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lionheart 1.1.0

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@LudvigOlsen LudvigOlsen released this 07 Dec 13:47
· 10 commits to main since this release

This release adds multiple CLI commands that:

  1. allow reproducing results from the article and seeing the effect of adding your own datasets:
  • Adds lionheart cross_validate command. Perform nested leave-one-dataset-out cross-validation on your dataset(s) and/or the included features.
  • Adds lionheart validate command. Validate a model on the included external dataset or a custom dataset.
  • Adds lionheart evaluate_univariates command. Evaluate each feature (cell-type) separately on your dataset(s) and/or the included features.
  1. expands what you can do with your own data:
  • Adds lionheart customize_thresholds command. Calculate the ROC curve and probability densities (for deciding probability thresholds) on your data and/or the included features for a custom model or an included model. Allows using probability thresholds suited to your own data when using lionheart predict_sample and lionheart validate.
  • Adds --custom_threshold_dirs argument in lionheart predict_sample. Allows passing the ROC curves and probability densities extracted with lionheart customize_thresholds.

Also:

  • Adds matplotlib as dependency.
  • Bumps generalize dependency requirement to 0.2.1.
  • Bumps utipy dependency requirement to 1.0.3.