Graph generation aims to sample discrete node and edge attributes while satisfying coupled structural constraints. Diffusion models for graphs often adopt largely factorized forward-noising, and many flow-matching methods start from factorized reference noise and coordinate-wise interpolation, so node-edge coupling is not encoded by the generative geometry and must be recovered implicitly by the core network, which can be brittle after discrete decoding. Bayesian Flow Networks (BFNs) evolve distribution parameters and naturally support discrete generation. But classical BFNs typically rely on factorized beliefs and independent channels, which limit geometric evidence fusion. We propose Variational Bayesian Flow Network (VBFN), which performs a variational lifting to a tractable joint Gaussian variational belief family governed by structured precisions. Each Bayesian update reduces to solving a symmetric positive definite linear system, enabling coupled node and edge updates within a single fusion step. We construct sample-agnostic sparse precisions from a representation-induced dependency graph, thereby avoiding label leakage while enforcing node-edge consistency. On synthetic and molecular graph datasets, VBFN improves fidelity and diversity, and surpasses baseline methods. The reproducible code is available at https://github.com/Cello2195/VBFN.
Molecular graph generation (MGG) is essentially a multi-class generative task, aimed at predicting categories of atoms and bonds under strict chemical and structural constraints. However, many prevailing diffusion paradigms learn to regress numerical embeddings and rely on a hard discretization rule during sampling to recover discrete labels. This introduces a fundamental discrepancy between training and sampling. While models are trained for point-wise numerical fidelity, the sampling process fundamentally relies on crossing categorical decision boundaries. This discrepancy forces the model to expend efforts on intra-class variations that become irrelevant after discretization, ultimately compromising diversity, structural statistics, and generalization performance. Therefore, we propose TopBF, a unified framework that (i) performs MGG directly in continuous parameter distributions, (ii) learns graph-topological understanding through a Quasi-Wasserstein optimal-transport coupling under geodesic costs, and (iii) supports controllable, property-conditioned generation during sampling without retraining the base model. TopBF innovatively employs cumulative distribution function (CDF) to compute category probabilities induced by the Gaussian channel, thereby unifying the training objective with the sampling discretization operation. Experiments on QM9 and ZINC250k demonstrate superior structural fidelity and efficient generation with improved performance.
Discrete graph generation has emerged as a powerful paradigm for modeling graph-structured data, yet state of the art models often rely on Graph Transformers or higher order architectures. We revisit this design assumption by introducing GenGNN, a modular message passing backbone for graph generation. GenGNN enables powerful generation by persisting edge fields through latent refinement of coupled node edge graph states, all without requiring global attention. Diffusion models integrating GenGNN achieve over 90 percent validity on standard benchmark datasets, performing within margins of Graph Transformer backbones and achieving up to 2x or even 5x faster inference. Systematic ablations isolate how GenGNN is resilient to oversmoothing during generative denoising, indicating each GenGNN component is necessary for downstream generation quality. Finally, representation-space analysis suggests GenGNN learns functionally similar representations to more theoretically-expressive architectures; even at deeper layers. As such, GenGNN uplifts local message-passing to challenge prevailing assumptions that performant discrete graph generation requires global attention or higher-order representations. Source Code Available Here
Generating signals on graphs requires permutation-equivariant models that exhibit stability with respect to relative structural perturbations. While favorable stability properties of Graph Neural Networks (GNNs) have been well documented, it is unclear how structural errors propagate through the dynamics of continuous generative flow models that are gaining traction for graph signal generation. In this paper, we analyze continuous normalized flow models parameterized by GNNs and show that permutation equivariance is preserved for both the resulting continuous-time ordinary differential equations and their discrete numerical approximations used as graph signal samplers. Our primary contribution is to derive explicit stability bounds on the generated probability distributions, which quantify how relative graph perturbations affect the final sampled signals. Motivated by these theoretical bounds, we introduce a stability-promoting regularized flow matching strategy that actively penalizes the spatial Lipschitz constant of the vector field during model training. Experiments using synthetic smooth signals on stochastic block model graphs and real-world fMRI signals on brain connectomes demonstrate that this bound-oriented approach yields generative models that are more robust to structural noise, without sacrificing output quality.