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CHANGELOG.md

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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

1.9.0 - 2025-01-24

Removed

  • Support for Python 3.10.

Added

  • Conda environment file (src/python/environment.yml) to reduce start up latency and improve reproducibility.

Changed

  • Upgrade to zensols.mimic version 1.8.0 and [zensols.deeplearn] version 1.13.3. The latter includes dependencies for PyTorch 2.1.2 and HuggingFace transformers 4.48.1.
  • Retrained models (0.1.1) using new dependencies and uploaded to Zenodo, which are downloaded automatically on first use.

1.8.0 - 2024-04-14

Changed

  • Release newly trained models with better performance and smaller file size (faster downloads).
  • Separated model training and inference configuration and process.
  • Removed model report for smaller model distribution files.
  • Retrained models with ScispaCy biological NER model en_ner_bionlp13cg_md.
  • Changed default to including non-empty sections that have no section type.

1.7.0 - 2024-03-07

Changed

  • Upgrade to zensols.deepnlp 1.13.0 and switch to its new model packing API.

1.6.0 - 2024-02-27

Added

  • Functionality to optionally add unclassified and/or non-empty sections in the prediction results (from SectionPredictor).

Changed

1.5.1 - 2024-01-17

Changed

1.5.0 - 2023-12-05

Changed

Added

  • Support for Python 3.11.

Removed

  • Support for Python 3.9.

1.4.3 - 2023-08-25

Changed

  • Model injection and assertion bug fixes.

1.4.2 - 2023-08-16

Changed

  • Inject model configuration to allow the SQLite connection manager with the model without any PostgreSQL drivers installed.

1.4.1 - 2023-08-16

Changed

  • Updated configuration to download model version 0.0.3.

1.4.0 - 2023-08-16

Added

  • Model training and packaging automation script for all models.

Changed

  • Model is downloaded and installed correctly using preemptive stash priming from the zensols.mimic library.
  • Upgraded zensols.mimic 1.4.0 and zensols.deepnlp 1.8.0
  • Handle carriage returns (\r) as a feature in the model.
  • Fix headers and sections matching up by removing newline tokens on prediction.
  • Retrain and default to highest performing models for model version 0.0.3.
  • Remove pt. to patient token replacements.

1.3.1 - 2023-06-28

Changed

  • Dependencies to force correct versions of torch, numpy and scipy.

1.3.0 - 2023-06-20

Changed

1.2.0 - 2023-06-09

Added

  • CLI summary output format.

Changed

  • Model training and automation process.
  • Remove PredictedSection and switch to its super class.
  • Upgraded to zensols.deepnlp 1.9.0.
  • Upgraded to zensols.mimic 1.2.0.

1.1.0 - 2023-04-05

Added

  • Automatically predict sections for note missing section annotations.
  • Output formatting added to raw notes.
  • More model training and packaging automation.

Changed

  • Fixed slow hospital admission persistence when persisting predicted notes.
  • Fix AgeType enumeration typo.
  • Upgraded zensols.deepnlp to 1.8.0.
  • Upgraded zensols.mimic to 1.1.0.

1.0.0 - 2023-02-10

Changed

0.0.1 - 2022-06-22

Added

  • Initial version.