A Quiet Failure in Calibrated Virtual Screening: Marginal Conformal Prediction Under-Covers the Minority Class, and a Class-Conditional Fix Recovers It

arXiv:2607.06605v1 Announce Type: new Abstract: 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 mi...