Decoupled Self-supervised Learning for Non-Homophilou Graphs
Abstract
This paper studies the problem of conducting self-supervised learning for node representation learning on graphs. Most existing self-supervised learning methods assume the graph is homophilous, where linked nodes often belong to the same class or have similar features. However, such assumptions of homophily do not always hold in real-world graphs. We address this problem by developing a decoupled self-supervised learning (DSSL) framework for graph neural networks. DSSL imitates a generative process of nodes and links from latent variable modeling of the semantic structure, which decouples different underlying semantics between different neighborhoods into the self-supervised learning process. Our DSSL framework is agnostic to the encoders and does not need prefabricated augmentations, thus is flexible to different graphs. To effectively optimize the framework, we derive the evidence lower bound of the self-supervised objective and develop a scalable training algorithm with variational inference. We provide a theoretical analysis to justify that DSSL enjoys the better downstream performance. Extensive experiments on various types of graph benchmarks demonstrate that our proposed framework can achieve better performance compared with competitive baselines.
Benchmark Results
Tested on 7 datasets 11 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 | |
| 156 | MVGRL | 0.8680
±0.0050 best reported | best at pub: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) Difference within reported uncertainty; not counted as underperformance. |
| 177 | DGI | 0.8630
±0.0020 best reported | best at pub: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 278 | GraphCL | 0.8428
±0.0091 | prev best: Rethinking the Promotion Brought by Contrastive Learning to Semi-Supervised Node Classification (IJCAI 2020) |
| 423 | DSSL | 0.8306
±0.0053 | This paper |
| 435 | DeepWalk | 0.8290 best reported | best at pub: Graph Representation Learning: A Survey (2019) |
| 630 | VGAE | 0.8059
±0.0035 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 654 | GAE | 0.8011
±0.0022 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 697 | LINE | 0.7893
±0.0055 | prev best: Graph Representation Learning: A Survey (2019) |
| 724 | MLP | 0.7768 | |
| 913 | struc2vec | 0.3026
±0.0152 | This paper |
| # | 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 | |
| 66 | DGI | 0.7890
±0.0020 best reported | best at pub: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 87 | MVGRL | 0.7808
±0.0006 best reported | |
| 350 | MLP | 0.7289
±0.0010 | |
| 395 | GraphCL | 0.7246
±0.0179 | prev best: Contrastive Laplacian Eigenmaps (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 625 | VGAE | 0.6990
±0.0057 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 664 | LINE | 0.6879
±0.0041 | This paper |
| 692 | DeepWalk | 0.6785
±0.0079 | |
| 739 | GAE | 0.6639
±0.0024 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) Improvement within reported uncertainty; not highlighted. |
| 860 | struc2vec | 0.5338
±0.0062 | This paper |
| # | 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 | |
| 144 | BGRL | 0.8134
±0.0050 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: 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 | |
| 223 | DeepWalk | 0.8652
±0.0012 best reported | |
| 299 | VGAE | 0.8133
±0.0069 | |
| 303 | DSSL | 0.8298
±0.0049 | This paper |
| 304 | GAE | 0.7828
±0.0077 | prev best: Graph Masked Autoencoders with Transformers (2022) Improvement within reported uncertainty; not highlighted. |
| 331 | GraphCL | 0.8196
±0.0073 | prev best: Rethinking the Promotion Brought by Contrastive Learning to Semi-Supervised Node Classification (IJCAI 2020) |
| 401 | LINE | 0.8056
±0.0092 | This paper |
| 881 | struc2vec | 0.4083
±0.0185 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 304 | DGI | 0.5853
±0.0298 | prev best: Graph Representation Learning via Aggregation Enhancement (2022) best today: Adaptive Graph Mixture of Residual Experts: Unsupervised Learning on Diverse Graphs with Heterogeneous Specialization (2025) Improvement within reported uncertainty; not highlighted. |
| 351 | MVGRL | 0.7301
±0.0552 best reported | |
| 359 | DSSL | 0.7273
±0.0402 best reported | |
| 409 | BGRL | 0.6841
±0.0501 best reported | |
| 523 | VGAE | 0.5027
±0.0221 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) best today: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 526 | GAE | 0.5909
±0.1626 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) best today: Multi-View Graph Representation Learning Beyond Homophily (2023) Difference within reported uncertainty; not counted as underperformance. |
| 585 | struc2vec | 0.4931
±0.0322 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 588 | LINE | 0.4869
±0.0139 | This paper |
| 589 | GraphCL | 0.4867
±0.0437 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 595 | DeepWalk | 0.4231
±0.0221 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 24 | MLP | 0.9136
±0.0070 | |
| 138 | SAGE | 0.8269 | |
| 289 | DSSL | 0.6928
±0.0601 best reported | |
| 340 | MVGRL | 0.6430 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 350 | DGI | 0.6335 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 354 | GAE | 0.6309
±0.0987 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) best today: Multi-View Graph Representation Learning Beyond Homophily (2023) |
| 386 | VGAE | 0.5919 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 415 | BGRL | 0.5730 best reported | |
| 500 | DeepWalk | 0.4155
±0.0312 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 513 | GraphCL | 0.4722
±0.0450 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 538 | LINE | 0.4368
±0.0217 | This paper |
| 571 | struc2vec | 0.3022
±0.0587 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
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 | |
| 68 | BGRL | 0.6331
±0.0049 best reported | best today: Frequency-Corrupt Based Graph Self-Supervised Learning (WWW 2026) |
| 69 | DSSL | 0.6038
±0.0032 | This paper |
| 71 | GraphCL | 0.5843
±0.0031 | This paper |
| 72 | VGAE | 0.5829
±0.0021 | This paper |
| 73 | GAE | 0.5811
±0.0018 | This paper |
| 74 | LINE | 0.5759
±0.0017 | This paper |
| 75 | MVGRL | 0.5722
±0.0017 | This paper |
| 76 | DeepWalk | 0.5613
±0.0046 | This paper |
| 77 | DGI | 0.5368
±0.0019 | This paper |
| 78 | struc2vec | 0.5029
±0.0031 | This paper |
