Generating realistic graphs faces challenges in estimating accurate distribution of graphs in an embedding space while preserving structural characteristics. However, existing graph generation methods primarily focus on approximating the joint distribution of nodes and edges, often overlooking topological properties such as connected components and loops, hindering accurate representation of global structures. To address this issue, we propose a Topology-Aware diffusion-based Graph Generation (TAGG), which aims to sample synthetic graphs that closely resemble the structural characteristics of the original graph based on persistent homology. Specifically, we suggest two core components: 1) Persistence Diagram Matching (PDM) loss which ensures high topological fidelity of generated graphs, and 2) Topology-aware Attention Module (TAM) which induces the denoising network to capture the homological characteristics of the original graphs. Extensive experiments on conventional graph benchmarks demonstrate the effectiveness of our approach indicating high generation performance across various metrics, while achieving closer alignment with the distribution of topological features observed in the original graphs.

Graph diffusion models have made significant progress in learning structured graph data and have demonstrated strong potential for predictive tasks.

We introduce AUTOGRAPH, a scalable autoregressive model for attributed graph generation using decoder-only transformers. By flattening graphs into random sequences of tokens through a reversible process, AUTOGRAPH enables modeling graphs as sequences without relying on additional node features that are expensive to compute, in contrast to diffusion-based approaches.

We introduce AutoGraph, a scalable autoregressive model for attributed graph generation using decoder-only transformers. By flattening graphs into random sequences of tokens through a reversible process, AutoGraph enables modeling graphs as sequences without relying on additional node features that are expensive to compute, in contrast to diffusion-based approaches.

ABSTRACT Discrete diffusion models are a powerful class of generative models with strong performance across many domains. For efficiency, however, discrete diffusion typically parameterizes the generative (reverse) process with factorized distributions, which makes it difficult for the model to learn the target process in a small number of steps and necessitates a long, computationally expensive sampling procedure. To reduce the gap between the target and model distributions and enable few-step generation, we propose Forward-Learned Discrete Diffusion (FLDD), which introduces discrete diffusion with a learnable forward (noising) process. Rather than fixing a Markovian forward chain, we adopt a non-Markovian formulation with learnable marginal and posterior distributions. This allows the generative process to remain factorized while matching the target defined by the noising process. We train all parameters end-to-end under the standard variational objective. Experiments on various benchmarks show that, for a given number of sampling steps, our approach produces a higher quality samples than conventional discrete diffusion models using the same reverse parameterization. 1 INTRODUCTION In the last years, diffusion models have demonstrated strong performance across many continuous (Hoogeboom et al., 2024) and discrete (Lou et al.) domains . Recent work has shown that distillation approaches and advanced training techniques allow learning a few-step (Salimans et al., 2024), or sometimes even a single-step, generative (Xu et al., 2025) procedure in the continuous domain.

Energy-based models for discrete domains, such as graphs, explicitly capture relative likelihoods, naturally enabling composable probabilistic inference tasks like conditional generation or enforcing constraints at test-time. However, discrete energy-based models typically struggle with efficient and high-quality sampling, as off-support regions often contain spurious local minima, trapping samplers and causing training instabilities. This has historically resulted in a fidelity gap relative to discrete diffusion models. We introduce Graph Energy Matching (GEM), a generative framework for graphs that closes this fidelity gap. Motivated by the transport map optimization perspective of the Jordan-Kinderlehrer-Otto (JKO) scheme, GEM learns a permutation-invariant potential energy that simultaneously provides transport-aligned guidance from noise toward data and refines samples within regions of high data likelihood. Further, we introduce a sampling protocol that leverages an energy-based switch to seamlessly bridge: (i) rapid, gradient-guided transport toward high-probability regions to (ii) a mixing regime for exploration of the learned graph distribution. On molecular graph benchmarks, GEM matches or exceeds strong discrete diffusion baselines. Beyond sample quality, explicit modeling of relative likelihood enables targeted exploration at inference time, facilitating compositional generation, property-constrained sampling, and geodesic interpolation between graphs.

Generating novel graph structures that optimize given objectives while obeying some given underlying rules is fundamental for chemistry, biology and social science research. This is especially important in the task of molecular graph generation, whose goal is to discover novel molecules with desired properties such as drug-likeness and synthetic accessibility, while obeying physical laws such as chemical valency. However, designing models that finds molecules that optimize desired properties while incorporating highly complex and non-differentiable rules remains to be a challenging task. Here we propose Graph Convolutional Policy Network (GCPN), a general graph convolutional network based model for goal-directed graph generation through reinforcement learning. The model is trained to optimize domain-specific rewards and adversarial loss through policy gradient, and acts in an environment that incorporates domain-specific rules. Experimental results show that GCPN can achieve 61% improvement on chemical property optimization over state-of-the-art baselines while resembling known molecules, and achieve 184% improvement on the constrained property optimization task.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated