Your Discrete Graph Diffusion Model is Secretly Memorizing

Abstract

Discrete graph diffusion models (GDMs) corrupt the graph structure by adding noise independently to nodes and edges under a Markovian noise model. In the unconditional setting without node features, an equivariant denoiser trained on a single graph is able to generate novel graphs and sample-level metrics such as edge overlap and WL kernel similarity find no evidence of memorization. In this work, we challenge this view and show for the first time that graph diffusion models indeed exhibit memorization. Analyzing the reverse diffusion trajectories of GDMs trained on two-block stochastic block models (SBMs), we find a strong train-data bias: the model recovers a corrupted training graph almost perfectly compared to a held-out test graph. We term this conditional memorization, as it surfaces only when the reverse trajectory is conditioned on a corrupted training graph and is not apparent during inference. It coincides with a growing generalization gap, where the training loss improves as the loss on held-out graphs degrades, and it cannot be mitigated by early stopping. The onset of memorization always precedes the emergence of community structure in the generated graphs, thus every checkpoint earlier produces structureless graphs. This behavior holds across all node sizes we test.