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Dual-Axis RCCL: Representation-Complete Convergent Learning for Organic Chemical Space

arXiv 2512.14418 ↗First posted 16 Dec 2025cs.LGcited by 0

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Abstract (arXiv)

Machine learning is profoundly reshaping molecular and materials modeling; however, given the vast scale of chemical space (10^30-10^60), it remains an open scientific question whether models can achieve convergent learning across this space. We introduce a Dual-Axis Representation-Complete Convergent Learning (RCCL) strategy, enabled by a molecular representation that integrates graph convolutional network (GCN) encoding of local valence environments, grounded in modern valence bond theory, together with no-bridge graph (NBG) encoding of ring/cage topologies, providing a quantitative measure of chemical-space coverage. This framework formalizes representation completeness, establishing a principled basis for constructing datasets that support convergent learning for large models. Guided by this RCCL framework, we develop the FD25 dataset, systematically covering 13,302 local valence units and 165,726 ring/cage topologies, achieving near-complete combinatorial coverage of organic molecules with H/C/N/O/F elements. Graph neural networks trained on FD25 exhibit representation-complete convergent learning and strong out-of-distribution generalization, with an overall prediction error of approximately 1.0 kcal/mol MAE across external benchmarks. Our results establish a quantitative link between molecular representation, structural completeness, and model generalization, providing a foundation for interpretable, transferable, and data-efficient molecular intelligence.

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References · 14

  1. 2017Neural Message Passing for Quantum Chemistrycited by 3,487
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  9. 2021Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction predictioncited by 68
  10. 2019Alchemy: A Quantum Chemistry Dataset for Benchmarking AI Modelscited by 36
  11. 2021Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphscited by 31
  12. 2023PubChemQC B3LYP/6-31G*//PM6 dataset: the Electronic Structures of 86 Million Molecules using B3LYP/6-31G* calculationscited by 12
2 more
  1. 2025Graph Neural Networks in Modern AI-aided Drug Discoverycited by 12
  2. 2024Advancing Molecular Machine Learning Representations with Stereoelectronics-Infused Molecular Graphscited by 2

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