[CPBench] Tasks and Models - Regression#948
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lehendo wants to merge 9 commits intosunlabuiuc:masterfrom
Open
[CPBench] Tasks and Models - Regression#948lehendo wants to merge 9 commits intosunlabuiuc:masterfrom
lehendo wants to merge 9 commits intosunlabuiuc:masterfrom
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Extends PyHealth with a full suite of regression and survival analysis tasks. Listed below is a summary of what I have implemented.
LOS regression: LengthOfStayRegression{MIMIC3,MIMIC4,eICU,OMOP} — continuous float LOS (days) as an alternative to the existing 10-bucket multiclass variants
CKD survival: MIMIC4CKDSurvAnalysis — time-to-ESRD on MIMIC-IV with time_invariant, time_variant, and heterogeneous settings; uses CKD-EPI 2021 eGFR, proper censoring logic, and a pre-filter for efficiency (ported from add/task.mimic_ckd)
METABRIC: METABRICDataset + METABRICSurvivalOS / METABRICSurvivalRFS — overall and relapse-free survival for breast cancer patients (cBioPortal format)
SEER: SEERDataset + SEERSurvivalTask — overall survival from NCI SEER cancer registry exports
Survival metrics (pyhealth/metrics/survival.py): Harrell's C-index and IPCW Brier score in pure NumPy, exposed via survival_metrics_fn