LDMol: Text-to-Molecule Diffusion Model with Structurally Informative Latent Space

Abstract

With the emergence of diffusion models as the frontline of generative models, many researchers have proposed molecule generation techniques with conditional diffusion models. However, the unavoidable discreteness of a molecule makes it difficult for a diffusion model to connect raw data with highly complex conditions like natural language. To address this, we present a novel latent diffusion model dubbed LDMol for text-conditioned molecule generation. LDMol comprises a molecule autoencoder that produces a learnable and structurally informative feature space, and a natural language-conditioned latent diffusion model. In particular, recognizing that multiple SMILES notations can represent the same molecule, we employ a contrastive learning strategy to extract feature space that is aware of the unique characteristics of the molecule structure. LDMol outperforms the existing baselines on the text-to-molecule generation benchmark, suggesting a potential for diffusion models can outperform autoregressive models in text data generation with a better choice of the latent domain. Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-guided molecule editing, demonstrating its versatility as a diffusion model.