v0.9.1

Changelog

Changed

• Improve negation patterns
• Abstent disorders now set the negation to True when matched as ABSENT
• Default qualifier is now None instead of False (empty string)

Fixed

• span_getter is not incompatible with on_ents_only anymore
• ContextualMatcher now supports empty matches (e.g. lookahead/lookbehind) in assign patterns

Pull Requests

• Fix negations by @percevalw in #216
• Chore: bump version to 0.9.1 by @percevalw in #218

Full Changelog: v0.9.0...v0.9.1

v0.9.0

Changelog

Added

• New to_duration method to convert an absolute date into a date relative to the note_datetime (or None)

Changes

• Input and output of components are now specified by span_getter and span_setter arguments.
• 💥 Score / disorders / behaviors entities now have a fixed label (passed as an argument), instead of being dynamically set from the component name. The following scores may have a different name than the current one in your pipelines:
  • eds.emergency.gemsa → emergency_gemsa
  • eds.emergency.ccmu → emergency_ccmu
  • eds.emergency.priority → emergency_priority
  • eds.charlson → charlson
  • eds.elston_ellis → elston_ellis
  • eds.SOFA → sofa
  • eds.adicap → adicap
  • eds.measuremets → size, weight, ... instead of eds.size, eds.weight, ...
• eds.dates now separate dates from durations. Each entity has its own label:
  • spans["dates"] → entities labelled as date with a span._.date parsed object
  • spans["durations"] → entities labelled as duration with a span._.duration parsed object
• the "relative" / "absolute" / "duration" mode of the time entity is now stored in
  the mode attribute of the span._.date/duration
• the "from" / "until" period bound, if any, is now stored in the span._.date.bound attribute
• to_datetime now only return absolute dates, converts relative dates into absolute if doc._.note_datetime is given, and None otherwise

Fixed

• export_to_brat issue with spans of entities on multiple lines.

Pull Requests

• Fix export_to_brat when there are spaces before new lines by @TheooJ in #211
• Refacto of the extensions by @percevalw in #213
• chore: bump version to 0.9.0 by @percevalw in #215

New Contributors

• @TheooJ made their first contribution in #211

Full Changelog: v0.8.1...v0.9.0

v0.8.1

Post-release to synchronize Zenodo

v0.8.1

What's changed

Fix release to allow installation from source.

Pull Requests

• Ship cython files in sdist by @percevalw in #210

Full Changelog: v0.8.0...v0.8.1

v0.8.0

Changelog

Added

• New trainable component for multi-label, multi-class span qualification (any attribute/extension)
• Add range measurements (like la tumeur fait entre 1 et 2 cm) to eds.measurements matcher
• Add eds.CKD component
• Add eds.COPD component
• Add eds.alcohol component
• Add eds.cerebrovascular_accident component
• Add eds.congestive_heart_failure component
• Add eds.connective_tissue_disease component
• Add eds.dementia component
• Add eds.diabetes component
• Add eds.hemiplegia component
• Add eds.leukemia component
• Add eds.liver_disease component
• Add eds.lymphoma component
• Add eds.myocardial_infarction component
• Add eds.peptic_ulcer_disease component
• Add eds.peripheral_vascular_disease component
• Add eds.solid_tumor component
• Add eds.tobacco component
• Add eds.spaces (or eds.normalizer with spaces=True) to detect space tokens, and add ignore_space_tokens to EDSPhraseMatcher and SimstringMatcher to skip them
• Add ignore_space_tokens option in most components
• eds.tables: new pipeline to identify formatted tables
• New merge_mode parameter in eds.measurements to normalize existing entities or detect
  measures only inside existing entities
• Tokenization exceptions (Mr., Dr., Mrs.) and non end-of-sentence periods are now tokenized with the next letter in the eds tokenizer

Changed

• Disable EDSMatcher preprocessing auto progress tracking by default
• Moved dependencies to a single pyproject.toml: support for pip install -e '.[dev,docs,setup]'
• ADICAP matcher now allow dot separators (e.g. B.H.HP.A7A0)

Fixed

• Abbreviation and number tokenization issues in the eds tokenizer
• eds.adicap : reparsed the dictionnary used to decode the ADICAP codes (some of them were wrongly decoded)
• Fix build for python 3.9 on Mac M1/M2 machines.

What's changed

Pull Requests

• docs: mention INRIA in the acknowledgment by @percevalw in #170
• Umls fixes by @percevalw in #183
• fix typo by @gammaeva in #179
• add link and definiton for sofa in documentation by @strayMat in #182
• CI fail exploration by @Thomzoy in #189
• Repare parsing errors of the ADICAP dict by @etienneguevel in #187
• Move dependencies to pyproject.toml by @percevalw in #190
• Add tokenization exceptions and detect some false positive EOS by @percevalw in #192
• Bump version to 0.8.0 by @percevalw in #194
• Update docs by @percevalw in #196
• Ignore space tokens by @percevalw in #198
• pipe tables by @aricohen93 in #180
• Range measurements by @percevalw in #195
• SpanQualifier trainable component by @percevalw in #193
• 18 pipes from the Charlson Comorbidity Index by @Thomzoy in #205
• Bump version to v0.8.0 by @percevalw in #209

New Contributors

• @gammaeva made their first contribution in #179
• @strayMat made their first contribution in #182

Full Changelog: v0.7.4...v0.8.0

v0.7.4

Changelog

Added

• eds.history : Add the option to consider only the closest dates in the sentence (dates inside the boundaries and if there is not, it takes the closest date in the entire sentence).
• eds.negation : It takes into account following past participates and preceding infinitives.
• eds.hypothesis: It takes into account following past participates hypothesis verbs.
• eds.negation & eds.hypothesis : Introduce new patterns and remove unnecessary patterns.
• eds.dates : Add a pattern for preceding relative dates (ex: l'embolie qui est survenue à 10 jours).
• Improve patterns in the eds.pollution component to account for multiline footers
• Add QuickExample object to quickly try a pipeline.
• Add UMLS terminology matcher eds.umls
• New RegexMatcher method to create spans from groupdicts
• New eds.dates option to disable time detection

Changed

• Improve date detection by removing false positives

Fixed

• eds.hypothesis : Remove too generic patterns.
• EDSTokenizer : It now tokenizes "rechereche d'" as ["recherche", "d'"], instead of ["recherche", "d", "'"].
• Fix small typos in the documentation and in the docstring.
• Harmonize processing utils (distributed custom_pipe) to have the same API for Pandas and Pyspark
• Fix BratConnector file loading issues with complex file hierarchies

Pull Requests

• 👓 Feedbacks from EDS-TeVa study by @Aremaki in #157
• feat: 🩺 Update negation and hypothesis pipelines by @Aremaki in #162
• Harmonize processing utils by @aricohen93 in #160
• Update pattern footer (pollution) by @aricohen93 in #159
• feat: add UMLS terminology (#147) by @percevalw in #165
• Relax pydantic version constraints by @percevalw in #167
• Allow back spacy dot components for backward compatibility by @percevalw in #152
• Update docs by @percevalw in #168
• Bump version to 0.7.3 by @percevalw in #169
• Quick example by @Thomzoy in #166
• Update index.md by @Thomzoy in #171
• Fix brat file path search for complex file hierarchies by @percevalw in #172
• Improve dates by @percevalw in #149
• Bump version to 0.7.4 by @percevalw in #173

Full Changelog: v0.7.2...v0.7.4

v0.7.2

Changelog

Added

• Improve the eds.history component by taking into account the date extracted from eds.dates component.
• New pop up when you click on the copy icon in the termynal widget (docs).
• Add NER eds.elston-ellis pipeline to identify Elston Ellis scores
• Add flags=re.MULTILINE to eds.pollution and change pattern of footer

Fixed

• Remove the warning in the eds.sections when eds.normalizer is in the pipe.
• Fix filter_spans for strictly nested entities
• Fill eds.remove-lowercase "assign" metadata to run the pipeline during EDSPhraseMatcher preprocessing

Pull Requests

• Update patterns pollution by @aricohen93 in #145
• feat: ✨ Improve eds.history component with eds.dates by @Aremaki in #144
• Small fixes by @percevalw in #146
• Elston and Ellis by @etienneguevel in #148
• Fix setup.py by @percevalw in #151
• Patch patterns norm by @aricohen93 in #150
• Bump version to 0.7.2 by @percevalw in #153

