GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials
Abstract
Graph Neural Networks (GNNs) are a promising deep learning approach for circumventing many real-world problems on graph-structured data. However, these models usually have at least one of four fundamental limitations: over-smoothing, over-fitting, difficult to train, and strong homophily assumption. For example, Simple Graph Convolution (SGC) is known to suffer from the first and fourth limitations. To tackle these limitations, we identify a set of key designs including (D1) dilated convolution, (D2) multi-channel learning, (D3) self-attention score, and (D4) sign factor to boost learning from different types (homophily and heterophily) and scales (small, medium, and large) of networks, and combine them into a graph neural network, GPNet, a simple and efficient one-layer model. We theoretically analyze the model and show that it can approximate various graph filters by adjusting the self-attention score and sign factor. Experiments show that GPNet consistently outperforms baselines in terms of average rank, average accuracy, complexity, and parameters on semi-supervised and full-supervised tasks, and achieves competitive performance compared to state-of-the-art model with inductive learning task.
Benchmark Results
Tested on 8 datasets 28 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 | |
| 50 | FAGCN | 0.8885
±0.0136 best reported | 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) |
| 99 | JKNet+DropEdge | 0.8800 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 373 | IncepGCN+DropEdge | 0.8350 | This paper |
| 384 | ARMA | 0.8340 | This paper |
| 544 | MixHop-learn | 0.8190
±0.0040 | 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 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 47 | JKNet+DropEdge | 0.8020 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 62 | JKNet | 0.7920 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 350 | MLP | 0.7289
±0.0010 | |
| 371 | IncepGCN+DropEdge | 0.7270 | This paper |
| 390 | ARMA | 0.7250 | This paper |
| 522 | MixHop-learn | 0.7140
±0.0080 | 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 | |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 25 | JKNet+DropEdge | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 210 | MLP | 0.8690
±0.0074 | |
| 217 | ARMA | 0.8678
±0.0021 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) |
| 391 | MixHop-learn | 0.8080
±0.0060 | This paper |
| 514 | IncepGCN+DropEdge | 0.7950 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | EnGCN | 0.9714
±0.0003 | |
| 2 | SAGN+SLE | 0.9710 | |
| 3 | GAMLP(JK) | 0.9704
±0.0001 | |
| 14 | GraphSAGE | 0.9660 | |
| 26 | GaAN | 0.9640 | Improvement within reported uncertainty; not highlighted. |
| 46 | GPNet | 0.9580 | This paper |
| 55 | SAGE-LSTM | 0.9540 | This paper |
| 71 | SAGE-mean | 0.9500 | This paper |
| 73 | SGC | 0.9490 | This paper |
| 82 | DGI | 0.9414
±0.0003 best reported | best at pub: Calibrating and Improving Graph Contrastive Learning (TMLR 2021) |
| 91 | FastGCN | 0.9370 | This paper |
| 109 | SAGE-GCN | 0.9300 | 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 | |
| 28 | GPRGNN | 0.9295
±0.0131 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 39 | GGCN | 0.9213
±0.0305 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: Graph Wave Networks (WWW 2025) |
| 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: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 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) |
| 93 | GPNet | 0.8784 | This paper |
| 118 | Conn-NSD | 0.8616
±0.0220 | This paper |
| 141 | GloGNN | 0.8524
±0.0490 best reported | best at pub: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 160 | UDGNN_GCN | 0.8460
±0.0530 | This paper |
| 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) |
| 276 | MixHop | 0.7784
±0.0770 | This paper |
| 325 | LINKX | 0.7460
±0.0840 | This paper |
| 330 | SGC | 0.7440
±0.0600 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 390 | DeepGCNs | 0.7027
±0.0710 | This paper |
| 415 | Geom-GCN | 0.6760 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 15 | GGCN | 0.9230
±0.0367 best reported | best at pub: Understanding convolution on graphs via energies (TMLR 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best at pub: Comprehensive Graph Gradual Pruning for Sparse Training in Graph Neural Networks (2022) best today: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 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) |
| 38 | FAGCN | 0.8852
±0.0133 best reported | best at pub: Comprehensive Graph Gradual Pruning for Sparse Training in Graph Neural Networks (2022) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 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. |
| 76 | Conn-NSD | 0.8595
±0.0770 | This paper |
| 74 | GloGNN | 0.8595
±0.0510 | prev best: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 105 | UDGNN_GCN | 0.8432
±0.0730 | This paper |
| 111 | GPNet | 0.8410
±0.0010 | This paper |
| 123 | LINKX | 0.8346
±0.0061 best reported | best today: Differentiable Cluster Graph Neural Network (2024) Difference within reported uncertainty; not counted as underperformance. |
| 138 | SAGE | 0.8269 | |
| 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) |
| 183 | MixHop | 0.7950
±0.0630 best reported | best at pub: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 252 | SGC | 0.7350
±0.0430 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 296 | DeepGCNs | 0.6838
±0.0590 | This paper |
| 342 | Geom-GCN | 0.6412 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: Steering Graph Neural Networks with Pinning Control (2023) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) |
| 23 | GPNet | 0.7861
±0.0020 | This paper |
| 29 | UDGNN_GCN | 0.7453
±0.0120 | This paper |
| 45 | GloGNN | 0.7133
±0.0242 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 48 | GGCN | 0.7114
±0.0180 | This paper |
| 52 | GCN | 0.7033 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 64 | LINKX | 0.6842
±0.0140 | This paper |
| 72 | GPRGNN | 0.6748
±0.0040 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 76 | SGC | 0.6710
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 79 | APPNP | 0.6670
±0.0270 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 92 | Conn-NSD | 0.6521
±0.0200 | This paper |
| 103 | GCNII | 0.6386
±0.0300 | prev best: Simplifying approach to Node Classification in Graph Neural Networks (2021) Improvement within reported uncertainty; not highlighted. |
| 107 | FAGCN | 0.6344
±0.0205 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 124 | Geom-GCN | 0.6090 | This paper |
| 129 | MixHop | 0.6050
±0.0250 | This paper |
| 133 | H2GCN | 0.6030
±0.0231 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 169 | MLP | 0.5429 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 205 | DeepGCNs | 0.4875
±0.0260 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 18 | GPNet | 0.7157
±0.0010 | This paper |
| 19 | GloGNN | 0.7121
±0.0184 best reported | best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 24 | UDGNN_GCN | 0.6813
±0.0260 | This paper |
| 39 | H2GCN | 0.6190
±0.0140 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) best today: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 40 | LINKX | 0.6181
±0.0180 | This paper |
| 46 | GCN | 0.6067 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 67 | GAT | 0.5630
±0.0220 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 68 | APPNP | 0.5590
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 69 | GGCN | 0.5567
±0.0187 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 76 | GPRGNN | 0.5435
±0.0087 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 81 | SGC | 0.5230
±0.0230 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 117 | Conn-NSD | 0.4519
±0.0160 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 127 | MixHop | 0.4380
±0.0150 | This paper |
| 139 | FAGCN | 0.4243
±0.0210 | prev best: Non-Local Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 172 | MLP | 0.3930
±0.0079 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 176 | GCNII | 0.3847
±0.0160 | prev best: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 179 | Geom-GCN | 0.3832
±0.0092 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Difference within reported uncertainty; not counted as underperformance. |
| 238 | DeepGCNs | 0.3123
±0.0140 | This paper |
