GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers
Abstract
Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self--attention, the core module of GTs, preserves only low-frequency signals in graph features, leading to ineffectiveness in capturing other important signals like high-frequency ones. Some recent GT models help alleviate this issue, but their flexibility and expressiveness are still limited since the filters they learn are fixed on predefined graph spectrum or spectral order. To tackle this challenge, we propose a Graph Fourier Kolmogorov-Arnold Transformer (GrokFormer), a novel GT model that learns highly expressive spectral filters with adaptive graph spectrum and spectral order through a Fourier series modeling over learnable activation functions. We demonstrate theoretically and empirically that the proposed GrokFormer filter offers better expressiveness than other spectral methods. Comprehensive experiments on 10 real-world node classification datasets across various domains, scales, and graph properties, as well as 5 graph classification datasets, show that GrokFormer outperforms state-of-the-art GTs and GNNs. Our code is available at https://github.com/GGA23/GrokFormer
Benchmark Results
Tested on 6 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 | |
| 11 | NAGphormer | 0.9614
±0.0016 best reported | |
| 18 | Specformer | 0.9580
±0.0026 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) Difference within reported uncertainty; not counted as underperformance. |
| 29 | SGFormer | 0.9434
±0.0023 | best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 31 | GrokFormer | 0.9552
±0.0052 | This paper |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | |
| 34 | H2GCN | 0.9548
±0.0043 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 35 | JacobiConv | 0.9543
±0.0023 | This paper |
| 39 | HiGCN | 0.9533
±0.0037 | This paper |
| 44 | NodeFormer | 0.9527
±0.0022 | This paper |
| 57 | GraphGPS | 0.9506
±0.0013 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) |
| 76 | HopGNN | 0.9449
±0.0033 | This paper |
| 99 | PolyFormer | 0.9408
±0.0137 | This paper |
| 118 | ChebyNet | 0.9377
±0.0032 | prev best: Spectral Graph Attention Network with Fast Eigen-approximation (2020) |
| 127 | BernNet | 0.9368
±0.0028 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 390 | MLP | 0.9128
±0.0063 | |
| 463 | Transformer | 0.8958
±0.0105 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | This paper |
| 2 | PolyFormer | 0.9808
±0.0027 | This paper |
| 3 | SGFormer | 0.9796
±0.0081 | This paper |
| 4 | HopGNN | 0.9786
±0.0016 | This paper |
| 5 | NAGphormer | 0.9785
±0.0026 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 6 | GAT | 0.9782
±0.0028 | prev best: Clarify Confused Nodes via Separated Learning (2023) |
| 7 | GPRGNN | 0.9777
±0.0015 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 8 | Specformer | 0.9775
±0.0053 | This paper |
| 9 | GCN | 0.9774
±0.0035 | prev best: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) |
| 10 | HiGCN | 0.9765
±0.0035 | This paper |
| 11 | H2GCN | 0.9764
±0.0050 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 13 | GraphGPS | 0.9760
±0.0005 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 14 | JacobiConv | 0.9756
±0.0028 | This paper |
| 17 | SAGE | 0.9739
±0.0018 | |
| 20 | BernNet | 0.9736
±0.0030 | This paper |
| 24 | ChebyNet | 0.9725
±0.0078 | This paper |
| 34 | NodeFormer | 0.9680
±0.0063 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention (WWW 2026) Difference within reported uncertainty; not counted as underperformance. |
| 58 | MLP | 0.9597
±0.0007 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 20 | H2GCN | 0.8345
±0.0026 | prev best: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 29 | GrokFormer | 0.8557
±0.0065 | This paper |
| 31 | GAT | 0.8322
±0.0078 | prev best: Unleashing the Potential of Text-attributed Graphs: Automatic Relation Decomposition via Large Language Models (2024) best today: Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning (2025) Improvement within reported uncertainty; not highlighted. |
| 32 | Specformer | 0.8515
±0.0063 | This paper |
| 33 | HopGNN | 0.8473
±0.0059 | This paper |
| 39 | JacobiConv | 0.8413
±0.0049 | This paper |
| 45 | PolyFormer | 0.8362
±0.0017 | This paper |
| 46 | BernNet | 0.8356
±0.0061 | This paper |
