Revisiting Graph Autoencoders as Implicit Contrastive Learners
Abstract
Graph autoencoders (GAEs) and graph contrastive learning (GCL) are two major paradigms for self-supervised representation learning on graphs, yet they are often studied in isolation and treated as fundamentally different approaches. In this work, we revisit GAEs through the lens of contrastive learning and show that both structure-based and feature-based GAEs can be conceptualized as implicitly graph contrastive learners. This perspective reveals that many existing GAEs differ primarily in how contrastive views are constructed, rather than in their learning objectives or architectures. Building on this insight, we introduce a unified formulation that highlights contrastive view design as a central and previously less explored dimension in GAEs. In particular, we identify asymmetric contrastive views, arising from mismatches in subgraph views, as an important yet underexplored design axis in prior GAE research. We formalize this insight within a unified framework and conduct systematic experiments on representative graph learning tasks to examine its impact on performance and efficiency. Our results show that interpreting GAEs as implicit contrastive learners offers a clearer understanding of existing models and provides practical guidance for designing effective and scalable graph autoencoders.
Benchmark Results
Tested on 9 datasets 21 baseline values reported too low Non-standard metric on 3 datasets
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 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 151 | lrGAE 6 | 0.9350
±0.0030 | This paper |
| 150 | GiGaMAE | 0.9350
±0.0050 | This paper |
| 161 | MaskGAE | 0.9342
±0.0026 best reported | |
| 164 | GraphMAE | 0.9341
±0.0010 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) Difference within reported uncertainty; not counted as underperformance. |
| 167 | lrGAE 7 | 0.9340
±0.0050 | This paper |
| 166 | S3GCL | 0.9340
±0.0020 | This paper |
| 165 | AUG-MAE | 0.9340
±0.0080 | This paper |
| 172 | BGRL | 0.9337
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 186 | CCA-SSG | 0.9325
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 193 | lrGAE 8 | 0.9320
±0.0040 | This paper |
| 192 | GraphMAE2 | 0.9320
±0.0050 | This paper |
| 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) |
| 208 | S2GAE | 0.9310
±0.0030 | This paper |
| 213 | DGI | 0.9309
±0.0008 best reported | |
| 229 | GGD | 0.9290
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 236 | SEEGERA | 0.9281
±0.0045 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 342 | EPAGCL | 0.9200
±0.0030 | 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 | |
| 529 | GAE_f | 0.8010
±0.0020 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 | |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 57 | S2GAE | 0.9094
±0.0008 best reported | best at pub: HC-GAE: The Hierarchical Cluster-based Graph Auto-Encoder for Graph Representation Learning (NeurIPS 2024) |
| 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) |
| 85 | GiGaMAE | 0.9020
±0.0045 best reported | best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 93 | GGD | 0.9010
±0.0090 best reported | best at pub: Rethinking and Scaling Up Graph Contrastive Learning: An Extremely Efficient Approach with Group Discrimination (NeurIPS 2022) |
| 98 | AUG-MAE | 0.9008
±0.0012 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 100 | GraphMAE | 0.9002
±0.0024 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 111 | GraphMAE2 | 0.8990
±0.0030 best reported | best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 117 | lrGAE 7 | 0.8980
±0.0020 | This paper |
| 124 | lrGAE 8 | 0.8970
±0.0030 | This paper |
| 132 | S3GCL | 0.8960
±0.0020 | This paper |
| 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) |
| 140 | MaskGAE | 0.8950
±0.0010 | This paper |
| 153 | lrGAE 6 | 0.8910
±0.0030 | This paper |
| 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) |
| 189 | SEEGERA | 0.8839
±0.0026 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 210 | DGI | 0.8798
±0.0081 best reported | best at pub: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) |
