Topology Reorganized Graph Contrastive Learning with Mitigating Semantic Drift
Abstract
Graph contrastive learning (GCL) is an effective paradigm for node representation learning in graphs. The key components hidden behind GCL are data augmentation and positive-negative pair selection. Typical data augmentations in GCL, such as uniform deletion of edges, are generally blind and resort to local perturbation, which is prone to producing under-diversity views. Additionally, there is a risk of making the augmented data traverse to other classes. Moreover, most methods always treat all other samples as negatives. Such a negative pairing naturally results in sampling bias and likewise may make the learned representation suffer from semantic drift. Therefore, to increase the diversity of the contrastive view, we propose two simple and effective global topological augmentations to compensate current GCL. One is to mine the semantic correlation between nodes in the feature space. The other is to utilize the algebraic properties of the adjacency matrix to characterize the topology by eigen-decomposition. With the help of both, we can retain important edges to build a better view. To reduce the risk of semantic drift, a prototype-based negative pair selection is further designed which can filter false negative samples. Extensive experiments on various tasks demonstrate the advantages of the model compared to the state-of-the-art methods.
Benchmark Results
Tested on 4 datasets 19 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 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) |
| 73 | GMI | 0.7869
±0.0016 best reported | |
| 87 | MVGRL | 0.7808
±0.0006 best reported | |
| 201 | GRACE | 0.7450
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 225 | GraphTP-T | 0.7410
±0.0020 | This paper |
| 240 | GraphTP-F | 0.7380
±0.0030 | This paper |
| 340 | COSTA_MV | 0.7290
±0.0030 | This paper |
| 350 | MLP | 0.7289
±0.0010 | |
| 354 | COSTA_SV | 0.7280
±0.0030 | This paper |
| 427 | HomoGCL | 0.7230
±0.0070 | This paper |
| 505 | GCA | 0.7150
±0.0030 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) Improvement within reported uncertainty; not highlighted. |
| 640 | GBT | 0.6940
±0.0050 | This paper |
| 692 | DeepWalk | 0.6785
±0.0079 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 709 | Raw features | 0.6730 best reported | best at pub: UGSL: A Unified Framework for Benchmarking Graph Structure Learning (2023) |
| # | 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 | |
| 122 | GraphTP-T | 0.9372
±0.0014 | This paper |
| 125 | GraphTP-F | 0.9369
±0.0013 | This paper |
| 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) |
| 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: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 213 | DGI | 0.9309
±0.0008 best reported | |
| 222 | HomoGCL | 0.9300
±0.0020 best reported | best at pub: HomoGCL: Rethinking Homophily in Graph Contrastive Learning (KDD 2023) best today: Multiplex Graph Contrastive Learning with Soft Negatives (2024) Difference within reported uncertainty; not counted as underperformance. |
| 235 | GBT | 0.9282
±0.0040 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Str-GCL: Structural Commonsense Driven Graph Contrastive Learning (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 276 | COSTA_MV | 0.9256
±0.0045 | This paper |
| 309 | COSTA_SV | 0.9230
±0.0025 | This paper |
| 390 | MLP | 0.9128
±0.0063 | |
| 408 | GMI | 0.9081
±0.0015 best reported | best at pub: Localized Graph Contrastive Learning (2022) best today: Energy-Balanced Hyperspherical Graph Representation Learning via Structural Binding and Entropic Dispersion (2025) Difference within reported uncertainty; not counted as underperformance. |
| 444 | DeepWalk | 0.9005
±0.0008 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 531 | Raw features | 0.7999
±0.0090 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Model-Driven Graph Contrastive Learning (2025) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 109 | GraphTP-F | 0.8993
±0.0014 | This paper |
| 137 | GraphTP-T | 0.8954
±0.0018 | 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) |
| 157 | HomoGCL | 0.8900
±0.0010 best reported | best at pub: HomoGCL: Rethinking Homophily in Graph Contrastive Learning (KDD 2023) best today: Multiplex Graph Contrastive Learning with Soft Negatives (2024) |
| 160 | GCA | 0.8894
±0.0015 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 165 | GBT | 0.8885
±0.0025 best reported | best at pub: Rethinking and Scaling Up Graph Contrastive Learning: An Extremely Efficient Approach with Group Discrimination (NeurIPS 2022) best today: Str-GCL: Structural Commonsense Driven Graph Contrastive Learning (WWW 2025) |
| 179 | MVGRL | 0.8861
±0.0064 best reported | best at pub: Training MLPs on Graphs without Supervision (2024) |
| 194 | COSTA_MV | 0.8832
±0.0003 | This paper |
| 198 | COSTA_SV | 0.8826
±0.0003 | This paper |
| 210 | DGI | 0.8798
±0.0081 best reported | best at pub: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) best today: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) |
| 278 | DeepWalk | 0.8628
±0.0007 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 320 | MLP | 0.8463 | |
| 342 | GMI | 0.8422
±0.0052 best reported | best at pub: Localized Graph Contrastive Learning (2022) |
| 456 | Raw features | 0.7381 | This paper |
| # | 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) |
| 30 | GraphTP-F | 0.9381
±0.0002 | This paper |
| 43 | DGI | 0.9350
±0.0030 best reported | best at pub: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) |
| 51 | GCA | 0.9332
±0.0012 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 55 | GraphTP-T | 0.9330
±0.0001 | This paper |
| 69 | GRACE | 0.9295
±0.0003 | prev best: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) best today: A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning (TMLR 2025) Improvement within reported uncertainty; not highlighted. |
| 74 | GBT | 0.9295
±0.0017 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) Difference within reported uncertainty; not counted as underperformance. |
| 75 | COSTA_SV | 0.9295
±0.0012 | This paper |
| 81 | COSTA_MV | 0.9294
±0.0010 | This paper |
| 88 | MLP | 0.9280
±0.0020 | |
| 94 | HomoGCL | 0.9274
±0.0022 best reported | best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 116 | MVGRL | 0.9211
±0.0012 | This paper |
| 152 | GMI | 0.9108
±0.0056 | prev best: Eliciting Structural and Semantic Global Knowledge in Unsupervised Graph Contrastive Learning (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 158 | Raw features | 0.9040 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) |
| 188 | DeepWalk | 0.8461
±0.0022 | This paper |
