HyperDiffusionFields (HyDiF): Diffusion-Guided Hypernetworks for Learning Implicit Molecular Neural Fields
This work addresses molecular modeling for computational chemistry and drug discovery, offering a novel field-based approach that is incremental in combining existing techniques like hypernetworks and diffusion models.
The authors tackled the problem of modeling 3D molecular conformers by introducing HyperDiffusionFields (HyDiF), which represents molecules as continuous fields using neural implicit fields and a diffusion-guided hypernetwork, enabling generative tasks like molecular inpainting and property prediction with demonstrated scalability to larger biomolecules.
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.