Frequency-Corrupt Based Graph Self-Supervised Learning
Abstract
Graph self-supervised learning (GSSL) alleviates the graph data labeling bottleneck without supervision, enabling wide application in domains like recommendation systems and social network analysis. High-frequency signals are valuable in GSSL for capturing local structural preferences, thereby enriching graph representations and boosting model performance. However, in practical applications, two critical problems hinder the efficient and robust use of these signals. First, the locality of high-frequency signals limits their full utilization by the model. Second, over-reliance on specific high-frequency signals will affect the model's generalization. To address the above problems, we propose the Frequency-Corrupt Based Graph Self-Supervised Learning (FC-GSSL) algorithm. Specifically, we generate corrupted graphs biased toward high-frequency signals by corrupting nodes and edges according to their low-frequency contributions. These corrupted graphs are fed as input to an autoencoder, with low-frequency and general features serving as the supervision. This compels the model to effectively fuse high- and low-frequency signals, thereby integrating and utilizing more valuable high-frequency information. Additionally, we design multiple sampling strategies and form diverse corrupted graphs based on the intersections and union between the results obtained from these strategies. By aligning the node representations from these views, the model can identify valuable frequency combinations, which helps reduce the negative impact of specific high-frequency components and improve generalization. FC-GSSL optimizes the design of GSSL for web applications, significantly improving model performance on complex web-related graphs, such as social networks and citation networks. This work makes a direct contribution to advancing the "Graph Algorithms and Modeling for the Web" research track. Experimental results on 14 datasets across multiple tasks illustrate the superiority of the proposed approach.
Benchmark Results
Tested on 6 datasets 11 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 18 | FC-GSSL | 0.4194
±0.0092 | This paper |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 77 | GraphPAE | 0.3855
±0.0135 | This paper |
| 242 | Sp^2GCL | 0.3470
±0.0092 | This paper |
| 247 | MVGRL | 0.3464
±0.0020 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 252 | GraphMAE2 | 0.3448
±0.0026 | This paper |
| 280 | MaskGAE | 0.3344
±0.0034 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 283 | AUG-MAE | 0.3342
±0.0038 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 299 | GraphMAE | 0.3215
±0.0133 | prev best: Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models (NeurIPS 2024) |
| 309 | VGAE | 0.3157
±0.0075 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 335 | DGI | 0.3067
±0.0063 best reported | best at pub: Toward General Digraph Contrastive Learning: A Dual Spatial Perspective (2025) |
| 356 | BGRL | 0.2986 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 400 | CCA-SSG | 0.2782
±0.0060 best reported | best at pub: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 420 | S2GAE | 0.2617
±0.0038 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 5 | FC-GSSL | 0.8231
±0.0051 | This paper |
| 6 | GraphPAE | 0.8051
±0.0125 | This paper |
| 16 | GraphMAE | 0.7950
±0.0057 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 20 | GraphMAE2 | 0.7913
±0.0019 | This paper |
| 22 | Sp^2GCL | 0.7888
±0.0104 | This paper |
| 27 | CCA-SSG | 0.7500
±0.0075 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 30 | MaskGAE | 0.7450
±0.0087 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 34 | MVGRL | 0.7319
±0.0042 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 37 | AUG-MAE | 0.7219
±0.0155 best reported | best at pub: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 52 | GCN | 0.7033 | |
