Temporal Evaluation of Uncertainty Quantification Under Distribution Shift

Paper i proceeding, 2025

Uncertainty quantification is emerging as a critical tool in high-stakes decision-making processes, where trust in automated predictions that lack accuracy and precision can be time-consuming and costly. In drug discovery, such high-stakes decisions are based on modeling the properties of potential drug compounds on biological assays. So far, existing uncertainty quantification methods have primarily been evaluated using public datasets that lack the temporal context necessary to understand their performance over time. In this work, we address the pressing need for a comprehensive, large-scale temporal evaluation of uncertainty quantification methodologies in the context of assay-based molecular property prediction. Our novel framework benchmarks three ensemble-based approaches to uncertainty quantification and explores the effect of adding lower-quality data during training in the form of censored labels. We investigate the robustness of the predictive performance and the calibration and reliability of predictive uncertainty by the models as time evolves. Moreover, we explore how the predictive uncertainty behaves in response to varying degrees of distribution shift. By doing so, our analysis not only advances the field but also provides practical implications for real-world pharmaceutical applications.