabel flag

Check that the training instances correspond with the multilabel flag,
adding the multilabel flag if required.

* Add textcat score to early stopping check

* Add more checks to debug-data for textcat

* Add example training data for textcat

* Add more checks to textcat train CLI

* Check configuration when extending base model
* Fix typos

* Update textcat example data

* Provide licensing details and licenses for data
* Remove two labels with no positive instances from jigsaw-toxic-comment
data.


Co-authored-by: Ines Montani <ines@ines.io>
2019-09-15 22:31:31 +02:00
Sofie Van Landeghem
0b4b4f1819 Documentation for Entity Linking (#4065)
* document token ent_kb_id

* document span kb_id

* update pipeline documentation

* prior and context weights as bool's instead

* entitylinker api documentation

* drop for both models

* finish entitylinker documentation

* small fixes

* documentation for KB

* candidate documentation

* links to api pages in code

* small fix

* frequency examples as counts for consistency

* consistent documentation about tensors returned by predict

* add entity linking to usage 101

* add entity linking infobox and KB section to 101

* entity-linking in linguistic features

* small typo corrections

* training example and docs for entity_linker

* predefined nlp and kb

* revert back to similarity encodings for simplicity (for now)

* set prior probabilities to 0 when excluded

* code clean up

* bugfix: deleting kb ID from tokens when entities were removed

* refactor train el example to use either model or vocab

* pretrain_kb example for example kb generation

* add to training docs for KB + EL example scripts

* small fixes

* error numbering

* ensure the language of vocab and nlp stay consistent across serialization

* equality with =

* avoid conflict in errors file

* add error 151

* final adjustements to the train scripts - consistency

* update of goldparse documentation

* small corrections

* push commit

* typo fix

* add candidate API to kb documentation

* update API sidebar with EntityLinker and KnowledgeBase

* remove EL from 101 docs

* remove entity linker from 101 pipelines / rephrase

* custom el model instead of existing model

* set version to 2.2 for EL functionality

* update documentation for 2 CLI scripts
2019-09-12 11:38:34 +02:00
Sofie Van Landeghem
482c7cd1b9 pulling tqdm imports in functions to avoid bug (tmp fix) (#4263) 2019-09-09 16:32:11 +02:00
Ines Montani
dad5621166 Tidy up and auto-format [ci skip] 2019-08-31 13:39:31 +02:00
adrianeboyd
82159b5c19 Updates/bugfixes for NER/IOB converters (#4186)
* Updates/bugfixes for NER/IOB converters

* Converter formats `ner` and `iob` use autodetect to choose a converter if
  possible

* `iob2json` is reverted to handle sentence-per-line data like
  `word1|pos1|ent1 word2|pos2|ent2`

  * Fix bug in `merge_sentences()` so the second sentence in each batch isn't
    skipped

* `conll_ner2json` is made more general so it can handle more formats with
  whitespace-separated columns

  * Supports all formats where the first column is the token and the final
    column is the IOB tag; if present, the second column is the POS tag

  * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O`
    separates documents

  * Add option for segmenting sentences (new flag `-s`)

  * Parser-based sentence segmentation with a provided model, otherwise with
    sentencizer (new option `-b` to specify model)

  * Can group sentences into documents with `n_sents` as long as sentence
    segmentation is available

  * Only applies automatic segmentation when there are no existing delimiters
    in the data

* Provide info about settings applied during conversion with warnings and
  suggestions if settings conflict or might not be not optimal.

* Add tests for common formats

* Add '(default)' back to docs for -c auto

* Add document count back to output

* Revert changes to converter output message

* Use explicit tabs in convert CLI test data

* Adjust/add messages for n_sents=1 default

* Add sample NER data to training examples

* Update README

* Add links in docs to example NER data

* Define msg within converters
2019-08-29 12:04:01 +02:00
adrianeboyd
8fe7bdd0fa Improve token pattern checking without validation (#4105)
* Fix typo in rule-based matching docs

* Improve token pattern checking without validation

Add more detailed token pattern checks without full JSON pattern validation and
provide more detailed error messages.

Addresses #4070 (also related: #4063, #4100).

