HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption
Abstract
[S U M M A R Y] Self-supervised auto-encoders have emerged as a successful framework for representation learning in computer vision and natural language processing in recent years, However, their application to graph data has been met with limited performance due to the non-Euclidean and complex structure of graphs in comparison to images or text, as well as the limitations of conventional auto-encoder architectures. In this paper, we investigate factors impacting the performance of auto-encoders on graph data and propose a novel auto-encoder model for graph representation learning. Our model incorporates a hierarchical adaptive masking mechanism to incrementally increase the difficulty of training in order to mimic the process of human cognitive learning, and a trainable corruption scheme to enhance the robustness of learned representations. Through extensive experimentation on ten benchmark datasets, we demonstrate the superiority of our proposed method over state-of-the-art graph representation learning models.
Benchmark Results
Tested on 6 datasets 16 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 140 | HAT-GAE | 0.9358
±0.0024 | This paper |
| 164 | GraphMAE | 0.9301
±0.0026 | prev best: Calibrating and Improving Graph Contrastive Learning (TMLR 2021) best today: Rethinking and Simplifying Bootstrapped Graph Latents (2023) |
| 172 | BGRL | 0.9337
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 186 | CCA-SSG | 0.9325
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 206 | MVGRL | 0.9310
±0.0040 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 213 | DGI | 0.9309
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 227 | HAT-GAE-TC | 0.9292
±0.0018 | This paper |
| 264 | HAT-GAE-HM | 0.9265
±0.0011 | This paper |
| 348 | GATE | 0.9191
±0.0014 | This paper |
| 352 | GAE | 0.9185
±0.0006 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 390 | MLP | 0.9128
±0.0063 | |
| 398 | InfoGCL | 0.9117
±0.0022 | This paper |
| 437 | HAT-GAE-AM | 0.9039
±0.0020 | This paper |
| 471 | GPT-GNN | 0.8927
±0.0028 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 79 | BGRL | 0.9034
±0.0019 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 100 | GraphMAE | 0.8832
±0.0016 | prev best: Calibrating and Improving Graph Contrastive Learning (TMLR 2021) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 139 | GRACE | 0.8953
±0.0035 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 159 | CCA-SSG | 0.8896
±0.0013 best reported | best at pub: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) best today: Str-GCL: Structural Commonsense Driven Graph Contrastive Learning (WWW 2025) |
| 179 | MVGRL | 0.8861
±0.0064 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 183 | HAT-GAE | 0.8855
±0.0018 | This paper |
| 210 | DGI | 0.8798
±0.0081 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) |
| 225 | HAT-GAE-TC | 0.8769
±0.0026 | This paper |
| 227 | HAT-GAE-HM | 0.8767
±0.0016 | This paper |
| 240 | HAT-GAE-AM | 0.8741
±0.0003 | This paper |
| 239 | InfoGCL | 0.8741
±0.0034 | This paper |
| 262 | GATE | 0.8671
±0.0029 | This paper |
| 264 | GAE | 0.8666
±0.0007 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 320 | MLP | 0.8463 | |
| 377 | GPT-GNN | 0.8336
±0.0015 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | EnGCN | 0.9714
±0.0003 | |
| 2 | SAGN+SLE | 0.9710 | |
| 3 | GAMLP(JK) | 0.9704
±0.0001 | |
| 14 | GraphSAGE | 0.9660 | |
| 36 | HAT-GAE | 0.9606
±0.0010 | This paper |
| 38 | GraphMAE | 0.9601
±0.0008 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Difference within reported uncertainty; not counted as underperformance. |
| 39 | GAT | 0.9600
±0.0010 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Difference within reported uncertainty; not counted as underperformance. |
| 58 | GCN | 0.9530
±0.0010 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Difference within reported uncertainty; not counted as underperformance. |
| 63 | CCA-SSG | 0.9511
±0.0018 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Improvement within reported uncertainty; not highlighted. |
| 64 | GATE | 0.9510
±0.0031 | This paper |
| 68 | GRACE | 0.9501
