Conformal Prediction for Molecular Properties under Label Shift

Hyeonsu Lee, Juyeon Kim, Erkhembayar Jadamba, Seungjin Choi, Hyunjin Shin

Keywords: Drug development, Machine learning, Conformal prediction, Label shift

TL;DR: By weighting conformal scores using marginal label probability ratios, our method produces statistically rigorous prediction intervals without retraining.

Abstract: Drug discovery and development underpins healthcare but remains costly and failure-prone. A critical bottleneck lies in predicting molecular properties such as solubility, potency, and toxicity, which directly determine whether a candidate can advance from preclinical to clinical trials. Artificial Intelligence (AI) has accelerated this process, yet its reliability is often undermined by distribution shift, as experimental conditions frequently diverge from training data. In addition, conventional point predictions provide only single-value estimates, offering limited guidance for high-stakes experimental design. We address these challenges with a conformal prediction framework tailored to label shift. By weighting conformal scores using marginal label probability ratios, our method produces statistically rigorous prediction intervals without retraining. This enables robust uncertainty quantification even when property distributions drift, directly tackling one of the most pervasive obstacles to applying AI in real-world drug development. By moving beyond accuracy alone to provide actionable confidence measures, our approach enhances the trustworthiness of AI-driven predictions. This further aligns predictive modeling with regulatory demands for transparency and uncertainty reporting and ultimately supports more reliable decision-making in billion-dollar development pipelines.

Submission Number: 99