| 95 | BGRL | 0.6486
±0.0063 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 114 | VGAE | 0.6232
±0.0190 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 134 | DGI | 0.6027
±0.0070 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 135 | S2GAE | 0.6024
±0.0037 | This paper |
| 169 | MLP | 0.5429 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 12 | FC-GSSL | 0.7403
±0.0084 | This paper |
| 17 | GraphPAE | 0.7205
±0.0140 | This paper |
| 20 | GraphMAE2 | 0.7027
±0.0088 | This paper |
| 22 | S2GAE | 0.6860
±0.0056 | This paper |
| 23 | MaskGAE | 0.6853
±0.0044 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 37 | Sp^2GCL | 0.6261
±0.0087 | This paper |
| 38 | AUG-MAE | 0.6257
±0.0067 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 42 | CCA-SSG | 0.6158
±0.0198 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 44 | GraphMAE | 0.6113
±0.0060 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 46 | GCN | 0.6067 | |
| 50 | MVGRL | 0.6009
±0.0044 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 108 | BGRL | 0.4624
±0.0070 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) |
| 141 | VGAE | 0.4250
±0.0135 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 144 | DGI | 0.4222
±0.0063 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) |
| 172 | MLP | 0.3930
±0.0079 |
MoleculeNet
| # | Model | RMSE ↓ | Paper |
|---|---|---|---|
| 1 | SE(3)-I MPPH | 0.3540
±0.0530 | |
| 2 | ECFP-4 + RF | 0.5600
±0.0660 | |
| 3 | GPSE + GPS | 0.6820 | |
| 52 | GraphPAE | 2.0580
±0.1900 best reported | best at pub: Graph Positional Autoencoders as Self-supervised Learners (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 56 | InfoGraph | 2.1040 best reported | best at pub: GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 66 | FC-GSSL | 2.2790
±0.2330 | This paper |
| 69 | GIN | 2.3460
±0.1220 | |
| 70 | AUG-MAE | 2.3950
±0.1580 | This paper |
| 76 | StructMAE | 2.5680
±0.2620 | This paper |
| 83 | GraphMAE | 2.7400
±0.2330 | This paper |
| 92 | GraphMAE2 | 2.9130
±0.2930 | This paper |
| 101 | GraphCL | 3.1660
±0.0270 best reported | |
| 104 | JOAO | 3.2820
±0.0020 best reported | |
| 117 | Sp^2GCL | 4.1440
±0.5730 | This paper |
| 128 | MVGRL | 9.0240
±1.9820 | This paper |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DC-GNN | 0.8669
±0.0022 | |
| 2 | M2M-GNN | 0.8594
±0.0040 | |
| 3 | GloGNN | 0.8574
±0.0042 | |
| 29 | GIN | 0.8268
±0.0032 | |
| 51 | MLP | 0.7534
±0.0064 | |
| 58 | FC-GSSL | 0.7350
±0.0040 | This paper |
| 59 | GraphPAE | 0.7179
±0.0037 | This paper |
| 60 | S2GAE | 0.7024
±0.0009 | This paper |
| 61 | AUG-MAE | 0.6990
±0.0043 | This paper |
| 63 | Sp^2GCL | 0.6880
±0.0045 | This paper |
| 64 | GraphMAE | 0.6797
±0.0021 | This paper |
| 65 | GraphMAE2 | 0.6786
±0.0042 | This paper |
| 66 | MaskGAE | 0.6384
±0.0003 | This paper |
| 67 | CCA-SSG | 0.6346
±0.0036 best reported | best at pub: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 68 | BGRL | 0.6331
±0.0049 | prev best: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 72 | VGAE | 0.5829
±0.0021 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LargeScaleNet | 0.6582
±0.0036 | |
| 2 | S² DirGCN | 0.6495
±0.0033 | |
| 3 | FaberNet | 0.6462
±0.0101 | |
| 31 | GCN | 0.4602
±0.0026 | |
| 38 | BGRL | 0.4302
±0.0062 best reported | best at pub: Simple and Asymmetric Graph Contrastive Learning without Augmentations (NeurIPS 2023) |
| 41 | FC-GSSL | 0.4200
±0.0011 | This paper |
| 42 | GraphPAE | 0.4185
±0.0004 | This paper |
| 43 | CCA-SSG | 0.4078
±0.0001 | prev best: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 45 | MaskGAE | 0.4059
±0.0004 | This paper |
| 46 | S2GAE | 0.4032
±0.0012 | This paper |
| 47 | GraphMAE | 0.4030
±0.0004 | This paper |
| 50 | Sp^2GCL | 0.3909
±0.0002 | This paper |
| 51 | GraphMAE2 | 0.3897
±0.0003 | This paper |
| 55 | AUG-MAE | 0.3710
±0.0013 | This paper |
| 56 | MLP | 0.3670
±0.0021 |