±0.0036 | prev best: Relational Self-Supervised Learning on Graphs (2022) Improvement within reported uncertainty; not highlighted. |
| 74 | BGRL | 0.9490
±0.0400 best reported | best at pub: Relational Self-Supervised Learning on Graphs (2022) Difference within reported uncertainty; not counted as underperformance. |
| 79 | MVGRL | 0.9421
±0.0010 | This paper |
| 82 | DGI | 0.9414
±0.0003 best reported | best at pub: Calibrating and Improving Graph Contrastive Learning (TMLR 2021) |
| 95 | InfoGCL | 0.9356
±0.0033 | This paper |
| 98 | GPT-GNN | 0.9351
±0.0020 | This paper |
| 117 | GAE | 0.9027
±0.0022 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 58 | MLP | 0.9597
±0.0007 | |
| 69 | BGRL | 0.9580
±0.0040 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| 77 | GRACE | 0.9574
±0.0006 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 106 | CCA-SSG | 0.9559
±0.0007 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 109 | HAT-GAE | 0.9557
±0.0021 | This paper |
| 117 | GraphMAE | 0.9550
±0.0010 best reported | best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 125 | MVGRL | 0.9544
±0.0027 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) Improvement within reported uncertainty; not highlighted. |
| 146 | GAE | 0.9520
±0.0010 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 167 | DGI | 0.9489
±0.0009 best reported | |
| 170 | HAT-GAE-TC | 0.9469
±0.0015 | This paper |
| 198 | InfoGCL | 0.9401
±0.0025 | This paper |
| 201 | HAT-GAE-HM | 0.9395
±0.0017 | This paper |
| 216 | GATE | 0.9352
±0.0041 | This paper |
| 225 | HAT-GAE-AM | 0.9328
±0.0003 | This paper |
| 226 | GPT-GNN | 0.9327
±0.0016 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±0.0001 | |
| 2 | GraphCON-GCN | 0.9960 | |
| 3 | GCNII | 0.9953
±0.0001 | |
| 21 | GCN | 0.9850 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) |
| 57 | GAT | 0.9732
±0.0032 | Improvement within reported uncertainty; not highlighted. |
| 92 | GIN | 0.8724
±0.0002 | |
| 109 | GAE | 0.7570 best reported | best at pub: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) |
| 112 | HAT-GAE | 0.7472
±0.0028 | This paper |
| 114 | GraphMAE | 0.7450
±0.0029 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 117 | BGRL | 0.7363
±0.0016 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 119 | CCA-SSG | 0.7334
±0.0017 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 120 | GATE | 0.7325
±0.0018 | This paper |
| 121 | InfoGCL | 0.7314
±0.0010 | This paper |
| 122 | GPT-GNN | 0.7276
±0.0029 | This paper |
| 126 | GRACE | 0.6971
±0.0017 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 136 | MVGRL | 0.6850
±0.0021 | This paper |
| 148 | DGI | 0.6380
±0.0020 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) best today: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 173 | MLP | 0.4620 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 43 | DGI | 0.9221
±0.0029 | prev best: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) Improvement within reported uncertainty; not highlighted. |
| 48 | CCA-SSG | 0.9337
±0.0020 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) |
| 53 | BGRL | 0.9331
±0.0013 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) Difference within reported uncertainty; not counted as underperformance. |
| 62 | HAT-GAE | 0.9317
±0.0025 | This paper |
| 63 | GraphMAE | 0.9313
±0.0015 best reported | best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 69 | GRACE | 0.9301
±0.0003 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) best today: A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning (TMLR 2025) |
| 79 | HAT-GAE-TC | 0.9295
±0.0005 | This paper |
| 88 | MLP | 0.9280
±0.0020 | |
| 95 | GPT-GNN | 0.9271
±0.0009 | This paper |
| 116 | MVGRL | 0.9211
±0.0012 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) Difference within reported uncertainty; not counted as underperformance. |
| 123 | GATE | 0.9204
±0.0011 | This paper |
| 130 | InfoGCL | 0.9189
±0.0024 | This paper |
| 147 | HAT-GAE-HM | 0.9128
±0.0025 | This paper |
| 148 | HAT-GAE-AM | 0.9120
±0.0014 | This paper |
| 163 | GAE | 0.9005
±0.0035 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) Improvement within reported uncertainty; not highlighted. |
