# Generalized Graph Transformer Variational Autoencoder

arXiv: https://arxiv.org/abs/2512.00612 · HTML: https://mlsanity.com/paper/2512.00612/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 11 references that are in the map.
- First posted on arXiv 29 Nov 2025.

## Builds on (most cited first, 8 of 8)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [An Introduction to Variational Autoencoders](https://mlsanity.com/paper/1906.02691/) (2019)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Graph Transformer Networks](https://mlsanity.com/paper/1911.06455/) (2019)
- [GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoders](https://mlsanity.com/paper/1802.03480/) (2018)
- [Graph-Bert: Only Attention is Needed for Learning Graph Representations](https://mlsanity.com/paper/2001.05140/) (2020)
- [LPFormer: An Adaptive Graph Transformer for Link Prediction](https://mlsanity.com/paper/2310.11009/) (2023)

## Abstract (arXiv)

Graph link prediction has long been a central problem in graph representation learning in both network analysis and generative modeling. Recent progress in deep learning has introduced increasingly sophisticated architectures for capturing relational dependencies within graph-structured data. In this work, we propose the Generalized Graph Transformer Variational Autoencoder (GGT-VAE). Our model integrates Generalized Graph Transformer Architecture with Variational Autoencoder framework for link prediction. Unlike prior GraphVAE, GCN, or GNN approaches, GGT-VAE leverages transformer style global self-attention mechanism along with laplacian positional encoding to model structural patterns across nodes into a latent space without relying on message passing. Experimental results on several benchmark datasets demonstrate that GGT-VAE consistently achieves above-baseline performance in terms of ROC-AUC and Average Precision. To the best of our knowledge, this is among the first studies to explore graph structure generation using a generalized graph transformer backbone in a variational framework.