Spectral-Aware Augmentation for Enhanced Graph Representation Learning
Abstract
Graph Contrastive Learning (GCL) has demonstrated remarkable effectiveness in learning representations on graphs in recent years. To generate ideal augmentation views, the augmentation generation methods should preserve essential information while discarding less relevant details for downstream tasks. However, current augmentation methods usually involve random topology corruption in the spatial domain, which fails to adequately address information spread across different frequencies in the spectral domain. Our preliminary study highlights this issue, demonstrating that spatial random perturbations impact all frequency bands almost uniformly. Given that task-relevant information typically resides in specific spectral regions that vary across graphs, this one-size-fits-all approach can pose challenges. We argue that indiscriminate spatial random perturbation might unintentionally weaken task-relevant information, reducing its effectiveness. To tackle this challenge, we propose applying perturbations selectively, focusing on information specific to different frequencies across diverse graphs. In this paper, we present GASSER, a model that applies tailored perturbations to specific frequencies of graph structures in the spectral domain, guided by spectral hints. Through extensive experimentation and theoretical analysis, we demonstrate that the augmentation views generated by GASSER are adaptive, controllable, and intuitively aligned with the homophily ratios and spectrum of graph structures.
Benchmark Results
Tested on 7 datasets 34 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 130 | BGRL | 0.8730
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 134 | GRACE | 0.8720
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 156 | MVGRL | 0.8680
±0.0050 best reported | best at pub: ENGAGE: Explanation Guided Data Augmentation for Graph Representation Learning (2023) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 177 | DGI | 0.8630
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 216 | GASSER | 0.8527
±0.0010 | This paper |
| 217 | CCA-SSG+GASSER | 0.8527
±0.0010 | This paper |
| 248 | CCA-SSG | 0.8460
±0.0070 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 293 | GRACE+GASSER | 0.8410
±0.0026 | This paper |
| 394 | GCL-SPAN | 0.8330
±0.0049 | This paper |
| 414 | AF-GCL | 0.8316
±0.0013 | This paper |
| 415 | GCA | 0.8310
±0.0030 best reported | best at pub: Graph Contrastive Learning with Implicit Augmentations (2022) |
| 643 | MVGRL+GASSER | 0.8036
±0.0005 | This paper |
| 724 | MLP | 0.7768 best reported | best at pub: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 66 | DGI | 0.7890
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 87 | MVGRL | 0.7808
±0.0006 best reported | |
| 136 | BGRL | 0.7600
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 163 | GASSER | 0.7541
±0.0084 | This paper |
| 164 | CCA-SSG+GASSER | 0.7541
±0.0084 | This paper |
| 165 | CCA-SSG | 0.7540
±0.0100 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 201 | GRACE | 0.7450
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 205 | MVGRL+GASSER | 0.7448
±0.0073 | This paper |
| 206 | GRACE+GASSER | 0.7447
±0.0064 | This paper |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 461 | AF-GCL | 0.7196
±0.0042 | This paper |
| 478 | GCL-SPAN | 0.7175
±0.0049 | This paper |
| 505 | GCA | 0.7150
±0.0030 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 136 | CCA-SSG | 0.8840
±0.0060 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 144 | BGRL | 0.8830
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 194 | GRACE | 0.8730
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 196 | MVGRL | 0.8725
±0.0012 best reported | |
| 204 | DGI | 0.8708
±0.0017 best reported | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 243 | GCL-SPAN | 0.8545
±0.0016 best reported | |
| 255 | GCA | 0.8512
±0.0023 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 281 | GRACE+GASSER | 0.8397
±0.0052 | This paper |
| 301 | GASSER | 0.8300
±0.0061 | This paper |
| 302 | CCA-SSG+GASSER | 0.8300
±0.0061 | This paper |
| 346 | AF-GCL | 0.8150
±0.0070 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 387 | MVGRL+GASSER | 0.8080
±0.0019 | This paper |
| # | 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 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 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. |
| 191 | GCA | 0.9320
±0.0060 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 199 | GASSER | 0.9317
±0.0031 | 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) |
| 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) |
| 275 | GCL-SPAN | 0.9258
±0.0017 best reported | |
| 284 | AF-GCL | 0.9249
±0.0031 | This paper |
| 390 | MLP | 0.9128
±0.0063 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 247 | MVGRL | 0.3464
±0.0020 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 251 | GRACE | 0.3450
±0.0110 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 282 | MVGRL+GASSER | 0.3342
±0.0014 | This paper |
| 311 | GASSER | 0.3147
±0.0004 | This paper |
| 312 | CCA-SSG+GASSER | 0.3147
±0.0004 | This paper |
| 335 | DGI | 0.3067
±0.0063 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Toward General Digraph Contrastive Learning: A Dual Spatial Perspective (2025) |
| 340 | GRACE+GASSER | 0.3037
±0.0048 | This paper |
| 356 | BGRL | 0.2986 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 357 | GCL-SPAN | 0.2982
±0.0010 | This paper |
| 361 | GCA | 0.2965 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 375 | AF-GCL | 0.2894
±0.0069 | This paper |
| 400 | CCA-SSG | 0.2782
±0.0060 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 27 | CCA-SSG | 0.7500
±0.0075 best reported | best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 34 | MVGRL | 0.7319
±0.0042 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 52 | GCN | 0.6796
±0.0182 | prev best: Non-Local Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 74 | GASSER | 0.6723
±0.0178 | This paper |
| 75 | CCA-SSG+GASSER | 0.6723
±0.0178 | This paper |
| 89 | AF-GCL | 0.6528
±0.0053 | This paper |
| 95 | BGRL | 0.6486
±0.0063 | This paper |
| 105 | GCA | 0.6366
±0.0032 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 109 | GCL-SPAN | 0.6294
±0.0066 | This paper |
| 119 | GRACE | 0.6124
±0.0053 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 134 | DGI | 0.6027
±0.0070 | This paper |
| 157 | MVGRL+GASSER | 0.5658
±0.0041 | This paper |
| 169 | MLP | 0.5429 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 178 | GRACE+GASSER | 0.5248
±0.0013 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 42 | CCA-SSG | 0.6158
±0.0198 best reported | best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 46 | GCN | 0.6067 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 50 | MVGRL | 0.6009
±0.0044 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 83 | AF-GCL | 0.5210
±0.0067 | This paper |
| 89 | GASSER | 0.5034
±0.0056 | This paper |
| 90 | CCA-SSG+GASSER | 0.5034
±0.0056 | This paper |
| 98 | GCA | 0.4222
±0.0090 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Improvement within reported uncertainty; not highlighted. |
| 102 | GCL-SPAN | 0.4723
±0.0131 | This paper |
| 108 | BGRL | 0.4624
±0.0070 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 144 | DGI | 0.4222
±0.0063 | This paper |
| 154 | GRACE | 0.4109
±0.0085 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 157 | MVGRL+GASSER | 0.4079
±0.0029 | This paper |
| 172 | MLP | 0.3930
±0.0079 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 198 | GRACE+GASSER | 0.3689
±0.0082 | This paper |
