GLDM: hit molecule generation with constrained graph latent diffusion model.

ABSTRACT: Discovering hit molecules with desired biological activity in a directed manner is a promising but profound task in computer-aided drug discovery. Inspired by recent generative AI approaches, particularly Diffusion Models (DM), we propose Graph Latent Diffusion Model (GLDM)-a latent DM that preserves both the effectiveness of autoencoders of compressing complex chemical data and the DM's capabilities of generating novel molecules. Specifically, we first develop an autoencoder to encode the molecular data into low-dimensional latent representations and then train the DM on the latent space to generate molecules inducing targeted biological activity defined by gene expression profiles. Manipulating DM in the latent space rather than the input space avoids complicated operations to map molecu

SUBMITTER: Wang C 

PROVIDER: S-EPMC10998532 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature