Diffusion on Graph: Augmentation of Graph Structure for Node Classification
Abstract
Graph diffusion models have recently been proposed to synthesize entire graphs, such as molecule graphs. Although existing methods have shown great performance in generating entire graphs for graph-level learning tasks, no graph diffusion models have been developed to generate synthetic graph structures, that is, synthetic nodes and associated edges within a given graph, for node-level learning tasks. Inspired by the research in the computer vision literature using synthetic data for enhanced performance, we propose Diffusion on Graph (DoG), which generates synthetic graph structures to boost the performance of GNNs. The synthetic graph structures generated by DoG are combined with the original graph to form an augmented graph for the training of node-level learning tasks, such as node classification and graph contrastive learning (GCL). To improve the efficiency of the generation process, a Bi-Level Neighbor Map Decoder (BLND) is introduced in DoG. To mitigate the adverse effect of the noise introduced by the synthetic graph structures, a low-rank regularization method is proposed for the training of graph neural networks (GNNs) on the augmented graphs. Extensive experiments on various graph datasets for semi-supervised node classification and graph contrastive learning have been conducted to demonstrate the effectiveness of DoG with low-rank regularization. The code of DoG is available at.
Benchmark Results
Tested on 7 datasets 13 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 | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 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) |
| 233 | SGFormer | 0.8482
±0.0085 best reported | best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Difference within reported uncertainty; not counted as underperformance. |
| 291 | Exphormer | 0.8410
±0.0080 | This paper |
| 366 | S^2GC | 0.8350
±0.0020 | This paper |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 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 | |
| 89 | SGFormer | 0.7798
±0.0091 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 264 | S^2GC | 0.7360
±0.0050 | This paper |
| 344 | Exphormer | 0.7290
±0.0040 | This paper |
| 350 | MLP | 0.7289
±0.0010 |
| # | 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 | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 56 | SGFormer | 0.9037
±0.0020 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) best today: VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention (WWW 2026) |
| 105 | Exphormer | 0.8906
±0.0024 best reported | best today: VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention (WWW 2026) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 433 | S^2GC | 0.8020
±0.0050 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | This paper |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 8 | Exphormer | 0.9580
±0.0020 best reported | best at pub: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 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) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 25 | APPNP | 0.9400
±0.0030 | prev best: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) Improvement within reported uncertainty; not highlighted. |
| 31 | S^2GC | 0.9380
±0.0010 | prev best: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 34 | SGFormer | 0.9370
±0.0040 | This paper |
| 43 | DGI | 0.9350
±0.0030 best reported | best at pub: 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) |
| 53 | BGRL | 0.9331
±0.0013 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) Difference within reported uncertainty; not counted as underperformance. |
| 57 | SGCL | 0.9330
±0.0020 | prev best: Rethinking and Simplifying Bootstrapped Graph Latents (2023) Improvement within reported uncertainty; not highlighted. |
| 63 | GraphMAE | 0.9300
±0.0010 | prev best: Rethinking and Simplifying Bootstrapped Graph Latents (2023) Improvement within reported uncertainty; not highlighted. |
| 88 | MLP | 0.9280
±0.0020 | |
| 98 | GGD | 0.9270
±0.0040 | prev best: Negative-Free Self-Supervised Gaussian Embedding of Graphs (2024) |
| 116 | MVGRL | 0.9211
±0.0012 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) Difference within reported uncertainty; not counted as underperformance. |
| 152 | GMI | 0.9108
±0.0056 best reported | best at pub: Topology Reorganized Graph Contrastive Learning with Mitigating Semantic Drift (2024) Difference within reported uncertainty; not counted as underperformance. |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | This paper |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 5 | ACM-GCN | 0.9510
±0.0320 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 53 | GraphSAGE | 0.9000
±0.0365 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | This paper |
| 16 | ACM-GCN | 0.4160
±0.0110 | |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 28 | ACM-GCN | 0.6900
±0.0170 | prev best: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) best today: Directed Homophily-Aware Graph Neural Network (2025) Improvement within reported uncertainty; not highlighted. |
| 50 | DoG | 0.7060
±0.0140 | This paper |
| 52 | GCN | 0.7033 | |
| 169 | MLP | 0.5429 |
