Commit Graph

21 Commits

Author SHA1 Message Date
Matthew Honnibal
6f5e308d17
Support negative examples in partial NER annotations (#8106)
* Support a cfg field in transition system

* Make NER 'has gold' check use right alignment for span

* Pass 'negative_samples_key' property into NER transition system

* Add field for negative samples to NER transition system

* Check neg_key in NER has_gold

* Support negative examples in NER oracle

* Test for negative examples in NER

* Fix name of config variable in NER

* Remove vestiges of old-style partial annotation

* Remove obsolete tests

* Add comment noting lack of support for negative samples in parser

* Additions to "neg examples" PR (#8201)

* add custom error and test for deprecated format

* add test for unlearning an entity

* add break also for Begin's cost

* add negative_samples_key property on Parser

* rename

* extend docs & fix some older docs issues

* add subclass constructors, clean up tests, fix docs

* add flaky test with ValueError if gold parse was not found

* remove ValueError if n_gold == 0

* fix docstring

* Hack in environment variables to try out training

* Remove hack

* Remove NER hack, and support 'negative O' samples

* Fix O oracle

* Fix transition parser

* Remove 'not O' from oracle

* Fix NER oracle

* check for spans in both gold.ents and gold.spans and raise if so, to prevent memory access violation

* use set instead of list in consistency check

Co-authored-by: svlandeg <sofie.vanlandeghem@gmail.com>
Co-authored-by: Sofie Van Landeghem <svlandeg@users.noreply.github.com>
2021-06-17 17:33:00 +10:00
Adriane Boyd
6788d90f61
Preserve existing ENT_KB_ID annotation in NER (#7988)
* Preserve existing ENT_KB_ID annotation in NER

Preserve `ent_kb_id` annotation on existing entity spans, which is not
preserved by the transition system.

* Simplify kb_id assignment

* Simplify further
2021-05-06 18:49:55 +10:00
Matthew Honnibal
0fb8d437c0
Fix sentence fragments bug (#7056, #7035) (#7057)
* Add test for #7035

* Update test for issue 7056

* Fix test

* Fix transitions method used in testing

* Fix state eol detection when rebuffer

* Clean up redundant fix
2021-02-14 13:38:13 +11:00
Matthew Honnibal
1d20e21f3e Add labels implicitly for parser and ner 2021-01-27 12:54:47 +11:00
Adriane Boyd
43a752a2a0
Fix assertion in default get oracle sequence usage (#6738)
Remove assertion for default debug value in 
`get_oracle_sequence_from_state`.
2021-01-16 16:07:39 +01:00
Matthew Honnibal
f0c696b4aa Fix failed merge of #6694 patch 2021-01-16 13:44:11 +11:00
Matthew Honnibal
7b3f0c6f1b
Questionable fix for parser training bug with misaligned sentences (#6694)
* Questionable fix for parser training bug with misaligned sentences

* Fix

Co-authored-by: Adriane Boyd <adrianeboyd@gmail.com>
2021-01-15 14:18:24 +01:00
svlandeg
ed53bb979d cleanup 2021-01-13 14:20:05 +01:00
svlandeg
5b598bd1d5 formatting 2021-01-12 17:28:41 +01:00
svlandeg
dd12c6c8fd allow missing information in deps and heads annotations 2021-01-07 19:10:32 +01:00
Sofie Van Landeghem
8c1a23209f
Getting scores out of beam_parser (#6684)
* clean up of ner tests

* beam_parser tests

* implement get_beam_parses and scored_parses for the dep parser

* we don't have to add the parse if there are no arcs
2021-01-07 16:28:27 +11:00
Sofie Van Landeghem
402dbc5bae
Getting scores out of beam_ner (#6575)
* small fixes and formatting

* bring test_issue4313 up-to-date, currently fails

* formatting

* add get_beam_parses method back

* add scored_ents function

* delete tag map
2021-01-06 12:02:32 +01:00
Sofie Van Landeghem
29b59086f9
Prevent 0-length mem alloc (#6653)
* prevent 0-length mem alloc by adding asserts

* fix lexeme mem allocation
2021-01-06 12:50:17 +11:00
Matthew Honnibal
8656a08777
Add beam_parser and beam_ner components for v3 (#6369)
* Get basic beam tests working

