Leave-tissue-out cross-validation#192
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PascalIversen merged 50 commits intodevelopmentfrom Apr 25, 2025
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Pull Request Overview
This PR adds support for a "tissue" column and introduces leave-tissue-out (LTO) cross-validation.
- Updated documentation and function signatures to include "LTO" as a valid test mode.
- Added a TISSUE_IDENTIFIER constant in utils and passed tissue-related information through dataset loading and cross-validation methods.
- Extended DrugResponseDataset to store tissue data and enforce its usage in LTO CV.
Reviewed Changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| drevalpy/experiment.py | Updated docstring for test_mode to include LTO. |
| drevalpy/datasets/utils.py | Added constant TISSUE_IDENTIFIER to handle tissue column. |
| drevalpy/datasets/loader.py | Updated function signatures and data loading to support tissue info. |
| drevalpy/datasets/dataset.py | Extended DrugResponseDataset to store tissues and updated CV logic. |
bug found by bot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Other tissues should always be in test set? Edit: all tissued mapped now :) |
JudithBernett
approved these changes
Apr 23, 2025
| response=response_data[measure].values, | ||
| cell_line_ids=response_data[CELL_LINE_IDENTIFIER].values, | ||
| drug_ids=response_data[DRUG_IDENTIFIER].values, | ||
| tissues=response_data[TISSUE_IDENTIFIER].values, |
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gibt das hier nicht ein problem wenn response_data[tissue] nicht existiert?
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ja das existiert jetzt aber bei unseren default datasets immer :)
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Wishing you much success! |
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Datasets are required to have "tissue" column. Will break everything before we update zenodo, since our datasets don't have these columns yet 🗡️
Optional for custom datasets.
Will also break viz maybe.