Synthetic Data from Diffusion Models Improve Drug Discovery Prediction
This addresses data sparsity for researchers in drug discovery, enabling easier exploration of questions across multiple datasets, though it appears incremental as it builds on existing diffusion and GNN methods.
The paper tackles data sparsity in drug discovery AI by proposing a diffusion GNN model, Syngand, to generate synthetic ligand and pharmacokinetic data, showing promising results on downstream regression tasks with datasets like AqSolDB, LD50, and hERG central.
Artificial intelligence (AI) is increasingly used in every stage of drug development. Continuing breakthroughs in AI-based methods for drug discovery require the creation, improvement, and refinement of drug discovery data. We posit a new data challenge that slows the advancement of drug discovery AI: datasets are often collected independently from each other, often with little overlap, creating data sparsity. Data sparsity makes data curation difficult for researchers looking to answer key research questions requiring values posed across multiple datasets. We propose a novel diffusion GNN model Syngand capable of generating ligand and pharmacokinetic data end-to-end. We show and provide a methodology for sampling pharmacokinetic data for existing ligands using our Syngand model. We show the initial promising results on the efficacy of the Syngand-generated synthetic target property data on downstream regression tasks with AqSolDB, LD50, and hERG central. Using our proposed model and methodology, researchers can easily generate synthetic ligand data to help them explore research questions that require data spanning multiple datasets.