--- a +++ b/docs-source/source/biscuit.rst @@ -0,0 +1,66 @@ +.. currentmodule:: slideflow.biscuit + +slideflow.biscuit +================= + +This module contains an official implementation of `BISCUIT <https://www.nature.com/articles/s41467-022-34025-x>`__, an uncertainty quantification and confidence thresholding algorithm for whole-slide images. The original implementation, which includes instructions for reproducing experimental results reported in the manuscript, is available on `GitHub <https://github.com/jamesdolezal/biscuit>`__. + +This module is requires the ``slideflow-noncommercial`` package, which can be installed with: + +.. code-block:: bash + + pip install slideflow-noncommercial + +See :ref:`uncertainty` for more information. + +.. autofunction:: find_cv +.. autofunction:: get_model_results + +biscuit.Experiment +****************** +.. autoclass:: Experiment +.. autofunction:: slideflow.biscuit.Experiment.display +.. autofunction:: slideflow.biscuit.Experiment.plot_uq_calibration +.. autofunction:: slideflow.biscuit.Experiment.results +.. autofunction:: slideflow.biscuit.Experiment.thresholds_from_nested_cv +.. autofunction:: slideflow.biscuit.Experiment.train +.. autofunction:: slideflow.biscuit.Experiment.train_nested_cv + +biscuit.hp +********** + +.. autofunction:: slideflow.biscuit.hp.nature2022 + +biscuit.threshold +***************** +.. autofunction:: slideflow.biscuit.threshold.apply +.. autofunction:: slideflow.biscuit.threshold.detect +.. autofunction:: slideflow.biscuit.threshold.from_cv +.. autofunction:: slideflow.biscuit.threshold.plot_uncertainty +.. autofunction:: slideflow.biscuit.threshold.process_group_predictions +.. autofunction:: slideflow.biscuit.threshold.process_tile_predictions + +biscuit.utils +************* + +.. autofunction:: slideflow.biscuit.utils.auc +.. autofunction:: slideflow.biscuit.utils.auc_and_threshold +.. autofunction:: slideflow.biscuit.utils.df_from_cv +.. autofunction:: slideflow.biscuit.utils.eval_exists +.. autofunction:: slideflow.biscuit.utils.find_cv +.. autofunction:: slideflow.biscuit.utils.find_cv_early_stop +.. autofunction:: slideflow.biscuit.utils.find_eval +.. autofunction:: slideflow.biscuit.utils.find_model +.. autofunction:: slideflow.biscuit.utils.get_model_results +.. autofunction:: slideflow.biscuit.utils.get_eval_results +.. autofunction:: slideflow.biscuit.utils.model_exists +.. autofunction:: slideflow.biscuit.utils.prediction_metrics +.. autofunction:: slideflow.biscuit.utils.read_group_predictions +.. autofunction:: slideflow.biscuit.utils.truncate_colormap + +biscuit.delong +************** + +.. autofunction:: slideflow.biscuit.delong.fastDeLong +.. autofunction:: slideflow.biscuit.delong.delong_roc_variance +.. autofunction:: slideflow.biscuit.delong.delong_roc_test