Rethinking Semi-Supervised Node Classification with Self-Supervised Graph Clustering
Abstract
The emergence of graph neural networks (GNNs) has offered a powerful tool for semi-supervised node classification tasks. Subsequent studies have achieved further improvements through refining the message passing schemes in GNN models or exploiting various data augmentation techniques to mitigate limited supervision. In real graphs, nodes often tend to form tightly-knit communities/clusters, which embody abundant signals for compensating label scarcity in semi-supervised node classification but are not explored in prior methods. Inspired by this, this paper presents NCGC that integrates self-supervised graph clustering and semi-supervised classification into a unified framework. Firstly, we theoretically unify the optimization objectives of GNNs and spectral graph clustering, and based on that, develop soft orthogonal GNNs (SOGNs) that leverage a refined message passing paradigm to generate node representations for both classification and clustering. On top of that, NCGC includes a self-supervised graph clustering module that enables the training of SOGNs for learning representations of unlabeled nodes in a self-supervised manner. Particularly, this component comprises two non-trivial clustering objectives and a Sinkhorn-Knopp normalization that transforms predicted cluster assignments into balanced soft pseudo-labels. Through combining the foregoing clustering module with the classification model using a multi-task objective containing the supervised classification loss on labeled data and self-supervised clustering loss on unlabeled data, NCGC promotes synergy between them and achieves enhanced model capacity. Our extensive experiments showcase that the proposed NCGC framework consistently and considerably outperforms popular GNN models and recent baselines for semi-supervised node classification on seven real graphs, when working with various classic GNN backbones.
Benchmark Results
Tested on 5 datasets 47 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: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT* | 0.8897
±0.0014 best reported | |
| 45 | GCNII | 0.8893
±0.0137 best reported | best at pub: Language is All a Graph Needs (2023) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 55 | JKNet | 0.8870 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 70 | DAGNN | 0.8840 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 87 | GRAND | 0.8815 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 108 | APPNP | 0.8787 best reported | best at pub: Orthogonal Graph Neural Networks (AAAI 2021) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 141 | GraphSAGE* | 0.8708
±0.0085 best reported | best at pub: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 162 | GPR-GNN | 0.8670
±0.0103 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 174 | NCGC (GCNII) | 0.8640
±0.0020 | This paper |
| 186 | NormProp | 0.8607 | This paper |
| 223 | SGC | 0.8509
±0.0648 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) Difference within reported uncertainty; not counted as underperformance. |
| 227 | DND-Net | 0.8498
±0.0056 | This paper |
| 257 | Violin | 0.8449
±0.0066 | This paper |
| 307 | GraphMix | 0.8394
±0.0057 best reported | best at pub: GraphMix: Improved Training of GNNs for Semi-Supervised Learning (2019) |
| 486 | Meta-PN | 0.8233
±0.0079 | This paper |
| 501 | GAM | 0.8228
±0.0048 best reported | best at pub: Rethinking Graph Regularization for Graph Neural Networks (AAAI 2020) |
| 526 | PTA | 0.8203
±0.0105 | This paper |
| 587 | MGCN | 0.8123
±0.0043 | prev best: Mixed Graph Contrastive Network for Semi-Supervised Node Classification (2022) Improvement within reported uncertainty; not highlighted. |
| 724 | MLP | 0.7768 | |
| 735 | M3S | 0.7730
±0.0046 | 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 | |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 18 | GCN* | 0.9296
±0.0015 best reported | |
| 20 | GAT* | 0.9233
±0.0018 best reported | |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 109 | GRAND | 0.8902 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 125 | GraphSAGE | 0.8864
±0.0030 best reported | best at pub: Non-backtracking Graph Neural Networks (TMLR 2023) |
| 141 | SGC | 0.8832
±0.0055 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 191 | GPR-GNN | 0.8738
±0.0063 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 210 | MLP | 0.8690
±0.0074 | |
| 226 | DAGNN | 0.8640 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 329 | NCGC (GCNII) | 0.8203
±0.0032 | This paper |
| 333 | Meta-PN | 0.8190
±0.0045 | This paper |
| 343 | NormProp | 0.8153
±0.0001 | This paper |
