Learning to Select Source Domains: Proxy-Rewarded Policy Optimization for Molecular OOD Generalization

Molecular property prediction under severe out-of-distribution (OOD) shifts remains challenging because conventional scaffold splits can retain local structural similarity between training and test molecules, while adaptation from heterogeneous source domains may cause negative transfer. We introduce SCOPE-Bench, a scaffold-cluster benchmark constructed by partitioning Bemis-Murcko scaffolds in an explicit physicochemical descriptor space, and POMA, a retrieve-compose-adapt framework for source-domain selection when target property labels are unavailable. POMA uses unlabeled target structures to retrieve labeled source scaffolds as proxy targets. A policy is trained from reductions in proxy-task mean absolute error after adaptation, and the selected source subset is then used for target adaptation with covariance alignment at the whole-molecule and BRICS-derived substructure levels. We evaluate HOMO, LUMO, and HOMO-LUMO gap prediction on QM9 using three 3D molecular backbones and 15 target-scaffold tasks. Relative to conventional scaffold splitting, prediction errors on SCOPE-Bench increase by up to 8.0-fold, with a mean increase of 5.9-fold. Relative to the supervised baseline under the strict OOD split, POMA reduces mean absolute error by up to 11.2%, with an average relative reduction of 6.2% over the nine backbone-property combinations. These results support adaptive source selection as a useful strategy for molecular prediction under strong structural distribution shifts.