.. 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