Framelet Message Passing
Abstract
Graph neural networks (GNNs) have achieved champion in wide applications. Neural message passing is a typical key module for feature propagation by aggregating neighboring features. In this work, we propose a new message passing based on multiscale framelet transforms, called Framelet Message Passing. Different from traditional spatial methods, it integrates framelet representation of neighbor nodes from multiple hops away in node message update. We also propose a continuous message passing using neural ODE solvers. It turns both discrete and continuous cases can provably achieve network stability and limit oversmoothing due to the multiscale property of framelets. Numerical experiments on real graph datasets show that the continuous version of the framelet message passing significantly outperforms existing methods when learning heterogeneous graphs and achieves state-of-the-art performance on classic node classification tasks with low computational costs.
Benchmark Results
Tested on 5 datasets 32 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: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: 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) |
| 55 | JKNet | 0.8870 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 87 | GRAND | 0.8815 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: 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: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 223 | SGC | 0.8509
±0.0648 best reported | |
| 283 | CGNN | 0.8420
±0.0100 best reported | best at pub: Continuous Graph Neural Networks (ICML 2019) |
| 317 | GDE | 0.8380
±0.0050 | This paper |
| 344 | FMP ode | 0.8360
±0.0080 | This paper |
| 510 | FMP mlp | 0.8220
±0.0070 | This paper |
| 724 | MLP | 0.7768 best reported | best at pub: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| # | 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: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 62 | JKNet | 0.7920 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 122 | GRAND | 0.7657 best reported | best at pub: Discovering Data Geometry: Energy-Driven Neural Diffusion (ICLR 2023) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 259 | SAGE | 0.7361
±0.0190 | |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 368 | FMP ode | 0.7270
±0.0090 | This paper |
| 391 | GDE | 0.7250
±0.0050 | This paper |
| 486 | FMP mlp | 0.7170
±0.0040 | This paper |
| 590 | CGNN | 0.7050
±0.0123 best reported | best at pub: GRAND: Graph Neural Diffusion (ICML 2021) best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) |
| # | 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: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 109 | GRAND | 0.7970
±0.0030 | prev best: Graph-Coupled Oscillator Networks (ICML 2022) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) Improvement within reported uncertainty; not highlighted. |
| 116 | SAGE | 0.8881
±0.0015 | |
| 125 | GraphSAGE | 0.8864
±0.0030 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Non-backtracking Graph Neural Networks (TMLR 2023) |
| 141 | SGC | 0.8832
±0.0055 best reported | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 430 | CGNN | 0.8020
±0.0030 | This paper |
| 459 | GDE | 0.7990
±0.0030 best reported | best at pub: GRAND: Graph Neural Diffusion (ICML 2021) best today: Beltrami Flow and Neural Diffusion on Graphs (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 491 | FMP ode | 0.7960
±0.0090 | This paper |
| 531 | FMP mlp | 0.7940
±0.0030 | 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 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 70 | GCNII | 0.8918
±0.0443 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) |
| 95 | FMP ode | 0.8760
±0.0520 | This paper |
| 159 | ASGAT | 0.8460
±0.0580 | This paper |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 428 | GCN-JKNet | 0.6650
±0.0660 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 5 | FMP ode | 0.9380
±0.0150 | This paper |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 54 | ASGAT | 0.8690
±0.0420 | This paper |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 138 | SAGE | 0.8269 | |
| 157 | GraphSAGE | 0.8196
±0.0739 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 335 | GCN-JKNet | 0.6460
±0.0870 | This paper |
