Inverse Molecular Design with Multi-Conditional Diffusion Guidance

Inverse molecular design with diffusion models holds great potential for advancements in material and drug discovery. Despite success in unconditional molecule generation, integrating multiple properties such as synthetic score and gas permeability as condition constraints into diffusion models remains unexplored. We introduce multi-conditional diffusion guidance. The proposed Transformer-based denoising model has a condition encoder that learns the representations of numerical and categorical conditions. The denoising model, consisting of a structure encoder-decoder, is trained for denoising under the representation of conditions. The diffusion process becomes graph-dependent to accurately estimate graph-related noise in molecules, unlike the previous models that focus solely on the marginal distributions of atoms or bonds. We extensively validate our model for multi-conditional polymer and small molecule generation. Results demonstrate our superiority across metrics from distribution learning to condition control for molecular properties. An inverse polymer design task for gas separation with feedback from domain experts further demonstrates its practical utility.