Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog
and this project adheres to Semantic Versioning.

[Unreleased]

[1.8.0] - 2025-01-11

Removed

• Support for Python 3.10.

Added

• Clinical [PubMedBert SBERT embeddings] configuration.
• [PyRuSH] Clincal clinical sententence chunker

Changed

• Upgraded to [zensols.util] version 1.15.

[1.7.0] - 2024-04-14

Removed

• Deprecated feature document parser mednlp_combine_medfirst_doc_parser from
  resource library.

Changed

• Renamed MeddicalFeatureDocumentParser to MedCatFeatureDocumentParser
  since the parser only adds MedCAT CUIs.
• Fixed the configured parser that adds both ScispaCy biomed entities and
  MedCAT CUIs in mednlp_combine_biomed_doc_parser.
• Separated combiner with non-combiner models in configuration space. The
  non-combiners (biomed ScispaCy and MedCAT) are parses that are used in their
  respective combiners. These are then used by a new composite parser that
  uses both (mednlp_combine_biomed_doc_parser). Unit test case added for
  all configured parsers.

[1.6.0] - 2024-02-27

Added

• Added a ScispaCy biomedical document parser, which is enabled by setting
  mednlp_default:doc_parser = mednlp_combine_biomed_doc_parser. This uses
  better linguistic features and detects more entity span(s).

Changed

• Fixed normalize token and sentence/token indexes from being clobbered by
  combined medical parsers.
• Fixed numeric entity feature from the combined medical parser is non-zero
  for medical entities.
• Combined medical parser defines linguistic and medical features in the
  document parser object instance.

[1.5.0] - 2023-12-05

Changed

• Upgrade libraries: numpy, lxml, scikitlearn, scipy, medcat.
• Added scispacy dependency.

Added

• Support for Python 3.11.

Removed

• Support for Python 3.9.

[1.4.1] - 2023-09-08

Changed

• Fix unit tests using the model provided for the MedCAT tutorials.
• Re-enable GitHub workflow unit tests CI.

[1.4.0] - 2023-08-16

Downstream moderate risk update release.

Changed

• Switch order of medical specific and general spaCy language parsing and
  chunking. Now the medical parser is the source parser and the default spaCy
  parser is the target in MappingCombinerFeatureDocumentParser. This was
  done to get better sentence chunking as MedCAT (used in the medical parser)
  does not sentence chunk well as it was not designed for it.
• Upgrade to [zensols.util] 1.13.0
• Fix cui2vec weight archive re-download on each access.
• Mapping combiner default is to use token's character absolute index.

[1.3.2] - 2023-06-29

Added

• Feature document parser shortcut from application factory.

Changed

• Resource library configuration to clean up model resources after download.

[1.3.1] - 2023-06-27

Changed

• Updated to [zensols.nlp] to 1.7.2 and use its new feature to auto load any
  missing spaCy base model(s).
• Remove configuration file requirement from the CLI.
• Fix spaCy dependency requirement to align with scipy and [zensols.nlp].

[1.3.0] - 2023-06-20

Changed

• Fix contraction tokenization. This was done by swapping the target and
  source parser in the lang.conf:mednlp_combine_doc_parser resource library
  configuration.

[1.2.0] - 2023-06-09

Changed

• Upgrade to [medcat] 1.7.0.
• Better UTS error handling with raised exceptions and messages.

[1.1.0] - 2023-04-05

Changed

• Install missing models and packages on start up.
• Updated [zensols.install] to 0.2.1
• Updated [zensols.nlp] to 1.6.0.

[1.0.0] - 2023-02-02

Changed

• Updated [zensols.util] to 1.12.1.
• Updated [zensols.nlp] to 1.5.0.

[0.1.1] - 2022-10-02

Removed

• Make scispacy optional and remove the dependency. See the test cases in
  test.

[0.1.0] - 2022-10-01

Added

• Unit test in GitHub CI.

Changed

• Upgrade to spaCy 2.2, MedCAT 3.0, zensols.nlp 1.4.0.
• Make cui2vec a standard word embedding with vectorizer and layer.
• Replace entity splitter by not embedding named entities as default
  configuration.

Removed

• Support for Python 3.7, 3.8 from dropped support in zensols.util.

[0.0.2] - 2022-05-04

Added

• A CSV features dump example.

Changed

• Use token instead of sentence level mapping in cases where MedCAT creates
  unaligned sentence boundaries.
• Make medical parser stand-alone and use delegate mapping combiner instead of
  using a class hierarchy.
• Entity linker is now a token decorator.
• Protect against unk (unknown) keys in TUIs.

[0.0.1] - 2022-01-30

Added

• Initial version.

[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.8.0...HEAD
[1.8.0]: https://github.com/Paul Landes/mednlp/compare/v1.7.0...v1.8.0
[1.7.0]: https://github.com/Paul Landes/mednlp/compare/v1.6.0...v1.7.0
[1.6.0]: https://github.com/Paul Landes/mednlp/compare/v1.5.0...v1.6.0
[1.5.0]: https://github.com/Paul Landes/mednlp/compare/v1.4.1...v1.5.0
[1.4.1]: https://github.com/Paul Landes/mednlp/compare/v1.4.0...v1.4.1
[1.4.0]: https://github.com/Paul Landes/mednlp/compare/v1.3.2...v1.4.0
[1.3.2]: https://github.com/Paul Landes/mednlp/compare/v1.3.1...v1.3.2
[1.3.1]: https://github.com/Paul Landes/mednlp/compare/v1.3.0...v1.3.1
[1.3.0]: https://github.com/Paul Landes/mednlp/compare/v1.2.0...v1.3.0
[1.2.0]: https://github.com/Paul Landes/mednlp/compare/v1.1.0...v1.2.0
[1.1.0]: https://github.com/Paul Landes/mednlp/compare/v1.0.0...v1.1.0
[1.0.0]: https://github.com/Paul Landes/mednlp/compare/v0.1.1...v1.0.0
[0.1.1]: https://github.com/Paul Landes/mednlp/compare/v0.1.0...v0.1.1
[0.1.0]: https://github.com/Paul Landes/mednlp/compare/v0.0.2...v0.1.0
[0.0.2]: https://github.com/Paul Landes/mednlp/compare/v0.0.1...v0.0.2
[0.0.1]: https://github.com/Paul Landes/mednlp/compare/v0.0.0...v0.0.1