A Piece-wise Polynomial Filtering Approach for Graph Neural Networks
Abstract
Graph Neural Networks (GNNs) exploit signals from node features and the input graph topology to improve node classification task performance. However, these models tend to perform poorly on heterophilic graphs, where connected nodes have different labels. Recently proposed GNNs work across graphs having varying levels of homophily. Among these, models relying on polynomial graph filters have shown promise. We observe that solutions to these polynomial graph filter models are also solutions to an overdetermined system of equations. It suggests that in some instances, the model needs to learn a reasonably high order polynomial. On investigation, we find the proposed models ineffective at learning such polynomials due to their designs. To mitigate this issue, we perform an eigendecomposition of the graph and propose to learn multiple adaptive polynomial filters acting on different subsets of the spectrum. We theoretically and empirically show that our proposed model learns a better filter, thereby improving classification accuracy. We study various aspects of our proposed model including, dependency on the number of eigencomponents utilized, latent polynomial filters learned, and performance of the individual polynomials on the node classification task. We further show that our model is scalable by evaluating over large graphs. Our model achieves performance gains of up to 10\
Benchmark Results
Tested on 3 datasets 2 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 126 | FAGCN | 0.8968
±0.0097 best reported | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 306 | PP-GNN | 0.8523
±0.0136 | This paper |
| 320 | MLP | 0.8463 best reported | best at pub: Graph-less Neural Networks: Teaching Old MLPs New Tricks via Distillation (ICLR 2021) |
| 323 | TDGNN | 0.8452
±0.0092 | This paper |
| 373 | LGC | 0.8344
±0.0177 | This paper |
| 381 | SuperGAT | 0.8304
±0.0102 | This paper |
| 397 | GPR-GNN | 0.8238
±0.0160 | This paper |
| 425 | SGCN | 0.8065
±0.0278 | This paper |
| 480 | LR | 0.6492
±0.0259 | This paper |
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 | |
| 30 | GPR-GNN | 0.9291
±0.0132 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 46 | APPNP | 0.8189
±0.0585 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 59 | PP-GNN | 0.8973
±0.0490 | This paper |
| 61 | FAGCN | 0.8243
±0.0689 | prev best: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 185 | TDGNN | 0.8300
±0.0450 | This paper |
| 219 | LR | 0.8135
±0.0633 | This paper |
| 240 | LGC | 0.8020
±0.0428 | This paper |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Graph Wave Networks (WWW 2025) |
| 415 | Geom-GCN | 0.6760 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| 469 | SGCN | 0.6243
±0.0443 | This paper |
| 490 | SuperGAT | 0.6108
±0.0497 | prev best: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Improvement within reported uncertainty; not highlighted. |
| # | 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 | 0.9279
±0.0312 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Heterophily-Aware Graph Attention Network (2023) |
| 21 | APPNP | 0.8189
±0.0625 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 38 | FAGCN | 0.8852
±0.0133 best reported | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 128 | LR | 0.8324
±0.0564 | This paper |
| 135 | TDGNN | 0.8292
±0.0661 | This paper |
| 138 | SAGE | 0.8269 | |
| 144 | PP-GNN | 0.8243
±0.0427 | This paper |
| 170 | GCN | 0.6297
±0.0541 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Improvement within reported uncertainty; not highlighted. |
| 238 | LGC | 0.7459
±0.0342 | This paper |
| 342 | Geom-GCN | 0.6412 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: Steering Graph Neural Networks with Pinning Control (2023) |
| 356 | SGCN | 0.6252
±0.0510 best reported | best today: Causal-Based Supervision of Attention in Graph Neural Network: A Better and Simpler Choice towards Powerful Attention (IJCAI 2023) Difference within reported uncertainty; not counted as underperformance. |
| 416 | SuperGAT | 0.5730
±0.0853 | This paper |
