Comparative Evaluation of Deep Generative Models for Capturing Topological Features in Brain Structural Connectivity

Structural connectivity (SC) data are crucial for brain network analysis, but SC-based machine learning often suffers from limited data availability, hindering model generalization and robustness. Although data augmentation using deep generative models has attracted increasing attention, it remains unclear how different models capture the complex topological features of SC data. To clarify the learning characteristics of deep generative models for SC generation, this study compares three representative models: variational autoencoder (VAE), Wasserstein GAN with gradient penalty (WGAN-GP), and denoising diffusion probabilistic models (DDPM). We systematically evaluated these models using both synthetic datasets with known characteristics and real-world SC data. Generation quality was assessed using graph-theoretic metric comparisons and visual inspection of the generated adjacency matrices. WGAN-GP showed relatively stable performance across datasets and metrics, without severe performance degradation across evaluation settings. In contrast, VAE and DDPM performed well in specific aspects but were more sensitive to data characteristics. These findings suggest that WGAN-GP may serve as the most balanced baseline for future SC data augmentation studies, whereas VAE and DDPM may be useful depending on the target application and structural properties of interest. Furthermore, because all models struggled to fully reproduce strict global constraints such as planarity, our results suggest that standard generative models may be insufficient to capture the complex topological features of SC data. This highlights the importance of incorporating the desired structural properties into the training or generation process.