Fit omics batch, covariate, and smoking corrections on train only - #133
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Pin the Hub to uncorrected matrices plus sidecars, and keep Parkinson hybridization batches unmixed in k-fold. Co-authored-by: Cursor <cursoragent@cursor.com>
johmathe
approved these changes
Sep 12, 2026
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Summary
056dfdc4…(uncorrected matrices + sidecars). MoTrPAC covariates, AddNeuroMed ComBat, and smoking promoter-probe pick + median-center now fit on train and transform val/test.grouping=batchso hybridization-date batches stay unmixed. Smokingfull_num_nodesis the TSS probe matrix; gene pick happens after the split.louisa/omics-kfoldbecause corrections run after the new split.Test plan
pytest tests/data/test_corrections.py tests/data/test_parkinsons_geo_meta.py tests/data/test_dataset_config_consistency.pypython -m ogbench dataset=motrpac model=gcnpython -m ogbench dataset=addneuromed model=gcnpython -m ogbench dataset=smoking model=gcnpython -m ogbench dataset=parkinsons model=gcn dataset.split_params.split_type=k-fold dataset.split_params.data_seed=0