Improving structural plausibility in diffusion-based 3D molecule generation via property-conditioned training with distorted molecules

Abstract

Traditional drug design methods are costly and time-consuming due to their reliance on trial-and-error processes. As a result, computational methods, including diffusion models, designed for molecule generation tasks have gained significant traction. Despite their potential, they have faced criticism for producing physically implausible outputs. As a solution to this problem, we propose a conditional training framework resulting in a model capable of generating molecules of varying and controllable levels of structural plausibility. This framework consists of adding distorted molecules to training datasets, and then annotating each molecule with a label representing the extent of its distortion, and hence its quality. By training the model to distinguish between favourable and unfavourable molecular conformations alongside the standard molecule generation training process, we can selectively sample molecules from the high-quality region of learned space, resulting in improvements in the validity of generated molecules. In addition to the standard two datasets used by molecule generation methods (QM9 and GEOM), we also test our method on a druglike dataset derived from ZINC. We use our conditional method with EDM, the first E(3) equivariant diffusion model for molecule generation, as well as two further models—a more recent diffusion model and a flow matching model—which were built off EDM. We demonstrate improvements in validity as assessed by RDKit parsability and the PoseBusters test suite; more broadly, though, our findings highlight the effectiveness of conditioning methods on low-quality data to improve the sampling of high-quality data.