| 48 | NAGphormer | 0.8341
±0.0034 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 52 | HiGCN | 0.8314
±0.0078 | This paper |
| 55 | ChebyNet | 0.8295
±0.0045 | This paper |
| 57 | SGFormer | 0.8271
±0.0056 | This paper |
| 58 | GPRGNN | 0.8258
±0.0089 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 66 | Transformer | 0.8188
±0.0015 best reported | |
| 74 | NodeFormer | 0.8103
±0.0094 | prev best: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 120 | GraphGPS | 0.7926
±0.0057 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 237 | MLP | 0.7469
±0.0085 |
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 | |
| 8 | GrokFormer | 0.9459
±0.0208 | This paper |
| 21 | JacobiConv | 0.9344
±0.0213 | This paper |
| 22 | BernNet | 0.9328
±0.0148 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 28 | GPRGNN | 0.9295
±0.0131 | prev best: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 32 | SGFormer | 0.9246
±0.0148 | This paper |
| 34 | MLP | 0.9230
±0.0070 | |
| 37 | HiGCN | 0.9215
±0.0073 | This paper |
| 40 | H2GCN | 0.9189
±0.0393 | prev best: Global-Local Graph Neural Networks for Node-Classification (2024) Improvement within reported uncertainty; not highlighted. |
| 43 | NAGphormer | 0.9180
±0.0185 | This paper |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 72 | HopGNN | 0.8915
±0.0404 | prev best: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Improvement within reported uncertainty; not highlighted. |
| 73 | PolyFormer | 0.8902
±0.0544 | This paper |
| 78 | Transformer | 0.8875
±0.0630 | This paper |
| 87 | Specformer | 0.8823
±0.0038 | This paper |
| 113 | ChebyNet | 0.8622
±0.0245 | prev best: Heterophily-Aware Graph Attention Network (2023) Improvement within reported uncertainty; not highlighted. |
| 155 | NodeFormer | 0.8463
±0.0347 | This paper |
| 173 | GraphGPS | 0.8371
±0.0585 | This paper |
| 211 | GAT | 0.8082
±0.0213 | prev best: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Improvement within reported uncertainty; not highlighted. |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 7 | GrokFormer | 0.4298
±0.0148 | This paper |
| 19 | Specformer | 0.4193
±0.0104 | |
| 20 | HiGCN | 0.4181
±0.0052 | This paper |
| 21 | BernNet | 0.4179
±0.0101 | This paper |
| 23 | SGFormer | 0.4169
±0.0063 | prev best: Graph Triple Attention Network: A Decoupled Perspective (2024) |
| 28 | PolyFormer | 0.4151
±0.0071 | This paper |
| 34 | JacobiConv | 0.4117
±0.0064 | This paper |
| 42 | MLP | 0.4026
±0.0108 | |
| 49 | NAGphormer | 0.4008
±0.0150 | prev best: Graph Triple Attention Network: A Decoupled Perspective (2024) |
| 51 | Transformer | 0.3995
±0.0064 | prev best: Deformable Graph Transformer (2022) |
| 52 | GPRGNN | 0.3992
±0.0067 | This paper |
| 61 | HopGNN | 0.3933
±0.0279 | prev best: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Improvement within reported uncertainty; not highlighted. |
| 64 | ChebyNet | 0.3917
±0.0143 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) Difference within reported uncertainty; not counted as underperformance. |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 110 | GraphGPS | 0.3768
±0.0094 | prev best: Even Sparser Graph Transformers (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 136 | NodeFormer | 0.3690
±0.0100 best reported | best at pub: Even Sparser Graph Transformers (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) Difference within reported uncertainty; not counted as underperformance. |
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 | |
| 13 | GPRGNN | 0.8455
±0.0054 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 14 | Specformer | 0.8432
±0.0032 | This paper |
| 18 | GrokFormer | 0.8359
±0.0026 | This paper |
| 22 | JacobiConv | 0.8335
±0.0011 | This paper |
| 23 | BernNet | 0.8326
±0.0029 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) |
| 24 | H2GCN | 0.8320
±0.0055 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 29 | GIN | 0.8268
±0.0032 | |
| 31 | GCN | 0.8247
±0.0027 | This paper |
| 36 | GAT | 0.8153
±0.0055 | This paper |
| 39 | ChebyNet | 0.8109
±0.0033 | This paper |
| 43 | PolyFormer | 0.7927
±0.0026 | This paper |
| 49 | SGFormer | 0.7665
±0.0049 | This paper |
| 51 | MLP | 0.7534
±0.0064 | |
| 55 | NAGphormer | 0.7398
±0.0053 | This paper |
| 62 | NodeFormer | 0.6966
±0.0083 | This paper |
