Node-oriented Spectral Filtering for Graph Neural Networks
Abstract
Graph neural networks (GNNs) have shown remarkable performance on homophilic graph data while being far less impressive when handling non-homophilic graph data due to the inherent low-pass filtering property of GNNs. In general, since real-world graphs are often complex mixtures of diverse subgraph patterns, learning a universal spectral filter on the graph from the global perspective as in most current works may still suffer from great difficulty in adapting to the variation of local patterns. On the basis of the theoretical analysis of local patterns, we rethink the existing spectral filtering methods and propose the ode-oriented spectral iltering for raph eural etwork (namely NFGNN). By estimating the node-oriented spectral filter for each node, NFGNN is provided with the capability of precise local node positioning via the generalized translated operator, thus discriminating the variations of local homophily patterns adaptively. Meanwhile, the utilization of re-parameterization brings a good trade-off between global consistency and local sensibility for learning the node-oriented spectral filters. Furthermore, we theoretically analyze the localization property of NFGNN, demonstrating that the signal after adaptive filtering is still positioned around the corresponding node. Extensive experimental results demonstrate that the proposed NFGNN achieves more favorable performance.
Benchmark Results
Tested on 6 datasets 9 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 | 0.9294
±0.0066 | prev best: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9249
±0.0055 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 33 | GPRGNN | 0.9387
±0.0042 | |
| 66 | FAGCN | 0.9489
±0.0048 best reported | best today: Clarify Confused Nodes via Separated Learning (2023) |
| 67 | NFGNN | 0.9485
±0.0024 | This paper |
| 119 | ChebNet | 0.9358
±0.0019 | prev best: Elastic Graph Neural Networks (ICML 2021) |
| 127 | BernNet | 0.9368
±0.0028 best reported | best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 390 | MLP | 0.8817
±0.0062 | prev best: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Clarify Confused Nodes via Separated Learning (2023) |
| 470 | LINK | 0.8928
±0.0031 | This paper |
| # | 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 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.8804
±0.0051 | prev best: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 72 | GPRGNN | 0.8720
±0.0047 | |
| 81 | NFGNN | 0.9031
±0.0042 | This paper |
| 126 | FAGCN | 0.8968
±0.0097 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) |
| 180 | BernNet | 0.8861
±0.0041 | This paper |
| 216 | ChebNet | 0.8782
±0.0072 | prev best: Elastic Graph Neural Networks (ICML 2021) |
| 320 | MLP | 0.8178
±0.0076 | |
| 357 | LINK | 0.8371
±0.0032 | This paper |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GIANT-XRT | 0.7612
±0.0016 | |
| 2 | GEGCN | 0.7576
±0.0064 | |
| 3 | AGDN | 0.7522
±0.0007 | |
| 23 | GCN | 0.7300
±0.0017 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 25 | GraphSAGE | 0.7277
±0.0016 | |
| 37 | NFGNN | 0.7213
±0.0033 | This paper |
| 49 | APPNP | 0.7190
±0.0025 best reported | best today: A General Graph Spectral Wavelet Convolution via Chebyshev Order Decomposition (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 55 | GPRGNN | 0.7168
±0.0044 | prev best: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 64 | BernNet | 0.7140
±0.0037 | This paper |
| 107 | MLP | 0.5765
±0.0012 |
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 | |
| 14 | NFGNN | 0.9403
±0.0082 | This paper |
| 22 | BernNet | 0.9328
±0.0148 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. |
| 26 | BMGCN | 0.9300
±0.0057 | This paper |
| 28 | GPRGNN | 0.9292
±0.0061 | prev best: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 34 | MLP | 0.9226
±0.0071 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 46 | APPNP | 0.9118
±0.0070 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 | |
| 62 | LINK | 0.8961
±0.0152 | |
| 110 | ChebNet | 0.8628
±0.0262 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 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 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 17 | BernNet | 0.9213
±0.0164 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) Difference within reported uncertainty; not counted as underperformance. |
| 20 | NFGNN | 0.9190
±0.0091 | This paper |
| 21 | APPNP | 0.9180
±0.0063 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 22 | GPRGNN | 0.9136
±0.0070 | |
| 24 | MLP | 0.9136
±0.0070 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) Improvement within reported uncertainty; not highlighted. |
| 38 | FAGCN | 0.8852
±0.0133 | |
| 85 | ChebNet | 0.8533
±0.0104 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 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) |
| 387 | LINK | 0.5916 best reported | best at pub: Comprehensive Graph Gradual Pruning for Sparse Training in Graph Neural Networks (2022) |
| # | 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 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) |
| 39 | NFGNN | 0.4062
±0.0038 | 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) |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Heterophily-Aware Graph Attention Network (2023) |
| 52 | GPRGNN | 0.3930
±0.0027 | prev best: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 56 | FAGCN | 0.3970 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 88 | ChebNet | 0.3802
±0.0023 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) 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) |
| 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. |
| 418 | LINK | 0.2625
±0.0143 | prev best: Simplifying Node Classification on Heterophilous Graphs with Compatible Label Propagation (TMLR 2022) |
