# Graph Positional Autoencoders as Self-supervised Learners

arXiv: https://arxiv.org/abs/2505.23345 · HTML: https://mlsanity.com/paper/2505.23345/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 85 references that are in the map.
- First posted on arXiv 29 May 2025.

## Builds on (most cited first, 30 of 48)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [Graph Self-Supervised Learning: A Survey](https://mlsanity.com/paper/2103.00111/) (2021)
- [Graph Contrastive Learning Automated](https://mlsanity.com/paper/2106.07594/) (2021)
- [Long Range Graph Benchmark](https://mlsanity.com/paper/2206.08164/) (2022)
- [Representing Long-Range Context for Graph Neural Networks with Global Attention](https://mlsanity.com/paper/2201.08821/) (2022)
- [Self-Supervised Learning of Graph Neural Networks: A Unified Review](https://mlsanity.com/paper/2102.10757/) (2021)
- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [A Survey of Graph Neural Networks for Recommender Systems: Challenges, Methods, and Directions](https://mlsanity.com/paper/2109.12843/) (2021)
- [From Canonical Correlation Analysis to Self-supervised Graph Neural Networks](https://mlsanity.com/paper/2106.12484/) (2021)
- [Self-supervised Learning on Graphs: Contrastive, Generative,or Predictive](https://mlsanity.com/paper/2105.07342/) (2021)
- [GraphMAE2: A Decoding-Enhanced Masked Self-Supervised Graph Learner](https://mlsanity.com/paper/2304.04779/) (2023)
- [AM-GCN: Adaptive Multi-channel Graph Convolutional Networks](https://mlsanity.com/paper/2007.02265/) (2020)
- [Symmetric Graph Convolutional Autoencoder for Unsupervised Graph Representation Learning](https://mlsanity.com/paper/1908.02441/) (2019)

## Built on by (most cited first, 3 of 3)

- [Frequency-Corrupt Based Graph Self-Supervised Learning](https://mlsanity.com/paper/2604.15699/) (2026)
- [GraphSculptor: Sculpting Pre-training Coreset for Graph Self-supervised Learning](https://mlsanity.com/paper/2605.01310/) (2026)
- [MDTE: Minority-Aware Diffusion over Temporal Edge Events for Imbalanced Node Classification](https://mlsanity.com/paper/2608.24812/) (2026)

## Abstract (arXiv)

Graph self-supervised learning seeks to learn effective graph representations without relying on labeled data. Among various approaches, graph autoencoders (GAEs) have gained significant attention for their efficiency and scalability. Typically, GAEs take incomplete graphs as input and predict missing elements, such as masked nodes or edges. While effective, our experimental investigation reveals that traditional node or edge masking paradigms primarily capture low-frequency signals in the graph and fail to learn the expressive structural information. To address these issues, we propose Graph Positional Autoencoders (GraphPAE), which employs a dual-path architecture to reconstruct both node features and positions. Specifically, the feature path uses positional encoding to enhance the message-passing processing, improving GAE's ability to predict the corrupted information. The position path, on the other hand, leverages node representations to refine positions and approximate eigenvectors, thereby enabling the encoder to learn diverse frequency information. We conduct extensive experiments to verify the effectiveness of GraphPAE, including heterophilic node classification, graph property prediction, and transfer learning. The results demonstrate that GraphPAE achieves state-of-the-art performance and consistently outperforms baselines by a large margin.