# Deepened Graph Auto-Encoders Help Stabilize and Enhance Link Prediction

arXiv: https://arxiv.org/abs/2103.11414 · HTML: https://mlsanity.com/paper/2103.11414/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 35 references that are in the map.
- First posted on arXiv 21 Mar 2021.

## Builds on (most cited first, 17 of 17)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [DropEdge: Towards Deep Graph Convolutional Networks on Node Classification](https://mlsanity.com/paper/1907.10903/) (2019)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [Graphite: Iterative Generative Modeling of Graphs](https://mlsanity.com/paper/1803.10459/) (2018)
- [Identity Matters in Deep Learning](https://mlsanity.com/paper/1611.04231/) (2016)
- [Adversarially Regularized Graph Autoencoder for Graph Embedding](https://mlsanity.com/paper/1802.04407/) (2018)
- [Improving Graph Attention Networks with Large Margin-based Constraints](https://mlsanity.com/paper/1910.11945/) (2019)

## Built on by (most cited first, 4 of 4)

- [Norm Augmented Graph AutoEncoders for Link Prediction](https://mlsanity.com/paper/2502.05868/) (2025)
- [Concept-free Causal Disentanglement with Variational Graph Auto-Encoder](https://mlsanity.com/paper/2311.10638/) (2023)
- [GraphMinNet: Learning Dependencies in Graphs with Light Complexity Minimal Architecture](https://mlsanity.com/paper/2502.00282/) (2025)
- [A Survey on GNN-based Link Prediction: Techniques, Applications, and Challenges](https://mlsanity.com/paper/2607.16198/) (2026)

## Abstract (arXiv)

Graph neural networks have been used for a variety of learning tasks, such as link prediction, node classification, and node clustering. Among them, link prediction is a relatively under-studied graph learning task, with current state-of-the-art models based on one- or two-layer of shallow graph auto-encoder (GAE) architectures. In this paper, we focus on addressing a limitation of current methods for link prediction, which can only use shallow GAEs and variational GAEs, and creating effective methods to deepen (variational) GAE architectures to achieve stable and competitive performance. Our proposed methods innovatively incorporate standard auto-encoders (AEs) into the architectures of GAEs, where standard AEs are leveraged to learn essential, low-dimensional representations via seamlessly integrating the adjacency information and node features, while GAEs further build multi-scaled low-dimensional representations via residual connections to learn a compact overall embedding for link prediction. Empirically, extensive experiments on various benchmarking datasets verify the effectiveness of our methods and demonstrate the competitive performance of our deepened graph models for link prediction. Theoretically, we prove that our deep extensions inclusively express multiple polynomial filters with different orders.