Willie Neiswanger
Famous AuthorPublications
Trustworthy Protein-Ligand Binding Affinity Prediction via Reliability-Aware Multi-Engine Fusion
Accurate protein-ligand binding affinity prediction is central to computational drug discovery, yet modern docking engines frequently disagree without indicating which prediction to trust. Consensus scoring and ensemble methods improve mean accuracy but treat all predictions identically without interpretable confidence measures or uncertainty decomposition, ignoring the chemical context of each protein-ligand pair. To address this limitation, we introduce RELIABLE-BA (RELIABiLity-aware Evidential fusion for Binding Affinity), an evidential framework for multi-engine binding affinity prediction. Our model comprises three steps: (1) modeling each engine as an evidential expert via Normal-Inverse-Gamma distributions, (2) scaling epistemic uncertainty through learned reliability from molecular context while preserving each expert's predictive mean, and (3) fusing experts through closed-form aggregation that captures both individual uncertainty and inter-engine disagreement. Experiments on the PDBBind and BDB2020+ benchmarks demonstrate competitive point prediction with substantially improved uncertainty calibration, and additional validation on the SARS-CoV-2 Mpro dataset and 5HT2A receptor demonstrates applicability to clinically relevant drug targets. Crucially, these uncertainty estimates enable reliable filtering of protein-ligand pairs, reducing prediction error by up to 25% when retaining only high-confidence pairs. To our knowledge, RELIABLE-BA is the first multi-engine binding affinity prediction framework to combine evidential fusion with context-dependent reliability, offering a principled path toward trustworthy AI-guided drug discovery. Our code is publicly available at https://github.com/yongchand/RELIABLE-BA.
Neural Nonmyopic Bayesian Optimization in Dynamic Cost Settings
Bayesian optimization (BO) is a common framework for optimizing black-box functions, yet most existing methods assume static query costs and rely on myopic acquisition strategies. We introduce LookaHES, a nonmyopic BO framework designed for dynamic, history-dependent cost environments, where evaluation costs vary with prior actions, such as travel distance in spatial tasks or edit distance in sequence design. LookaHES combines a multi-step variant of $H$-Entropy Search with pathwise sampling and neural policy optimization, enabling long-horizon planning beyond twenty steps without the exponential complexity of existing nonmyopic methods. The key innovation is the integration of neural policies, including large language models, to effectively navigate structured, combinatorial action spaces such as protein sequences. These policies amortize lookahead planning and can be integrated with domain-specific constraints during rollout. Empirically, LookaHES outperforms strong myopic and nonmyopic baselines across nine synthetic benchmarks from two to eight dimensions and two real-world tasks: geospatial optimization using NASA night-light imagery and protein sequence design with constrained token-level edits. In short, LookaHES provides a general, scalable, and cost-aware solution for robust long-horizon optimization in complex decision spaces, which makes it a useful tool for researchers in machine learning, statistics, and applied domains. Our implementation is available at https://github.com/sangttruong/nonmyopia.