[Submitted on 13 Oct 2026]
Title:PMO-Dock: Benchmarking Docking, Specificity, and Generalization in Molecular Optimization
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Abstract:The Practical Molecular Optimization (PMO) benchmark standardized evaluation in molecular optimization, but it is built on simple property-based oracles that do not capture structure-based drug design. As the field has moved to docking-based objectives, evaluation practice has become unstandardized, and different methods report results on different docking tasks, often without a shared protocol for fair comparison or sample-efficiency constraints. To address this, we introduce Practical Molecular Optimization for Docking (PMO-Dock), a benchmark and protocol for docking-based optimization consisting of 25 tasks covering hit generation, lead optimization, and a new specificity task requiring strong on-target binding while penalizing off-target interactions. The protocol separates model development from final evaluation: validation tasks are used for hyperparameter tuning, and test tasks are held out for final evaluation and are not used during development. Evaluation on the test tasks is done under a strict oracle budget to reflect realistic drug-discovery settings. We benchmark four diverse high-performing methods spanning different optimization paradigms, Saturn (reinforcement learning), GenMol (discrete diffusion), Genetic-guided GFlowNet, and ChemLlama (LLM-based evolutionary search). Our results show no universally best method across tasks, additional analyses of hyperparameter transfer (cross-task and cross-category) and sensitivity show that transfer is often limited and varies by method, motivating method-dependent selection strategies. This benchmark provides a concrete standard for evaluating generalization to unseen tasks and sample efficiency under a limited test-time oracle budget.
Subjects:
Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
Cite as: arXiv:2610.19011 [cs.LG]
(or arXiv:2610.19011v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2610.19011
arXiv-issued DOI via DataCite (pending registration)
Submission history
From: Hrant Khachatrian [view email] [v1] Tue, 13 Oct 2026 18:07:37 UTC (1,976 KB)
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