ScaleMol: Defining and Leveraging Scales for 3D Molecular Generation

Small molecules lack a natural definition of scale, making it difficult to organize their generation from coarse structure to fine detail. We address this problem by introducing resolution-consistent molecular mass grids (MMGs), which define molecular scales through the spatial resolution of a molecular field. Coarse MMGs capture regional element content, while finer MMGs progressively resolve its spatial distribution, with exact consistency across scales. Based on this scale definition, we introduce ScaleMol, which explicitly predicts and supervises molecular fields from coarse to fine. On QM9 and GEOM-Drugs, ScaleMol improves atom and molecule stability over existing field-based generators, while controlled ablations verify the benefits of both MMGs and coarse-to-fine prediction. The same scale hierarchy also enables conditioning on a reference molecule at different resolutions without additional training. Together, our results provide a simple definition of scale for small molecules and demonstrate its utility for 3D molecular generation.