LON-GNN: Spectral GNNs with Learnable Orthonormal Basis
Abstract
In recent years, a plethora of spectral graph neural networks (GNN) methods have utilized polynomial basis with learnable coefficients to achieve top-tier performances on many node-level tasks. Although various kinds of polynomial bases have been explored, each such method adopts a fixed polynomial basis which might not be the optimal choice for the given graph. Besides, we identify the so-called over-passing issue of these methods and show that it is somewhat rooted in their less-principled regularization strategy and unnormalized basis. In this paper, we make the first attempts to address these two issues. Leveraging Jacobi polynomials, we design a novel spectral GNN, LON-GNN, with Learnable OrthoNormal bases and prove that regularizing coefficients becomes equivalent to regularizing the norm of learned filter function now. We conduct extensive experiments on diverse graph datasets to evaluate the fitting and generalization capability of LON-GNN, where the results imply its superiority.
Benchmark Results
Tested on 6 datasets 11 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 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 35 | JacobiConv | 0.9543
±0.0023 | This paper |
| 72 | LON-GNN | 0.9466
±0.0052 | This paper |
| 119 | ChebNet | 0.9377
±0.0032 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 127 | BernNet | 0.9363
±0.0035 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 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: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 59 | LON-GNN | 0.9093
±0.0082 | This paper |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 72 | GPRGNN | 0.9050
±0.0091 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 77 | JacobiConv | 0.9039
±0.0029 | This paper |
| 180 | BernNet | 0.8861
±0.0041 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 216 | ChebNet | 0.8782
±0.0072 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 320 | MLP | 0.8463 |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 10 | JacobiConv | 0.9295
±0.0246 | This paper |
| 17 | BernNet | 0.9213
±0.0164 | This paper |
| 19 | Jacobi+Learnable | 0.9191 | This paper |
| 21 | APPNP | 0.9181
±0.0196 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 22 | GPRGNN | 0.9137
±0.0181 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 24 | MLP | 0.9136
±0.0070 | |
| 85 | ChebNet | 0.8533
±0.0104 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 103 | LON-GNN | 0.8447
±0.0345 | This paper |
| 116 | Jacobi+OrthNorm | 0.8383 | This paper |
| 138 | SAGE | 0.8269 | |
| 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) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 21 | BernNet | 0.4179
±0.0101 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 34 | JacobiConv | 0.4117
±0.0064 | This paper |
| 41 | APPNP | 0.4046
±0.0064 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) Difference within reported uncertainty; not counted as underperformance. |
| 42 | MLP | 0.4026
±0.0108 | |
| 52 | GPRGNN | 0.3992
±0.0067 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 66 | LON-GNN | 0.3910
±0.0159 | This paper |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 88 | ChebNet | 0.3802
±0.0023 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 31 | JacobiConv | 0.7420
±0.0103 | This paper |
| 35 | LON-GNN | 0.7300
±0.0220 | 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) |
| 66 | BernNet | 0.6829
±0.0158 | This paper |
| 72 | GPRGNN | 0.6728
±0.0109 | prev best: Simplifying approach to Node Classification in Graph Neural Networks (2021) Improvement within reported uncertainty; not highlighted. |
| 79 | APPNP | 0.6670
±0.0270 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 140 | ChebNet | 0.5928
±0.0125 | This paper |
| 169 | MLP | 0.5429 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 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) |
| 47 | LON-GNN | 0.6061
±0.0169 | This paper |
| 60 | JacobiConv | 0.5738
±0.0125 | This paper |
| 68 | APPNP | 0.5590
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 76 | GPRGNN | 0.5015
±0.0192 | prev best: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Directed Homophily-Aware Graph Neural Network (2025) Improvement within reported uncertainty; not highlighted. |
| 86 | BernNet | 0.5139
±0.0092 best reported | best today: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) Difference within reported uncertainty; not counted as underperformance. |
| 120 | SAGE | 0.4460
±0.0130 | |
| 125 | ChebNet | 0.4386
±0.0164 best reported | best today: Scalable Graph Compressed Convolutions (2024) |
| 172 | MLP | 0.3930
±0.0079 |
