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]#

[1.7.0] - 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#

[1.0.0] - 2023-02-02#

Changed#

[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/v1.7.0…HEAD [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