Accelerating Inference in Molecular Diffusion Models with Latent
  Representations of Protein Structure
Ian Dunn David Ryan Koes
Diffusion generative models have emerged as a powerful framework for
addressing problems in structural biology and structure-based drug design.
These models operate directly on 3D molecular structures. Due to the
unfavorable scaling of graph neural networks (GNNs) with graph size as well as
the relatively slow inference speeds inherent to diffusion models, many
existing molecular diffusion models rely on coarse-grained representations of
protein structure to make training and inference feasible. However, such
coarse-grained representations discard essential information for modeling
molecular interactions and impair the quality of generated structures. In this
work, we present a novel GNN-based architecture for learning latent
representations of molecular structure. When trained end-to-end with a
diffusion model for de novo ligand design, our model achieves comparable
performance to one with an all-atom protein representation while exhibiting a
3-fold reduction in inference time.