[2603.20724] Multi-RF Fusion with Multi-GNN Blending for Molecular Property Prediction

Computer Science > Artificial Intelligence arXiv:2603.20724 (cs) [Submitted on 21 Mar 2026] Title:Multi-RF Fusion with Multi-GNN Blending for Molecular Property Prediction Authors:Zacharie Bugaud View a PDF of the paper titled Multi-RF Fusion with Multi-GNN Blending for Molecular Property Prediction, by Zacharie Bugaud View PDF HTML (experimental) Abstract:Multi-RF Fusion achieves a test ROC-AUC of 0.8476 +/- 0.0002 on ogbg-molhiv (10 seeds), placing #1 on the OGB leaderboard ahead of HyperFusion (0.8475 +/- 0.0003). The core of the method is a rank-averaged ensemble of 12 Random Forest models trained on concatenated molecular fingerprints (FCFP, ECFP, MACCS, atom pairs -- 4,263 dimensions total), blended with deep-ensembled GNN predictions at 12% weight. Two findings drive the result: (1) setting max_features to 0.20 instead of the default sqrt(d) gives a +0.008 AUC gain on this scaffold split, and (2) averaging GNN predictions across 10 seeds before blending with the RF eliminates GNN seed variance entirely, dropping the final standard deviation from 0.0008 to 0.0002. No external data or pre-training is used. Comments: Subjects: Artificial Intelligence (cs.AI); Machine Learning (cs.LG) Cite as: arXiv:2603.20724 [cs.AI]   (or arXiv:2603.20724v1 [cs.AI] for this version)   https://doi.org/10.48550/arXiv.2603.20724 Focus to learn more arXiv-issued DOI via DataCite (pending registration) Submission history From: Zacharie Bugaud [view email] [v1] Sat, 21 Mar 2026 09:18:37 UTC...