| 264 | GAE | 0.8666
±0.0007 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 274 | EPAGCL | 0.8640
±0.0040 | This paper |
| 320 | MLP | 0.8463 | |
| 470 | GAE_f | 0.7090
±0.0030 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 9 | GCN | 0.9774
±0.0035 | |
| 58 | MLP | 0.9597
±0.0007 | |
| 71 | lrGAE 8 | 0.9580
±0.0010 | This paper |
| 69 | BGRL | 0.9580
±0.0040 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 77 | GRACE | 0.9574
±0.0006 best reported | best at pub: Building Shortcuts between Distant Nodes with Biaffine Mapping for Graph Convolutional Networks (2023) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 87 | lrGAE 7 | 0.9570
±0.0020 | This paper |
| 101 | MaskGAE | 0.9560
±0.0020 | This paper |
| 106 | CCA-SSG | 0.9559
±0.0007 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 117 | GraphMAE | 0.9550
±0.0010 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 118 | GraphMAE2 | 0.9550
±0.0020 best reported | best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 119 | S2GAE | 0.9550
±0.0020 | This paper |
| 127 | lrGAE 6 | 0.9540
±0.0010 | This paper |
| 139 | S3GCL | 0.9530
±0.0030 | This paper |
| 147 | EPAGCL | 0.9520
±0.0020 | This paper |
| 148 | SEEGERA | 0.9520
±0.0010 | This paper |
| 146 | GAE | 0.9520
±0.0010 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 159 | GGD | 0.9500
±0.0040 | This paper |
| 167 | DGI | 0.9480
±0.0020 | prev best: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 280 | GAE_f | 0.5560
±0.0070 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 137 | GRACE | 0.9065
±0.0081 best reported | best at pub: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) |
| 147 | lrGAE 7 | 0.9050
±0.0080 | This paper |
| 148 | lrGAE (7) | 0.9050
±0.0080 | This paper |
| 203 | lrGAE 6 | 0.8990
±0.0040 | This paper |
| 210 | AUG-MAE | 0.8980
±0.0130 | prev best: Rethinking Graph Masked Autoencoders through Alignment and Uniformity (AAAI 2024) |
| 218 | EPAGCL | 0.8970
±0.0130 | This paper |
| 226 | GraphMAE2 | 0.8950
±0.0150 | prev best: UGMAE: A Unified Framework for Graph Masked Autoencoders (2024) |
| 231 | CCA-SSG | 0.8950
±0.0070 | This paper |
| 228 | GAE | 0.8950
±0.0150 | prev best: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) |
| 243 | BGRL | 0.8940
±0.0100 | prev best: Smoothed Graph Contrastive Learning via Seamless Proximity Integration (2024) |
| 260 | lrGAE 8 | 0.8930
±0.0070 | This paper |
| 258 | GraphMAE | 0.8930
±0.0110 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) |
| 266 | S2GAE | 0.8927
±0.0153 best reported | best at pub: Generative and Contrastive Paradigms Are Complementary for Graph Self-Supervised Learning (2023) best today: Explainable Graph Representation Learning via Graph Pattern Analysis (IJCAI 2025) |
| 282 | SEEGERA | 0.8890
±0.0120 | This paper |
| 304 | MaskGAE | 0.8860
±0.0060 | This paper |
| 394 | GAE_f | 0.8700
±0.0120 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 406 | S3GCL | 0.8650
±0.0090 | This paper |
| 440 | GGD | 0.8540
±0.0030 | This paper |
| 517 | DGI | 0.8320
±0.0130 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 112 | S2GAE | 0.8237
±0.0224 best reported | best at pub: Generative and Contrastive Paradigms Are Complementary for Graph Self-Supervised Learning (2023) best today: Explainable Graph Representation Learning via Graph Pattern Analysis (IJCAI 2025) |
| 116 | GraphMAE2 | 0.8230
±0.0090 | prev best: UGMAE: A Unified Framework for Graph Masked Autoencoders (2024) |
| 121 | MaskGAE | 0.8220
±0.0040 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 150 | lrGAE 6 | 0.8150
±0.0060 | This paper |
| 156 | lrGAE 7 | 0.8140
±0.0040 | This paper |
| 171 | lrGAE 8 | 0.8120
±0.0070 | This paper |
| 194 | EPAGCL | 0.8050
±0.0040 | This paper |
| 200 | GraphMAE | 0.8042
±0.0035 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations (2025) Difference within reported uncertainty; not counted as underperformance. |
| 236 | GAE | 0.7978
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 243 | S3GCL | 0.7960
±0.0050 | This paper |
| 251 | BGRL | 0.7940
±0.0060 | This paper |
| 275 | CCA-SSG | 0.7880
