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arXiv · 2610.16586

OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows

Yu-Tong Jin·Yi-Yang Tian·Qiwei Ye·Peng-Shuai Wang
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Abstract

Generating accurate 3D molecules requires jointly determining a variable number of atoms, their identities, and geometry across spatial scales: global shape emerges coarsely, whereas chemical bonds demand fine local precision. Existing atom-based diffusion and flow models operate largely at a single scale, while dense spatial fields become costly at high resolution. We introduce OctMole, a multiscale octree flow framework for 3D molecular generation. A hierarchical occupancy flow progressively resolves sparse molecular support from coarse to fine, and a joint atom flow assigns atom types and continuous in-cell offsets to occupied leaves. This decomposition combines efficient global structure with subcell geometric precision, while cell corruption improves robustness to generated support. On QM9 and GEOM-DRUG, OctMole achieves strong chemical, distributional, and geometric quality, with particularly clear gains over Uni-3DAR on GEOM-DRUG and substantial efficiency gains over dense 3D generation. As an additional capability, intermediate occupancy states and selected regions provide spatial conditioning without task-specific retraining, supporting multiscale shape conditioning, regional editing, linker generation, and shape interpolation. Code and pretrained checkpoints are available at https://github.com/octree-nn/octmole and https://huggingface.co/Disembo/octmole, respectively.

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Yu-Tong Jin, Yi-Yang Tian, Qiwei Ye, Peng-Shuai Wang. 2026-10-12. OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows. https://arxiv.org/abs/2610.16586

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