Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach
Abstract
Graph Neural Networks (GNNs), known as spectral graph filters, find a wide range of applications in web networks. To bypass eigendecomposition, polynomial graph filters are proposed to approximate graph filters by leveraging various polynomial bases for filter training. However, no existing studies have explored the diverse polynomial graph filters from a unified perspective for optimization. In this paper, we first unify polynomial graph filters, as well as the optimal filters of identical degrees into the Krylov subspace of the same order, thus providing equivalent expressive power theoretically. Next, we investigate the asymptotic convergence property of polynomials from the unified Krylov subspace perspective, revealing their limited adaptability in graphs with varying heterophily degrees. Inspired by those facts, we design a novel adaptive Krylov subspace approach to optimize polynomial bases with provable controllability over the graph spectrum so as to adapt various heterophily graphs. Subsequently, we propose AdaptKry, an optimized polynomial graph filter utilizing bases from the adaptive Krylov subspaces. Meanwhile, in light of the diverse spectral properties of complex graphs, we extend AdaptKry by leveraging multiple adaptive Krylov bases without incurring extra training costs. As a consequence, extended AdaptKry is able to capture the intricate characteristics of graphs and provide insights into their inherent complexity. We conduct extensive experiments across a series of real-world datasets. The experimental results demonstrate the superior filtering capability of AdaptKry, as well as the optimized efficacy of the adaptive Krylov basis. The code of AdaptKry is accessed at.
Benchmark Results
Tested on 3 datasets 3 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 8 | AdaptKry | 0.4270
±0.0114 | This paper |
| 11 | OptBasisGNN | 0.4239
±0.0052 | This paper |
| 21 | BernNet | 0.4179
±0.0101 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) 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 |
| 33 | SIGN | 0.4122
±0.0096 | |
| 34 | JacobiConv | 0.4117
±0.0064 | This paper |
| 40 | EvenNet | 0.4048
±0.0062 best reported | best at pub: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 42 | MLP | 0.4026
±0.0108 | |
| 53 | GPR-GNN | 0.3992
±0.0067 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) Difference within reported uncertainty; not counted as underperformance. |
| 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) |
| 237 | SGC | 0.3490
±0.0070 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 284 | ASGC | 0.3341
±0.0080 | 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 | |
| 10 | GPR-GNN | 0.5043
±0.0189 | prev best: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 35 | OptBasisGNN | 0.6362
±0.0076 | This paper |
| 36 | AdaptKry | 0.6331
±0.0076 | This paper |
| 46 | GCN | 0.6067 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 55 | ASGC | 0.5791
±0.0089 | This paper |
| 56 | ChebNetII | 0.5772
±0.0059 | This paper |
| 60 | JacobiConv | 0.5738
±0.0125 | This paper |
| 80 | EvenNet | 0.5271
±0.0085 | This paper |
| 81 | SGC | 0.5230
±0.0230 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 86 | BernNet | 0.5139
±0.0092 | prev best: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) Improvement within reported uncertainty; not highlighted. |
| 112 | SIGN | 0.4559
±0.0140 | |
| 120 | SAGE | 0.4460
±0.0130 | |
| 125 | ChebNet | 0.4081
±0.0042 | prev best: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Scalable Graph Compressed Convolutions (2024) Improvement within reported uncertainty; not highlighted. |
| 172 | MLP | 0.3930
±0.0079 |
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 | |
| 5 | AdaptKry | 0.8497
±0.0036 | This paper |
| 7 | ChebNetII | 0.8486
±0.0033 | This paper |
| 8 | OptBasisGNN | 0.8485
±0.0039 | This paper |
| 20 | GPR-GNN | 0.8354
±0.0032 | This paper |
| 23 | BernNet | 0.8326
±0.0029 | This paper |
| 29 | GIN | 0.8268
±0.0032 | |
| 30 | ChebNet | 0.8259
±0.0031 | This paper |
| 31 | GCN | 0.8247
±0.0027 | This paper |
| 34 | SIGN | 0.8213
±0.0028 | This paper |
| 37 | SGC | 0.8144
±0.0015 | This paper |
| 51 | MLP | 0.7534
±0.0064 |
