Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering
Abstract
While a growing body of literature has been studying new Graph Neural Networks (GNNs) that work on both homophilic and heterophilic graphs, little has been done on adapting classical GNNs to less-homophilic graphs. Although the ability to handle less-homophilic graphs is restricted, classical GNNs still stand out in several nice properties such as efficiency, simplicity, and explainability. In this work, we propose a novel graph restructuring method that can be integrated into any type of GNNs, including classical GNNs, to leverage the benefits of existing GNNs while alleviating their limitations. Our contribution is threefold: [label= *)] learning the weight of pseudo-eigenvectors for an adaptive spectral clustering that aligns well with known node labels, proposing a new density-aware homophilic metric that is robust to label imbalance, and reconstructing the adjacency matrix based on the result of adaptive spectral clustering to maximize homophilic scores. The experimental results show that our graph restructuring method can significantly boost the performance of six classical GNNs by an average of 25\
Benchmark Results
Tested on 6 datasets SOTA at publication on 1 3 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 28 | GPRGNN | 0.8460
±0.0400 | prev best: Graph-Coupled Oscillator Networks (ICML 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Improvement within reported uncertainty; not highlighted. |
| 34 | MLP | 0.9230
±0.0070 | |
| 46 | APPNP | 0.9131
±0.0197 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) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 170 | ARMA | 0.8397
±0.0377 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 | 0.7980
±0.0430 | prev best: Graph Pointer Neural Networks (AAAI 2021) |
| 243 | CHEV | 0.8000
±0.0480 | This paper |
| 257 | GCN | 0.7840
±0.0540 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 330 | SGC | 0.7440
±0.0600 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 24 | MLP | 0.9136
±0.0070 | |
| 82 | ARMA | 0.8562
±0.0213 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. |
| 138 | SAGE | 0.8269 | |
| 146 | GPRGNN (GDC) | 0.8240
±0.0470 | This paper |
| 158 | GAT | 0.8190
±0.0540 | prev best: Graph-Coupled Oscillator Networks (ICML 2022) |
| 166 | CHEV(GDC) | 0.8110
±0.0320 | This paper |
| 170 | GCN | 0.7920
±0.0630 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 252 | SGC | 0.7350
±0.0430 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 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 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 182 | GAT | 0.3560
±0.0070 | |
| 185 | CHEV | 0.3600
±0.0110 | This paper |
| 191 | ARMA (GDC) | 0.3590
±0.0050 | This paper |
| 237 | SGC | 0.3490
±0.0070 | |
| 255 | GPRGNN (GDC) | 0.3440
±0.0100 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.6650
±0.0260 | prev best: Non-Local Graph Neural Networks (2020) best today: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) Improvement within reported uncertainty; not highlighted. |
| 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) |
| 65 | ARMA | 0.6840
±0.0230 | This paper |
| 72 | GPRGNN | 0.6748
±0.0040 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 76 | SGC | 0.6710
±0.0290 | This paper |
| 78 | CHEV | 0.6680
±0.0180 | This paper |
| 79 | APPNP | 0.6670
±0.0270 | This paper |
| 108 | SAGE | 0.6340
±0.0300 | |
| 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 | 0.5570
±0.0240 | prev best: Non-Local Graph Neural Networks (2020) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) Improvement within reported uncertainty; not highlighted. |
| 67 | GAT | 0.5630
±0.0220 | prev best: Non-Local Graph Neural Networks (2020) |
| 68 | APPNP | 0.5590
±0.0290 | This paper |
| 70 | ARMA | 0.5560
±0.0170 | This paper |
| 72 | CHEV | 0.5500
±0.0200 | This paper |
| 76 | GPRGNN | 0.5435
±0.0087 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 81 | SGC | 0.5230
±0.0230 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 172 | MLP | 0.3930
±0.0079 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 best reported | best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 5 | GPRGNN | 0.8990
±0.0300 best reported | best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 37 | MLP | 0.8629
±0.0450 | |
| 48 | ARMA | 0.8450
±0.0030 | This paper |
| 54 | CHEV | 0.8430
±0.0320 | This paper |
| 53 | GAT | 0.8430
±0.0370 | prev best: Non-Local Graph Neural Networks (2020) |
| 63 | GCN | 0.8310
±0.0320 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 69 | GraphSAGE | 0.8118
±0.0556 | |
| 91 | SGC | 0.7780
±0.0470 | This paper |
