A Quiet Failure in Calibrated Virtual Screening: Marginal Conformal Prediction Under-Covers the Minority Class, and a Class-Conditional Fix Recovers It
Conformal prediction is being adopted in drug discovery to put an honest number on model reliability: pick an error rate alpha, and the method returns prediction sets containing the true label with probability at least 1 - alpha. We show this guarantee can be dangerous on imbalanced datasets. Across four datasets, standard (marginal) conformal prediction hits its global 90% coverage target while leaving the minority class badly exposed: realized minority coverage falls to 64.8% on blood-brain-barrier penetration and to 4.2% on clinical-trial toxicity, where the rare class is nearly abandoned. The failure is not tied to one model: a random forest, a graph network, and a frozen chemical lan...
| Authors | Muhammadjon Tursunbadalov, Mustafojon Tursunbadalov |
|---|---|
| Primary category | cs.LG |
| Published | 7 July 2026 |
| Last updated at source | 7 July 2026 |
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