GraphK: Variable-Size Graph Generation with Efficient Edge Construction

Generating realistic and diverse graphs is a key problem in machine learning, with applications in molecular discovery, circuit design, cybersecurity, and beyond. However, current graph generative models remain limited by scalability and novelty. Diffusion-based methods often require costly full-adjacency operations and long denoising chains, while many autoregressive and hybrid models have at least quadratic complexity. In addition, these models often imitate training graphs rather than generalize beyond them. We propose a lightweight autoregressive framework to address these issues. It uses a structure-guided topological ordering to serialize graphs into regular edge sequences, enabling near log-linear generation, and a two-phase training strategy that combines exploration-oriented augmentation with iterative refinement to reduce overfitting and promote controlled novelty. Experiments on molecular and non-molecular benchmarks show that our approach improves novelty while preserving high validity and uniqueness. The framework also supports both LSTM and Mamba-style causal sequence backbones, with large-memory accelerators enabling longer graph-sequence experiments beyond typical GPU limits.

The Deep Graph Generation's panorama spans two extremes: one-shot and sequential models. The former generates nodes and edges jointly, while the latter samples them autoregressively. Each method performs better in different graph domains depending on size and topology, but neither is applicable to all graph categories. For instance, one-shot methods struggle with generating large graphs, while sequential methods underperform on smaller graphs. A possible way to overcome these limitations is to flexibly combine the two methods in a unique system. In this work, we propose the FLAGG (Flexible Autoregressive Graph Generation) framework, which sequentially generates portions of graphs with one-shot models. FLAGG can apply any one-shot model to make it autoregressive, allowing flexibility in choosing the sequential policy. This policy is specified through a stochastic node removal process, which an Insertion Model learns to reverse. We evaluate FLAGG with the DiGress one-shot model on several data sets of different graph sizes and domains. We show that the approach outperforms both one-shot and autoregressive baselines in terms of sampling quality.

Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design. Yet, scaling these models to large graphs remains an open problem. We approach this question in the dense-graph setting through the lens of graphons, the size-agnostic limit objects of dense graph sequences, to study how structural graph statistics behave across node-size scales. This perspective leads to DiPhon, a diffusion framework for size-scalable graph generation. Specifically, we formulate a continuous diffusion process on the graphon space via a Jacobi stochastic differential equation (SDE), and propose DiPhon, a discretized graph-level process that mimics these dynamics on finite graphs. We further derive the corresponding reverse-time process, which requires access to the marginal score. For the Jacobi process, this score interestingly admits a tractable form, which we estimate from data via graph denoising and plug into the reverse process to generate graph samples. We prove that DiPhon matches exactly the first moment of the marginal distributions induced by the continuous graphon process, and approximates the second moment up to a closed-form discrepancy. Thus, DiPhon inherits key size-agnostic statistical properties of the graphon dynamics, providing a principled route toward scalable graph generation. Empirically, we demonstrate this scalability by training on small graphs and generating progressively larger graphs at inference time, without retraining, while preserving their core topological properties.