biomolecular modelers

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.

Abstract: Manifold-valued data, and consequently the distributions they induce, are prevalent across many domains, ranging from the locations of geospatial events, such as earthquakes, to biomolecular torsion angles that encode information about three-dimensional structure. While diffusion and flow-based generative models have been successfully extended to compact manifolds, sampling typically requires tens or hundreds of sequential network evaluations. We introduce RW-Flow, a theoretically grounded framework for learning one-step generative models on compact manifolds via Wasserstein gradient flows. The main challenge is identifiability: driving the velocity field to zero should guarantee that the model distribution matches the target distribution. We establish a necessary and sufficient condition for identifiability on compact, connected Riemannian manifolds. We specifically show that, for a symmetric, Lipschitz-continuous cost function, the velocity field induced by the Sinkhorn divergence is identifiable if and only if the associated Gibbs kernel is nondegenerate. This characterization provides a general principle for designing identifiable costs on compact manifolds. It also reveals that the squared geodesic distance, the natural manifold analogue of the squared Euclidean distance, does not always guarantee identifiability. Across benchmarks involving geospatial events, protein side chain torsion angles, RNA backbone torsion angles, and general manifolds discretized as triangular meshes, RW-Flow outperforms existing one-step methods in nearly all settings under fair comparison conditions.