Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations
Abstract
We present LaplaceGNN, a novel self-supervised graph learning framework that bypasses the need for negative sampling by leveraging spectral bootstrapping techniques. Our method integrates Laplacian-based signals into the learning process, allowing the model to effectively capture rich structural representations without relying on contrastive objectives or handcrafted augmentations. By focusing on positive alignment, LaplaceGNN achieves linear scaling while offering a simpler, more efficient, self-supervised alternative for graph neural networks, applicable across diverse domains. Our contributions are twofold: we precompute spectral augmentations through max-min centrality-guided optimization, enabling rich structural supervision without relying on handcrafted augmentations, then we integrate an adversarial bootstrapped training scheme that further strengthens feature learning and robustness. Our extensive experiments on different benchmark datasets show that LaplaceGNN achieves superior performance compared to state-of-the-art self-supervised graph methods, offering a promising direction for efficiently learning expressive graph representations.
Benchmark Results
Tested on 8 datasets 13 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 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 22 | LaplaceGNN | 0.9570
±0.0015 | This paper |
| 164 | GraphMAE | 0.9341
±0.0010 best reported | best at pub: 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) Difference within reported uncertainty; not counted as underperformance. |
| 184 | Supervised GCN | 0.9328
±0.0003 best reported | best at pub: Perfect Alignment May be Poisonous to Graph Contrastive Learning (ICML 2023) |
| 189 | Sp^2GCL | 0.9323
±0.0026 | This paper |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learn Beneficial Noise as Graph Augmentation (ICML 2025) Difference within reported uncertainty; not counted as underperformance. |
| 269 | SSGE | 0.9261
±0.0022 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | 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 | |
| 19 | LaplaceGNN | 0.9230
±0.0023 | This paper |
| 79 | BGRL | 0.9034
±0.0019 | This paper |
| 96 | Sp^2GCL | 0.9009
±0.0032 | This paper |
| 100 | GraphMAE | 0.9002
±0.0024 best reported | best at pub: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 139 | GRACE | 0.8953
±0.0035 | This paper |
| 154 | SSGE | 0.8905
±0.0058 | This paper |
| 205 | Supervised GCN | 0.8811
±0.0014 best reported | best at pub: Perfect Alignment May be Poisonous to Graph Contrastive Learning (ICML 2023) |
| 320 | MLP | 0.8463 |
| # | 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 | |
| 36 | LaplaceGNN | 0.9672
±0.0011 | This paper |
| 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. |
| 91 | Supervised GCN | 0.9565
±0.0016 | This paper |
| 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) |
| 193 | SSGE | 0.9410
±0.0021 | This paper |
| 206 | Sp^2GCL | 0.9377
±0.0025 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 | |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 60 | LaplaceGNN | 0.8234
±0.0038 | This paper |
| 84 | GraphMAE | 0.8052
±0.0032 best reported | best at pub: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 94 | GRACE | 0.8014
±0.0048 | This paper |
| 100 | BGRL | 0.8000
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) Difference within reported uncertainty; not counted as underperformance. |
| 114 | Sp^2GCL | 0.7942
±0.0019 | This paper |
| 128 | SSGE | 0.7919
±0.0057 | prev best: Negative-Free Self-Supervised Gaussian Embedding of Graphs (2024) Improvement within reported uncertainty; not highlighted. |
| 203 | Supervised GCN | 0.7719
±0.0012 | This paper |
| 237 | MLP | 0.7469
±0.0085 |
| # | 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 | |
| 15 | LaplaceGNN | 0.9486
±0.0016 | This paper |
| 45 | SSGE | 0.9346
±0.0045 best reported | best at pub: Negative-Free Self-Supervised Gaussian Embedding of Graphs (2024) Difference within reported uncertainty; not counted as underperformance. |
| 53 | BGRL | 0.9331
±0.0013 | This paper |
| 63 | GraphMAE | 0.9313
±0.0015 best reported | best at pub: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 68 | Supervised GCN | 0.9303
±0.0031 | This paper |
| 69 | GRACE | 0.9301
±0.0003 best reported | best at pub: A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning (TMLR 2025) |
| 88 | MLP | 0.9280
±0.0020 | |
| 100 | Sp^2GCL | 0.9261
±0.0024 | 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 | |
| 47 | LaplaceGNN | 0.9285
±0.0074 | This paper |
| 105 | InfoGCL | 0.9120
±0.0130 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 199 | MVGRL | 0.8993
±0.0616 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 257 | InfoGraph | 0.8930
±0.0514 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 258 | GraphMAE | 0.8930
±0.0110 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 325 | AugMAE | 0.8821
±0.0102 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 432 | Supervised GCN | 0.8563
±0.0584 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 120 | LaplaceGNN | 0.8221
±0.0042 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 200 | GraphMAE | 0.8042
±0.0035 | prev best: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) Improvement within reported uncertainty; not highlighted. |
| 214 | Supervised GCN | 0.8021
±0.0202 | This paper |
| 215 | InfoGCL | 0.8020
±0.0060 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 220 | AugMAE | 0.8011
±0.0043 | This paper |
| 338 | InfoGraph | 0.7750
±0.0074 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 356 | MVGRL | 0.7700
±0.0080 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: Graph Self-Supervised Learning with Learnable Structural and Positional Encodings (WWW 2025) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 22 | GraphMAE | 0.8270
±0.0100 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 23 | GCN | 0.8260
±0.0220 | |
| 25 | LaplaceGNN | 0.8241
±0.0042 | This paper |
| 104 | MVGRL | 0.8048
±0.0029 best reported | best at pub: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 108 | AugMAE | 0.8040
±0.0052 | This paper |
| 126 | InfoGCL | 0.8001
±0.0132 | prev best: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 146 | InfoGraph | 0.7940 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 151 | MLP | 0.7920
±0.0240 | |
| 156 | Supervised GCN | 0.7901
±0.0181 | This paper |
