Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited
Abstract
Designing spectral convolutional networks is a challenging problem in graph learning. ChebNet, one of the early attempts, approximates the spectral graph convolutions using Chebyshev polynomials. GCN simplifies ChebNet by utilizing only the first two Chebyshev polynomials while still outperforming it on real-world datasets. GPR-GNN and BernNet demonstrate that the Monomial and Bernstein bases also outperform the Chebyshev basis in terms of learning the spectral graph convolutions. Such conclusions are counter-intuitive in the field of approximation theory, where it is established that the Chebyshev polynomial achieves the optimum convergent rate for approximating a function. In this paper, we revisit the problem of approximating the spectral graph convolutions with Chebyshev polynomials. We show that ChebNet's inferior performance is primarily due to illegal coefficients learnt by ChebNet approximating analytic filter functions, which leads to over-fitting. We then propose ChebNetII, a new GNN model based on Chebyshev interpolation, which enhances the original Chebyshev polynomial approximation while reducing the Runge phenomenon. We conducted an extensive experimental study to demonstrate that ChebNetII can learn arbitrary graph convolutions and achieve superior performance in both full- and semi-supervised node classification tasks. Most notably, we scale ChebNetII to a billion graph ogbn-papers100M, showing that spectral-based GNNs have superior performance. Our code is available at.
Benchmark Results
Tested on 10 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 387 | ChebBase/k | 0.7252
±0.0029 | This paper |
| 576 | ChebBase | 0.7076
±0.0037 | 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 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 553 | ChebBase/k | 0.7925
±0.0031 | This paper |
| 673 | ChebBase | 0.7807
±0.0032 | This paper |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | SGC | 0.7910 | |
| 2 | GAMLP | 0.7036
±0.0002 | |
| 3 | GLEM-GNN | 0.7036
±0.0002 | |
| 21 | ChebNetII | 0.6718
±0.0032 | This paper |
| 35 | SAGE | 0.6644
±0.0017 | |
| 38 | SIGN | 0.6636
±0.0005 best reported | best at pub: Scalable and Adaptive Graph Neural Networks with Self-Label-Enhanced Training (2021) best today: Graph Learning at Scale: Characterizing and Optimizing Pre-Propagation GNNs (2025) |
| 50 | GPR-GNN | 0.6589
±0.0035 | This paper |
| 55 | NDLS | 0.6561
±0.0029 | prev best: Node Dependent Local Smoothing for Scalable Graph Learning (NeurIPS 2021) Improvement within reported uncertainty; not highlighted. |
| 59 | GBP | 0.6523
±0.0031 | prev best: Evaluating Deep Graph Neural Networks (2021) Improvement within reported uncertainty; not highlighted. |
| 95 | MLP | 0.4960
±0.0030 |
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 | |
| 23 | ChebNetII | 0.9328
±0.0147 | This paper |
| 22 | BernNet | 0.9328
±0.0148 best reported | best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 25 | PDE-GCN | 0.9324
±0.0203 | This paper |
| 30 | GPR-GNN | 0.9291
±0.0132 | prev best: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 34 | MLP | 0.8681
±0.0224 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Design your own universe: a physics-informed agnostic method for enhancing graph neural networks (2024) Improvement within reported uncertainty; not highlighted. |
| 46 | APPNP | 0.9064
±0.0170 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) Improvement within reported uncertainty; not highlighted. |
| 47 | TWIRLS | 0.9131
±0.0336 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 70 | GCNII | 0.8046
±0.0591 | prev best: Graph-Coupled Oscillator Networks (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 110 | ChebNet | 0.8628
±0.0262 | This paper |
| 170 | ARMA | 0.8397
±0.0377 | This paper |
| 220 | EGNN | 0.8134
±0.0156 | This paper |
| 257 | GCN | 0.7697
±0.0397 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 11 | GPR-GNN | 0.9157
±0.0196 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 16 | ChebNetII | 0.9230
±0.0148 | This paper |
| 17 | BernNet | 0.9213
±0.0164 | This paper |
| 21 | APPNP | 0.9152
±0.0181 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) |
| 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) |
