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Warn when fine-tuning chromosomes overlap with pretraining data - #184
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avantikalal merged 3 commits intoSep 20, 2026
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Add a warnings.warn() in tune_on_dataset() that checks whether the fine-tuning dataset's chromosomes overlap with the pretrained model's training chromosomes, which may indicate data leakage. The check uses chromosome metadata already stored in the checkpoint via data_params['train']['intervals']. It is skipped when either the pretrained model or the new dataset lacks interval information. Closes Genentech#59
main renamed interval_dataset's chromosomes from chr1 to seq1/seq2 (switch to bundled test genome), which silently broke this test's hardcoded chr1 overlap fixture during the merge with main. Update the fixture and assertion to use seq1 to match interval_dataset's actual chromosomes. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
avantikalal
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Sep 20, 2026
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Closes #59.
When calling
tune_on_dataset(), this checks whether the fine-tuning dataset's chromosomes overlap with the pretrained model's training chromosomes and emits awarnings.warn()if so, since this may indicate data leakage.The check uses chromosome metadata already stored in the checkpoint via
data_params['train']['intervals']. It is skipped when either the pretrained model or the new dataset lacks interval information (e.g. string-based sequences).Tests added:
test_lightning_model_finetune_chrom_overlap_warning: simulates a pretrained model trained on chr1, fine-tunes with a chr1 dataset, asserts warning firestest_lightning_model_finetune_no_chrom_warning: fine-tunes with string-based dataset, asserts no warning