DeFoG: Discrete Flow Matching for Graph Generation

Graph generative models are essential across diverse scientific domains by capturing complex distributions over relational data. Among them, graph diffusion models achieve superior performance but face inefficient sampling and limited flexibility due to the tight coupling between training and sampling stages. We introduce DeFoG, a novel graph generative framework that disentangles sampling from training, enabling a broader design space for more effective and efficient model optimization. DeFoG employs a discrete flow-matching formulation that respects the inherent symmetries of graphs. We theoretically ground this disentangled formulation by explicitly relating the training loss to the sampling algorithm and showing that DeFoG faithfully replicates the ground truth graph distribution. Building on these foundations, we thoroughly investigate DeFoG’s design space and propose novel sampling methods that significantly enhance performance and reduce the required number of refinement steps. Extensive experiments demonstrate state-of-the-art performance across synthetic, molecular, and digital pathology datasets, covering both unconditional and conditional generation settings. It also outperforms most diffusion-based models with just 5–10% of their sampling steps.