| 359 | Violin | 0.8123
±0.0042 | This paper |
| 367 | GraphMix | 0.8110
±0.0078 best reported | best at pub: GraphMix: Improved Training of GNNs for Semi-Supervised Learning (2019) |
| 382 | PTA | 0.8087
±0.0062 | This paper |
| 497 | GAM | 0.7960
±0.0063 best reported | best at pub: Rethinking Graph Regularization for Graph Neural Networks (AAAI 2020) |
| 510 | M3S | 0.7950
±0.0076 best reported | best at pub: Self-supervised Learning on Graphs: Deep Insights and New Directions (2020) |
| 660 | DND-Net | 0.7824
±0.0098 | This paper |
| 761 | MGCN | 0.7634
±0.0073 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT* | 0.9669
±0.0014 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN* | 0.9632
±0.0008 best reported | |
| 20 | GRAND | 0.9579
±0.0059 best reported | best at pub: Graph Wave Networks (WWW 2025) |
| 21 | APPNP | 0.9573
±0.0012 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 50 | SGC | 0.9511
±0.0009 best reported | |
| 56 | GraphSAGE* | 0.9508
±0.0026 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 87 | GCNII | 0.9430
±0.0020 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 112 | GPR-GNN | 0.9385
±0.0028 best reported | best at pub: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 253 | NCGC (GAT) | 0.9274
±0.0038 | This paper |
| 260 | DAGNN | 0.9269 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) |
| 266 | MGCN | 0.9264
±0.0024 best reported | best at pub: Mixed Graph Contrastive Network for Semi-Supervised Node Classification (2022) |
| 346 | NormProp | 0.9193
±0.0044 | This paper |
| 364 | JKNet | 0.9169 best reported | best at pub: Structure-Aware DropEdge Towards Deep Graph Convolutional Networks (2023) |
| 390 | MLP | 0.9128
±0.0063 | |
| 395 | GAM | 0.9123
±0.0032 | This paper |
| 486 | GraphMix | 0.8845
±0.0076 | This paper |
| 497 | M3S | 0.8709
±0.0052 | This paper |
| 532 | Meta-PN | 0.7932
±0.1271 | This paper |
| 551 | PTA | 0.7417
±0.0157 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN* | 0.9412
±0.0008 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 3 | GAT* | 0.9398
±0.0022 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 46 | GraphSAGE* | 0.9120
±0.0029 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization? (LoG 2025) |
| 52 | GCNII | 0.9104
±0.0041 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 144 | GRAND | 0.8937
±0.0041 best reported | best at pub: Graph Wave Networks (WWW 2025) |
| 230 | JKNet | 0.8760 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 320 | MLP | 0.8463 | |
| 324 | DAGNN | 0.8450
±0.0120 best reported | best at pub: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) |
| 350 | NCGC (GAT) | 0.8401
±0.0094 | This paper |
| 353 | MGCN | 0.8399
±0.0090 best reported | best at pub: Mixed Graph Contrastive Network for Semi-Supervised Node Classification (2022) |
| 397 | GPR-GNN | 0.8238
±0.0160 best reported | best at pub: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) Difference within reported uncertainty; not counted as underperformance. |
| 411 | GAM | 0.8164
±0.0036 | This paper |
| 448 | M3S | 0.7592
±0.0107 | This paper |
| 463 | NormProp | 0.7298
±0.0464 | This paper |
| 465 | Meta-PN | 0.7246
±0.0732 | This paper |
| 466 | GraphMix | 0.7154
±0.0045 | This paper |
| 487 | PTA | 0.5541
±0.0279 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN* | 0.9774
±0.0035 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 42 | APPNP | 0.9654
±0.0007 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 43 | GraphSAGE* | 0.9649
±0.0006 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 59 | GCNII | 0.9597
±0.0011 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | MLP | 0.9597
±0.0007 | |
| 70 | SGC | 0.9580
±0.0010 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 177 | GraphMix | 0.9449
±0.0084 best reported | best at pub: GraphMix: Improved Training of GNNs for Semi-Supervised Learning (2019) |
| 179 | NCGC (GCN) | 0.9441
±0.0029 | This paper |
| 188 | NormProp | 0.9428 | This paper |
| 189 | PTA | 0.9424
±0.0031 | This paper |
| 197 | DAGNN | 0.9401
±0.0060 best reported | best at pub: Building Shortcuts between Distant Nodes with Biaffine Mapping for Graph Convolutional Networks (2023) Difference within reported uncertainty; not counted as underperformance. |
| 215 | GPR-GNN | 0.9357
±0.0011 | This paper |
| 221 | GAM | 0.9331
±0.0151 | This paper |
| 227 | JKNet | 0.9325
±0.0082 best reported | best at pub: Towards Understanding Graph Neural Networks: An Algorithm Unrolling Perspective (2022) Difference within reported uncertainty; not counted as underperformance. |
| 248 | GRAND | 0.9264
±0.0012 | This paper |
| 262 | Meta-PN | 0.9206
±0.0123 | This paper |
| 274 | M3S | 0.8945
±0.0095 | This paper |
