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CHANGELOG.md

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Change Log

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

[current] -

  • We are working to include the calculation of bootstrap confidence intervals.

[1.2.1] - 2024-03-26

  • Minor bugfix affecting multi-thread calculation.

[1.2.0] - 2024-02-01

  • We included micro-average metrics. Now precision, recall and F-score in addition to previously reported metrics are calculated as micro-averages by averaging the confusion matrices over targets before calculating aggregated metrics (precision, recall, ect.).
  • We include the calculation of the average precision score (APS) in the plot notebook.

Changed

  • plot.ipynb, added calculation of average precision score (APS) in the plot notebook.
  • evaluation.py, micro-average calculation, some refactoring of the core functions.
  • parser.py, minor fixes and improvements.

[1.1.0] - 2024-01-24

  • We changed the way alternative identifiers in ontology files are considered. Now alternative identifiers are recognized in both the ground truth and prediction files and mapped to the "canonical" term.

Added

  • CHANGELOG.md, this file!

Changed

  • graph.py, changed the Graph class.
  • parser.py, changed the ground truth and prediction parsers in order to replace alternative identifiers with canonical terms.
  • plot.ipynb, cleaned up.

[1.0.0] - 2023-08-04

First release after CAFA5 challenge closed. The version used in Kaggle is provided under the 'Kaggle' branch. The 'main' branch includes instead a packed version of the code. While usage and performance has been improved the calculation is exactly the same.