{"paper":{"title":"When Three-Dimensional Conformer Ensembles Improve Molecular Property Prediction Beyond Two-Dimensional Fingerprints: A Systematic Study","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["q-bio.MN"],"primary_cat":"physics.chem-ph","authors_text":"Austin Jin, Bryan Cheng, Jasper Zhang","submitted_at":"2026-06-07T20:33:49Z","abstract_excerpt":"When do three-dimensional conformer ensembles improve molecular property prediction beyond two-dimensional fingerprints? We provide the first systematic, mechanistically grounded answer. Through ~1,000 experiments spanning 13 model configurations, 14 regression targets, and 2 classification targets across MoleculeNet, QM9, and MARCEL benchmarks, we discover selective complementarity: conformer ensemble statistics extracted via Distribution Kernel Operators (DKOs) yield statistically significant RMSE reductions on solvation-dependent properties (ESOL -11.0%, p < 10^{-9}; FreeSolv -13.5%, p < 3x"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.08825","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.08825/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}