* Check whether top-level attributes in patterns and attr for PhraseMatcher are
  in token pattern schema

* Check whether attribute value types are supported in general (as opposed to
  per attribute with full validation)

* Report various internal error types (OverflowError, AttributeError, KeyError)
  as ValueError with standard error messages

* Check for tagger/parser in PhraseMatcher pipeline for attributes TAG, POS,
  LEMMA, and DEP

* Add error messages with relevant details on how to use validate=True or nlp()
  instead of nlp.make_doc()

* Support attr=TEXT for PhraseMatcher

* Add NORM to schema

* Expand tests for pattern validation, Matcher, PhraseMatcher, and EntityRuler

* Remove unnecessary .keys()

* Rephrase error messages

* Add another type check to Matcher

Add another type check to Matcher for more understandable error messages
in some rare cases.

* Support phrase_matcher_attr=TEXT for EntityRuler

* Don't use spacy.errors in examples and bin scripts

* Fix error code

* Auto-format

Also try get Azure pipelines to finally start a build :(

* Update errors.py


Co-authored-by: Ines Montani <ines@ines.io>
Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2019-08-21 14:00:37 +02:00
Sofie Van Landeghem
0ba1b5eebc CLI scripts for entity linking (wikipedia & generic) (#4091)
* document token ent_kb_id

* document span kb_id

* update pipeline documentation

* prior and context weights as bool's instead

* entitylinker api documentation

* drop for both models

* finish entitylinker documentation

* small fixes

* documentation for KB

* candidate documentation

* links to api pages in code

* small fix

* frequency examples as counts for consistency

* consistent documentation about tensors returned by predict

* add entity linking to usage 101

* add entity linking infobox and KB section to 101

* entity-linking in linguistic features

* small typo corrections

* training example and docs for entity_linker

* predefined nlp and kb

* revert back to similarity encodings for simplicity (for now)

* set prior probabilities to 0 when excluded

* code clean up

* bugfix: deleting kb ID from tokens when entities were removed

* refactor train el example to use either model or vocab

* pretrain_kb example for example kb generation

* add to training docs for KB + EL example scripts

* small fixes

* error numbering

* ensure the language of vocab and nlp stay consistent across serialization

* equality with =

* avoid conflict in errors file

* add error 151

* final adjustements to the train scripts - consistency

* update of goldparse documentation

* small corrections

* push commit

* turn kb_creator into CLI script (wip)

* proper parameters for training entity vectors

* wikidata pipeline split up into two executable scripts

* remove context_width

* move wikidata scripts in bin directory, remove old dummy script

* refine KB script with logs and preprocessing options

* small edits

* small improvements to logging of EL CLI script
2019-08-13 15:38:59 +02:00
svlandeg
cd6c263fe4 format offsets 2019-07-23 11:31:29 +02:00
svlandeg
9f8c1e71a2 fix for Issue #4000 2019-07-22 13:34:12 +02:00
svlandeg
dae8a21282 rename entity frequency 2019-07-19 17:40:28 +02:00
svlandeg
21176517a7 have gold.links correspond exactly to doc.ents 2019-07-19 12:36:15 +02:00
svlandeg
e1213eaf6a use original gold object in get_loss function 2019-07-18 13:35:10 +02:00
svlandeg
ec55d2fccd filter training data beforehand (+black formatting) 2019-07-18 10:22:24 +02:00
Ines Montani
f2ea3e3ea2
Merge branch 'master' into feature/nel-wiki 2019-07-09 21:57:47 +02:00
Patrick Hogan
8c0586fd9c Update example and sign contributor agreement (#3916)
* Sign contributor agreement for askhogan

* Remove unneeded `seen_tokens` which is never used within the scope
2019-07-08 10:27:20 +02:00
svlandeg
b7a0c9bf60 fixing the context/prior weight settings 2019-07-03 17:48:09 +02:00
svlandeg
8840d4b1b3 fix for context encoder optimizer 2019-07-03 13:35:36 +02:00
svlandeg
3420cbe496 small fixes 2019-07-03 10:25:51 +02:00
svlandeg
2d2dea9924 experiment with adding NER types to the feature vector 2019-06-29 14:52:36 +02:00
svlandeg
c664f58246 adding prior probability as feature in the model 2019-06-28 16:22:58 +02:00
svlandeg
1c80b85241 fix tests 2019-06-28 08:59:23 +02:00
svlandeg
68a0662019 context encoder with Tok2Vec + linking model instead of cosine 2019-06-28 08:29:31 +02:00
svlandeg
dbc53b9870 rename to KBEntryC 2019-06-26 15:55:26 +02:00
svlandeg
1de61f68d6 improve speed of prediction loop 2019-06-26 13:53:10 +02:00