# Reconsidering the Performance of GAE in Link Prediction

arXiv: https://arxiv.org/abs/2411.03845 · HTML: https://mlsanity.com/paper/2411.03845/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 33 of its 51 references that are in the map.
- First posted on arXiv 6 Nov 2024.

## Builds on (most cited first, 30 of 33)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [LightGCN: Simplifying and Powering Graph Convolution Network for Recommendation](https://mlsanity.com/paper/2002.02126/) (2020)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [Inductive Representation Learning on Temporal Graphs](https://mlsanity.com/paper/2002.07962/) (2020)
- [Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction](https://mlsanity.com/paper/2106.06935/) (2021)
- [Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks](https://mlsanity.com/paper/1909.01315/) (2019)
- [Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning](https://mlsanity.com/paper/2010.16103/) (2020)
- [Inductive Matrix Completion Based on Graph Neural Networks](https://mlsanity.com/paper/1904.12058/) (2019)
- [Classic GNNs are Strong Baselines: Reassessing GNNs for Node Classification](https://mlsanity.com/paper/2406.08993/) (2024)
- [Graph Neural Networks for Link Prediction with Subgraph Sketching](https://mlsanity.com/paper/2209.15486/) (2022)
- [Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction](https://mlsanity.com/paper/2206.04216/) (2022)
- [Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking](https://mlsanity.com/paper/2306.10453/) (2023)
- [Neural Common Neighbor with Completion for Link Prediction](https://mlsanity.com/paper/2302.00890/) (2023)
- [Revisiting Link Prediction: A Data Perspective](https://mlsanity.com/paper/2310.00793/) (2023)
- [Pairwise Learning for Neural Link Prediction](https://mlsanity.com/paper/2112.02936/) (2021)
- [Pure Message Passing Can Estimate Common Neighbor for Link Prediction](https://mlsanity.com/paper/2309.00976/) (2023)
- [LPFormer: An Adaptive Graph Transformer for Link Prediction](https://mlsanity.com/paper/2310.11009/) (2023)

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

- [Relatron: Automating Relational Machine Learning over Relational Databases](https://mlsanity.com/paper/2602.22552/) (2026)
- [Plain Transformers are Surprisingly Powerful Link Predictors](https://mlsanity.com/paper/2602.01553/) (2026)
- [A Survey on GNN-based Link Prediction: Techniques, Applications, and Challenges](https://mlsanity.com/paper/2607.16198/) (2026)
- [Link prediction on multi-relational graphs from an influence propagation perspective](https://mlsanity.com/paper/2608.05016/) (2026)

## Abstract (arXiv)

Recent advancements in graph neural networks (GNNs) for link prediction have introduced sophisticated training techniques and model architectures. However, reliance on outdated baselines may exaggerate the benefits of these new approaches. To tackle this issue, we systematically explore Graph Autoencoders (GAEs) by applying model-agnostic tricks in recent methods and tuning hyperparameters. We find that a well-tuned GAE can match the performance of recent sophisticated models while offering superior computational efficiency on widely-used link prediction benchmarks. Our approach delivers substantial performance gains on datasets where structural information dominates and feature data is limited. Specifically, our GAE achieves a state-of-the-art Hits@100 score of 78.41% on the ogbl-ppa dataset. Furthermore, we examine the impact of various tricks to uncover the reasons behind our success and to guide the design of future methods. Our study emphasizes the critical need to update baselines for a more accurate assessment of progress in GNNs for link prediction. Our code is available at https://github.com/GraphPKU/Refined-GAE.