Graph Wave Networks
Abstract
Dynamics modeling has been introduced as a novel paradigm in message passing (MP) of graph neural networks (GNNs). Existing methods consider MP between nodes as a heat diffusion process, and leverage heat equation to model the temporal evolution of nodes in the embedding space. However, heat equation can hardly depict the wave nature of graph signals in graph signal processing. Besides, heat equation is essentially a partial differential equation (PDE) involving a first partial derivative of time, whose numerical solution usually has low stability, and leads to inefficient model training. In this paper, we would like to depict more wave details in MP, since graph signals are essentially wave signals that can be seen as a superposition of a series of waves in the form of eigenvector. This motivates us to consider MP as a wave propagation process to capture the temporal evolution of wave signals in the space. Based on wave equation in physics, we innovatively develop a graph wave equation to leverage the wave propagation on graphs. In details, we demonstrate that the graph wave equation can be connected to traditional spectral GNNs, facilitating the design of graph wave networks (GWNs) based on various Laplacians and enhancing the performance of the spectral GNNs. Besides, the graph wave equation is particularly a PDE involving a second partial derivative of time, which has stronger stability on graphs than the heat equation that involves a first partial derivative of time. Additionally, we theoretically prove that the numerical solution derived from the graph wave equation are constantly stable, enabling to significantly enhance model efficiency while ensuring its performance. Extensive experiments show that GWNs achieve state-of-the-art and efficient performance on benchmark datasets, and exhibit outstanding performance in addressing challenging graph problems, such as over-smoothing and heterophily. Our code is available at.
Benchmark Results
Tested on 5 datasets 10 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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 | prev best: Graph Neural Aggregation-diffusion with Metastability (2024) |
| 27 | GWN-fa | 0.9561
±0.0053 | This paper |
| 40 | ADC | 0.9533
±0.0027 | This paper |
| 42 | GWN-sym | 0.9531
±0.0065 | This paper |
| 56 | GraphSAGE | 0.9508
±0.0026 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 66 | FAGCN | 0.9489
±0.0048 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 71 | GADC | 0.9470
±0.0035 | This paper |
| 82 | CGNN | 0.9435
±0.0056 | prev best: Beltrami Flow and Neural Diffusion on Graphs (NeurIPS 2021) |
| 141 | GDC | 0.9356
±0.0033 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | 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) |
| 67 | GWN-fa | 0.9062
±0.0061 | This paper |
| 94 | GWN-sym | 0.9010
±0.0087 | This paper |
| 126 | FAGCN | 0.8968
±0.0097 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 144 | GRAND | 0.8937
±0.0041 | prev best: Graph Neural Aggregation-diffusion with Metastability (2024) |
| 178 | ADC | 0.8862
±0.0056 | This paper |
| 181 | GDC | 0.8856
±0.0038 | This paper |
| 195 | CGNN | 0.8831
±0.0065 | prev best: Beltrami Flow and Neural Diffusion on Graphs (NeurIPS 2021) |
| 221 | GADC | 0.8778
±0.0054 | This paper |
| 320 | MLP | 0.8463 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | This paper |
| 3 | GWN-sym | 0.9666
±0.0026 | This paper |
| 4 | CGNN | 0.9621
±0.0032 | prev best: Beltrami Flow and Neural Diffusion on Graphs (NeurIPS 2021) |
| 5 | GADC | 0.9616
±0.0029 | This paper |
| 6 | GraphSAGE | 0.9593
±0.0025 | prev best: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) |
| 7 | ADC | 0.9582
±0.0015 | This paper |
| 9 | FAGCN | 0.9579 | This paper |
| 10 | GRAND | 0.9577
±0.0028 | prev best: TIDE: Time Derivative Diffusion for Deep Learning on Graphs (ICML 2022) |
| 12 | GCN | 0.9514
±0.0025 | prev best: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) Improvement within reported uncertainty; not highlighted. |
| 16 | GDC | 0.9482
±0.0022 | This paper |
| 21 | GAT | 0.9437
±0.0028 | prev best: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) Improvement within reported uncertainty; not highlighted. |
| 88 | MLP | 0.9280
±0.0020 | |
| 138 | GIN | 0.9140
±0.0020 |
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 | |
| 5 | ACM-GCN | 0.9557
±0.0360 best reported | best at pub: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 29 | GWN-fa | 0.9294
±0.0445 | This paper |
| 30 | GPR-GNN | 0.9291
±0.0132 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Difference within reported uncertainty; not counted as underperformance. |
| 34 | MLP | 0.9230
±0.0070 | |
| 39 | GGCN | 0.9213
±0.0305 | prev best: Global-Local Graph Neural Networks for Node-Classification (2024) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 48 | Ordered GNN | 0.9082
±0.0418 | This paper |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 55 | GWN-sym | 0.8985
±0.0505 | This paper |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) Difference within reported uncertainty; not counted as underperformance. |
| 257 | GCN | 0.7933
±0.0447 | prev best: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 15 | GWN-fa | 0.4203
±0.0159 | This paper |
| 16 | ACM-GCN | 0.4198
±0.0089 best reported | best at pub: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 42 | MLP | 0.4026
±0.0108 | |
| 50 | GWN-sym | 0.3997
±0.0172 | This paper |
| 53 | GPR-GNN | 0.3992
±0.0067 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 91 | Ordered GNN | 0.3799
±0.0170 | This paper |