Full Changelog: v0.7.1...v0.7.2

v0.7.1

Changelog

Added

• Add new patterns (footer, web entities, biology tables, coding sections) to pipeline normalisation (pollution)

Changed

• Improved TNM detection algorithm
• Account for more modifiers in ADICAP codes detection

Fixed

• Add nephew, niece and daughter to family qualifier patterns
• EDSTokenizer (spacy.blank('eds')) now recognizes non-breaking whitespaces as spaces and does not split float numbers
• eds.dates pipeline now allows new lines as space separators in dates

Pull Requests

• add: new patterns to pollution by @Thomzoy in #132
• docs: fix cim10 docs by @percevalw in #130
• Remove print statement by @Thomzoy in #133
• fix: param sampling AdicapCode by @etienneguevel in #131
• Add nephew, niece and daughter to family qualifier patterns by @julienduquesne in #135
• Modification of the TNM ner by @etienneguevel in #136
• modification of the ADICAP ner by @etienneguevel in #137
• EDSTokenizer: split on non-breaking spaces and don't split float numbers by @percevalw in #141
• Allow newlines in dates by @percevalw in #142
• new pattern norm pollution by @aricohen93 in #139
• Bump version to 0.7.1 by @percevalw in #143

New Contributors

• @etienneguevel made their first contribution in #131
• @julienduquesne made their first contribution in #135

Full Changelog: v0.7.0...v0.7.1

v0.7.0

Changelog

Added

• New nested NER trainable nested_ner pipeline component
• Support for nested entities and attributes in BratDataConnector
• Pytorch wrappers and experimental training utils
• Add attribute section to entities
• Add new cases for separator pattern when components of the TNM score are separated by a forward slash
• Add NER eds.adicap pipeline to identify ADICAP codes

Changed

• Update of the ContextualMatcher (and all pipelines depending on it), rendering it more flexible to use
• Rename R component of score TNM as "resection_completeness"

Fixed

• Prevent section titles from capturing surrounding tokens, causing overlaps (#113)
• Enhance existing patterns for section detection and add patterns for previously ignored sections (introduction, evolution, modalites de sortie, vaccination) .
• Fix explain mode, which was always triggered, in eds.history factory.
• Fix test in eds.sections. Previously, no check was done
• Remove SOFA scores spurious span suffixes

Pull requests

• Change links to streamlit demo by @percevalw in #111
• Restore demo links by @percevalw in #112
• Prevent section titles from capturing surrounding tokens by @percevalw in #114
• Section upgrade by @paul-bssr in #115
• Nested NER trainable pipeline component by @percevalw in #84
• Fix history factory parameter type by @clementjumel in #117
• Rename R component (TNM) by @aricohen93 in #119
• Update separator pattern score TNM by @aricohen93 in #121
• add section info to entities by @aricohen93 in #120
• Adicap pipeline by @aricohen93 in #123
• ContextualMatcher + ADICAP Update by @Thomzoy in #124
• fix: handle single entity in contextual matcher by @Thomzoy in #126
• Adicap model by @percevalw in #127
• chore: bump version to 0.7.0 by @percevalw in #125
• v0.7.0 + fixed package_data by @percevalw in #129

New Contributors

• @paul-bssr made their first contribution in #115
• @clementjumel made their first contribution in #117

Full Changelog: v0.6.2...v0.7.0

v0.6.2

Changelog

Added

• New SimstringMatcher matcher to perform fuzzy term matching, and algorithm parameter in terminology components and eds.matcher component

Changed

• Add consultation date pattern "CS", and False Positive patterns for dates (namely phone numbers and pagination).
• Update the pipeline score eds.TNM. Now it is possible to return a dictionary where the results are either str or int values

Fixed

• Add new patterns to the negation qualifier
• Numpy header issues with binary distributed packages
• Simstring dependency on Windows

Pull Requests

• chore: add acknowledgement by @bdura in #102
• TNM by @aricohen93 in #103
• fix: eds.sentences behaviour with dates by @bdura in #99
• Add consultation date pattern and date False Positive by @JCharline in #107
• Simstring by @percevalw in #94
• Fix numpy header issues with binary packages by @percevalw in #109
• fix: add "non" preceding pattern by @bdura in #105
• Bump version to v0.6.2 by @percevalw in #110

New Contributors

• @JCharline made their first contribution in #107

Full Changelog: v0.6.1...v0.6.2