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[Submitted on 13 Oct 2026] Title:PMO-Dock: Benchmarking Docking, Specificity, and Generalization in Molecular Optimization View a PDF of the paper titled PMO-Dock: Benchmarking Docking, Specificity, and Generalization in Molecular Optimization, by Gor Simonyan and 4 other authors View PDF HTML (experimental) 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) Full-text links: Access Paper: View a PDF of the paper titled PMO-Dock: Benchmarking Docking, Specificity, and Generalization in Molecular Optimization, by Gor Simonyan and 4 other authors View PDF HTML (experimental) TeX Source view license Additional Features Audio Summary Current browse context: cs.LG new | recent | 2026-10 Change to browse by: cs q-bio q-bio.QM References & Citations NASA ADS Google Scholar Semantic Scholar Loading... Data provided by: Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) IArxiv recommender toggle IArxiv Recommender (What is IArxiv?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)