VecMol: Vector-Field Representations for 3D Molecule Generation

Abstract

Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types with continuous atomic coordinates, leading to intrinsic learning difficulties such as heterogeneous modality entanglement and geometry–chemistry coherence constraints. We propose VecMol, a novel representation that models 3D molecules as continuous vector fields over Euclidean space, where vectors point toward nearby atoms and implicitly encode molecular structure. The vector field is parameterized by a neural field and generated using a latent diffusion model, avoiding explicit graph generation and decoupling structure learning from discrete atom instantiation. Experiments on the QM9 and GEOM-Drugs benchmarks demonstrate that VecMol achieves competitive generation quality, suggesting vector-field-based representations as a promising new direction for 3D molecular generation.