Uncertainty Quantification in Molecular Machine Learning for Property Predictions under Data Shifts

Drug discovery and medicinal chemistry efforts are increasingly influenced by machine learning (ML), with compound property prediction as a central application. ML models have demonstrated strong performance in predicting various compound properties from chemical structure. However, these models can exhibit varying levels of prediction error, making uncertainty quantification (UQ) essential for informed decisions. Standard UQ metrics include the distance to the molecules in the training set and prediction variance, obtained through methods such as model ensembles or Bayesian modeling. Although several UQ methodologies have been developed in recent years, no single approach consistently outperformed others. Herein, we present a comprehensive benchmark of UQ strategies for ML-based prediction of absorption, distribution, metabolism, and excretion (ADME) properties, using both in-house and public data sets. We employed the recently introduced UNIQUE (UNcertaInty QUantification bEnchmarking) framework and evaluated UQ method performance under data shifts. Our findings indicate data-based UQ metrics (e.g., chemical distance), and model-based UQ metrics (e.g., predicted value and variance) may capture complementary aspects of uncertainty. Their combination through error models, designed to predict the original ML model's error, yielded higher-quality uncertainty estimates. These error models emerged as a promising strategy for enhancing UQ, showing robustness in under various degrees and types of data shift. Taken together, our work highlights the potential of combining diverse UQ metrics and error modeling to improve reliability in molecular property prediction. By establishing standardized evaluation setups and assessing UQ under data shifts, we provide a foundation for future UQ method development and benchmarking in the field.