| 27 | TWIRLS | 0.8983
±0.0229 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) Improvement within reported uncertainty; not highlighted. |
| 28 | PDE-GCN | 0.8973
±0.0135 | This paper |
| 35 | GCNII | 0.8426
±0.0213 | prev best: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 82 | ARMA | 0.8562
±0.0213 | This paper |
| 85 | ChebNet | 0.8533
±0.0104 best reported | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 117 | EGNN | 0.8380
±0.0460 best reported | Difference within reported uncertainty; not counted as underperformance. |
| 138 | SAGE | 0.8269 | |
| 170 | GCN | 0.6578
±0.0416 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) 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 | |
| 21 | BernNet | 0.4179
±0.0101 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 22 | ChebNetII | 0.4175
±0.0107 | This paper |
| 38 | GCNII | 0.3689
±0.0095 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 41 | APPNP | 0.3976
±0.0049 | |
| 42 | MLP | 0.4018
±0.0055 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 53 | GPR-GNN | 0.3991
±0.0062 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 55 | PDE-GCN | 0.3976
±0.0074 | This paper |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 85 | TWIRLS | 0.3813
±0.0081 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) Improvement within reported uncertainty; not highlighted. |
| 88 | ChebNet | 0.3802
±0.0023 best reported | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 111 | ARMA | 0.3767
±0.0054 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 224 | EGNN | 0.3516
±0.0064 | This paper |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DC-GNN | 0.8669
±0.0022 | |
| 2 | M2M-GNN | 0.8594
±0.0040 | |
| 3 | GloGNN | 0.8574
±0.0042 | |
| 7 | ChebNetII | 0.8486
±0.0033 | This paper |
| 11 | LINKX | 0.8471
±0.0052 | This paper |
| 20 | GPR-GNN | 0.8354
±0.0032 | This paper |
| 23 | BernNet | 0.8326
±0.0029 | This paper |
| 27 | GCNII | 0.8292
±0.0059 | This paper |
| 29 | GIN | 0.8268
±0.0032 | |
| 30 | ChebNet | 0.8259
±0.0031 | This paper |
| 31 | GCN | 0.8247
±0.0027 | This paper |
| 40 | LINK | 0.8079
±0.0049 | This paper |
| 51 | MLP | 0.7534
±0.0064 best reported | best today: Clarify Confused Nodes via Separated Learning (2023) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LargeScaleNet | 0.6582
±0.0036 | |
| 2 | S² DirGCN | 0.6495
±0.0033 | |
| 3 | FaberNet | 0.6462
±0.0101 | |
| 13 | LINKX | 0.5600
±0.0134 | This paper |
| 17 | LINK | 0.5397
±0.0018 | This paper |
| 24 | ChebNetII | 0.4853
±0.0031 | This paper |
| 26 | GCNII | 0.4721
±0.0028 | prev best: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 28 | ChebNet | 0.4676
±0.0024 | This paper |
| 29 | BernNet | 0.4634
±0.0032 | This paper |
| 31 | GCN | 0.4602
±0.0026 | prev best: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 32 | GPR-GNN | 0.4597
±0.0026 | This paper |
| 56 | MLP | 0.3670
±0.0021 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | SAGE | 0.8597
±0.0021 | |
| 2 | Polynormer | 0.8595
±0.0007 | |
| 3 | NID_SAGE | 0.8563
±0.0031 | |
| 6 | ChebNetII | 0.8233
±0.0028 | This paper |
| 7 | LINKX | 0.8204
±0.0007 | This paper |
| 9 | BernNet | 0.8167
±0.0017 | This paper |
| 13 | GPR-GNN | 0.8074
±0.0022 | This paper |
| 14 | LINK | 0.8054
±0.0003 | This paper |
| 16 | GCNII | 0.7894
±0.0011 | This paper |
| 23 | GCN | 0.7601
±0.0049 best reported | best today: Mixture of Weak & Strong Experts on Graphs (ICLR 2023) |
| 24 | GraphSAGE | 0.7576
±0.0004 | |
| 27 | ChebNet | 0.7271
±0.0066 | This paper |
| 31 | MLP | 0.7048
±0.0077 best reported | best today: FMP: Toward Fair Graph Message Passing against Topology Bias (2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DGT | 0.6609
±0.0022 | |
| 2 | ICG_u-NN | 0.6608
±0.0074 | |
| 3 | LINKX | 0.6606
±0.0019 | This paper |
| 11 | ChebNetII | 0.6503
±0.0027 | This paper |
| 13 | LINK | 0.6485
±0.0021 | This paper |
| 14 | GraphSAGE | 0.6473
±0.0011 | |
| 16 | GCN | 0.6434
±0.0012 best reported | best today: Deformable Graph Transformer (2022) |
| 18 | BernNet | 0.6427
±0.0031 | This paper |
| 23 | GCNII | 0.6339
±0.0061 | This paper |
| 27 | GPR-GNN | 0.6259
±0.0038 | This paper |
| 28 | ChebNet | 0.6231
±0.0037 | This paper |
| 33 | MLP | 0.6114
±0.0006 best reported | best today: Deformable Graph Transformer (2022) |