±0.0050 | This paper |
| 276 | AUG-MAE | 0.7880
±0.0120 | This paper |
| 334 | SEEGERA | 0.7760
±0.0120 | This paper |
| 351 | GRACE | 0.7720
±0.0150 | prev best: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) Improvement within reported uncertainty; not highlighted. |
| 374 | GGD | 0.7650
±0.0030 | This paper |
| 388 | DGI | 0.7620
±0.0180 | This paper |
| 422 | GAE_f | 0.7450
±0.0130 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 10 | GraphMAE2 | 0.8170
±0.0080 | prev best: UGMAE: A Unified Framework for Graph Masked Autoencoders (2024) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 22 | GraphMAE | 0.8270
±0.0100 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) |
| 23 | GCN | 0.8260
±0.0220 | |
| 27 | S2GAE | 0.8220
±0.0040 | |
| 28 | lrGAE 6 | 0.8230
±0.0070 | This paper |
| 29 | lrGAE 7 | 0.8230
±0.0040 | This paper |
| 31 | lrGAE 8 | 0.8220
±0.0020 | This paper |
| 35 | MaskGAE | 0.8200
±0.0050 | This paper |
| 48 | BGRL | 0.8150
±0.0070 | This paper |
| 89 | SEEGERA | 0.8080
±0.0060 | This paper |
| 91 | GAE | 0.8078
±0.0012 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 95 | S3GCL | 0.8070
±0.0140 | This paper |
| 103 | AUG-MAE | 0.8050
±0.0050 best reported | best at pub: Rethinking Graph Masked Autoencoders through Alignment and Uniformity (AAAI 2024) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 141 | GRACE | 0.7960
±0.0130 | prev best: Unifying Graph Contrastive Learning via Graph Message Augmentation (2024) |
| 147 | CCA-SSG | 0.7940
±0.0060 | This paper |
| 148 | EPAGCL | 0.7940
±0.0130 | This paper |
| 151 | MLP | 0.7920
±0.0240 | |
| 212 | GAE_f | 0.7690
±0.0150 | This paper |
| 224 | GGD | 0.7630
±0.0120 | This paper |
| 295 | DGI | 0.7070
±0.0140 | This paper |
Heterogeneous Graph Benchmarks
DBLP
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | HG-SCM | 0.9490
±0.0015 | |
| 2 | SeHGNN | 0.9489
±0.0018 | |
| 3 | AdvSynGNN | 0.9486
±0.0012 | |
| 4 | S2GAE | 0.9480
±0.0040 | This paper |
| 5 | lrGAE 7 | 0.9460
±0.0030 | This paper |
| 7 | lrGAE 6 | 0.9440
±0.0020 | This paper |
| 8 | lrGAE 8 | 0.9430
±0.0020 | This paper |
| 9 | SHGN | 0.9420
±0.0031 | This paper |
| 10 | MaskGAE | 0.9420
±0.0020 | This paper |
| 11 | GAE | 0.9410
±0.0030 | prev best: Deep Graph Contrastive Representation Learning (2020) |
| 15 | HGT | 0.9349
±0.0025 | This paper |
| 19 | RGCN | 0.9207
±0.0050 | This paper |
| 20 | HAN | 0.9205
±0.0062 | This paper |
| 36 | GCN | 0.8758
±0.0020 | |
| 65 | MLP | 0.8118
±0.0020 |
ACM
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | SignGT | 0.9545
±0.0049 | |
| 2 | NodeFormer | 0.9493
±0.0035 | |
| 3 | FAGCN | 0.9487
±0.0059 | |
| 8 | lrGAE 8 | 0.9410
±0.0010 | This paper |
| 11 | lrGAE 7 | 0.9400
±0.0030 | This paper |
| 13 | S2GAE | 0.9380
±0.0070 | This paper |
| 15 | MaskGAE | 0.9370
±0.0020 | This paper |
| 18 | lrGAE 6 | 0.9350
±0.0040 | This paper |
| 20 | SHGN | 0.9335
±0.0045 | This paper |
| 24 | GAE | 0.9330
±0.0050 | This paper |
| 34 | GCN | 0.9233
±0.0038 | |
| 35 | HAN | 0.9220
±0.0020 best reported | best at pub: Scalable Graph Neural Networks for Heterogeneous Graphs (2020) |
| 36 | HGT | 0.9190
±0.0030 best reported | best at pub: Scalable Graph Neural Networks for Heterogeneous Graphs (2020) Difference within reported uncertainty; not counted as underperformance. |
| 38 | RGCN | 0.9175
±0.0035 | prev best: Towards Human-like Perception: Learning Structural Causal Model in Heterogeneous Graph (2023) Improvement within reported uncertainty; not highlighted. |
IMDB
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | BERT-Base, Uncased | 0.9190 | |
| 2 | TAGs (70b) | 0.7157
±0.0042 | |
| 3 | UniMP | 0.6998
±0.0058 | |
| 4 | GIN | 0.6759
±0.0041 | |
| 5 | SHGN | 0.6736
±0.0057 | This paper |
| 7 | HGT | 0.6720
±0.0057 | This paper |
| 9 | lrGAE 8 | 0.6630
±0.0040 | This paper |
| 10 | lrGAE 6 | 0.6600
±0.0050 | This paper |
| 12 | MaskGAE | 0.6590
±0.0070 | This paper |
| 13 | S2GAE | 0.6570
±0.0050 | This paper |
| 14 | GAE | 0.6540
±0.0020 | This paper |
| 15 | RGCN | 0.6521
±0.0073 | |
| 16 | lrGAE 7 | 0.6520
±0.0060 | This paper |
| 19 | HAN | 0.6463
±0.0058 | This paper |