* Get basic beam tests working

* Compile _beam_utils

* Remove prints

* Test beam density

* Beam parser seems to train

* Draft beam NER

* Upd beam

* Add hypothesis as dev dependency

* Implement missing is-gold-parse method

* Implement early update

* Fix state hashing

* Fix test

* Fix test

* Default to non-beam in parser constructor

* Improve oracle for beam

* Start refactoring beam

* Update test

* Refactor beam

* Update nn

* Refactor beam and weight by cost

* Update ner beam settings

* Update test

* Add __init__.pxd

* Upd test

* Fix test

* Upd test

* Fix test

* Remove ring buffer history from StateC

* WIP change arc-eager transitions

* Add state tests

* Support ternary sent start values

* Fix arc eager

* Fix NER

* Pass oracle cut size for beam

* Fix ner test

* Fix beam

* Improve StateC.clone

* Improve StateClass.borrow

* Work directly with StateC, not StateClass

* Remove print statements

* Fix state copy

* Improve state class

* Refactor parser oracles

* Fix arc eager oracle

* Fix arc eager oracle

* Use a vector to implement the stack

* Refactor state data structure

* Fix alignment of sent start

* Add get_aligned_sent_starts method

* Add test for ae oracle when bad sentence starts

* Fix sentence segment handling

* Avoid Reduce that inserts illegal sentence

* Update preset SBD test

* Fix test

* Remove prints

* Fix sent starts in Example

* Improve python API of StateClass

* Tweak comments and debug output of arc eager

* Upd test

* Fix state test

* Fix state test
2020-12-13 09:08:32 +08:00
Ines Montani
bcd52e5486 Tidy up errors and warnings 2020-10-04 11:16:31 +02:00
Adriane Boyd
7e4cd7575c
Refactor Docs.is_ flags (#6044)
* Refactor Docs.is_ flags

* Add derived `Doc.has_annotation` method

  * `Doc.has_annotation(attr)` returns `True` for partial annotation

  * `Doc.has_annotation(attr, require_complete=True)` returns `True` for
    complete annotation

* Add deprecation warnings to `is_tagged`, `is_parsed`, `is_sentenced`
and `is_nered`

* Add `Doc._get_array_attrs()`, which returns a full list of `Doc` attrs
for use with `Doc.to_array`, `Doc.to_bytes` and `Doc.from_docs`. The
list is the `DocBin` attributes list plus `SPACY` and `LENGTH`.

Notes on `Doc.has_annotation`:

* `HEAD` is converted to `DEP` because heads don't have an unset state

* Accept `IS_SENT_START` as a synonym of `SENT_START`

Additional changes:

* Add `NORM`, `ENT_ID` and `SENT_START` to default attributes for
`DocBin`

* In `Doc.from_array()` the presence of `DEP` causes `HEAD` to override
`SENT_START`

* In `Doc.from_array()` using `attrs` other than
`Doc._get_array_attrs()` (i.e., a user's custom list rather than our
default internal list) with both `HEAD` and `SENT_START` shows a warning
that `HEAD` will override `SENT_START`

* `set_children_from_heads` does not require dependency labels to set
sentence boundaries and sets `sent_start` for all non-sentence starts to
`-1`

* Fix call to set_children_form_heads

Co-authored-by: Matthew Honnibal <honnibal+gh@gmail.com>
2020-09-17 00:14:01 +02:00
Adriane Boyd
a119667a36
Clean up spacy.tokens (#6046)
* Clean up spacy.tokens

* Update `set_children_from_heads`:
  * Don't check `dep` when setting lr_* or sentence starts
  * Set all non-sentence starts to `False`

* Use `set_children_from_heads` in `Token.head` setter
  * Reduce similar/duplicate code (admittedly adds a bit of overhead)
  * Update sentence starts consistently

* Remove unused `Doc.set_parse`

* Minor changes:
  * Declare cython variables (to avoid cython warnings)
  * Clean up imports

* Modify set_children_from_heads to set token range

Modify `set_children_from_heads` so that it adjust tokens within a
specified range rather then the whole document.

Modify the `Token.head` setter to adjust only the tokens affected by the
new head assignment.
2020-09-16 20:32:38 +02:00
Sofie Van Landeghem
8e7557656f
Renaming gold & annotation_setter (#6042)
* version bump to 3.0.0a16

* rename "gold" folder to "training"

* rename 'annotation_setter' to 'set_extra_annotations'

* formatting
2020-09-09 10:31:03 +02:00
Matthew Honnibal
737a1408d9 Improve implementation of fix #6010
Follow-ups to the parser efficiency fix.

* Avoid introducing new counter for number of pushes
* Base cut on number of transitions, keeping it more even
* Reintroduce the randomization we had in v2.
2020-09-02 14:42:32 +02:00
Matthew Honnibal
c1bf3a5602
Fix significant performance bug in parser training (#6010)
The parser training makes use of a trick for long documents, where we
use the oracle to cut up the document into sections, so that we can have
batch items in the middle of a document. For instance, if we have one
document of 600 words, we might make 6 states, starting at words 0, 100,
200, 300, 400 and 500.

The problem is for v3, I screwed this up and didn't stop parsing! So
instead of a batch of [100, 100, 100, 100, 100, 100], we'd have a batch
of [600, 500, 400, 300, 200, 100]. Oops.

The implementation here could probably be improved, it's annoying to
have this extra variable in the state. But this'll do.

This makes the v3 parser training 5-10 times faster, depending on document
lengths. This problem wasn't in v2.
2020-09-02 12:57:13 +02:00
Sofie Van Landeghem
ca491722ad
The Parser is now a Pipe (2) (#5844)
* moving syntax folder to _parser_internals

* moving nn_parser and transition_system

* move nn_parser and transition_system out of internals folder

* moving nn_parser code into transition_system file

* rename transition_system to transition_parser

* moving parser_model and _state to ml

* move _state back to internals

* The Parser now inherits from Pipe!

* small code fixes

* removing unnecessary imports

* remove link_vectors_to_models

* transition_system to internals folder

* little bit more cleanup

* newlines
2020-07-30 23:30:54 +02:00