{"ID":2853006,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2510.18122","arxiv_id":"2510.18122","title":"HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields","abstract":"We introduce HyperDiffusionFields (HyDiF), a framework that models 3D molecular conformers as continuous fields rather than discrete atomic coordinates or graphs. At the core of our approach is the Molecular Directional Field (MDF), a vector field that maps any point in space to the direction of the nearest atom of a particular type. We represent MDFs using molecule-specific neural implicit fields, which we call Molecular Neural Fields (MNFs). To enable learning across molecules and facilitate generalization, we adopt an approach where a shared hypernetwork, conditioned on a molecule, generates the weights of the given molecule's MNF. To endow the model with generative capabilities, we train the hypernetwork as a denoising diffusion model, enabling sampling in the function space of molecular fields. Our design naturally extends to a masked diffusion mechanism to support structure-conditioned generation tasks, such as molecular inpainting, by selectively noising regions of the field. Beyond generation, the localized and continuous nature of MDFs enables spatially fine-grained feature extraction for molecular property prediction, something not easily achievable with graph or point cloud based methods. Furthermore, we demonstrate that our approach scales to larger biomolecules, illustrating a promising direction for field-based molecular modeling.","short_abstract":"We introduce HyperDiffusionFields (HyDiF), a framework that models 3D molecular conformers as continuous fields rather than discrete atomic coordinates or graphs. At the core of our approach is the Molecular Directional Field (MDF), a vector field that maps any point in space to the direction of the nearest atom of a p...","url_abs":"https://arxiv.org/abs/2510.18122","url_pdf":"https://arxiv.org/pdf/2510.18122v1","authors":"[\"Sudarshan Babu\",\"Phillip Lo\",\"Xiao Zhang\",\"Aadi Srivastava\",\"Ali Davariashtiyani\",\"Jason Perera\",\"Michael Maire\",\"Aly A. Khan\"]","published":"2025-10-20T21:41:10Z","proceeding":"cs.LG","tasks":"[\"cs.LG\"]","methods":"[\"Diffusion Model\"]","has_code":false}