Partition-wise Graph Filtering: A Unified Perspective Through the Lens of Graph Coarsening
Abstract
Filtering-based graph neural networks (GNNs) constitute a distinct class of GNNs that employ graph filters to handle graph-structured data, achieving notable success in various graph-related tasks. Conventional methods adopt a graph-wise filtering paradigm, imposing a uniform filter across all nodes, yet recent findings suggest that this rigid paradigm struggles with heterophilic graphs. To overcome this, recent works have introduced node-wise filtering, which assigns distinct filters to individual nodes, offering enhanced adaptability. However, a fundamental gap remains: a comprehensive framework unifying these two strategies is still absent, limiting theoretical insights into the filtering paradigms. Moreover, through the lens of Contextual Stochastic Block Model, we reveal that a synthesis of graph-wise and node-wise filtering provides a sufficient solution for classification on graphs exhibiting both homophily and heterophily, suggesting the risk of excessive parameterization and potential overfitting with node-wise filtering. To address the limitations, this paper introduces Coarsening-guided Partition-wise Filtering (CPF). CPF innovates by performing filtering on node partitions. The method begins with partition-wise filtering, which filters node partitions obtained via graph coarsening algorithms, and then performs partition-wise filtering, refining node embeddings via filtering on clusters produced by $k$-means clustering over features. In-depth analysis is conducted for each phase of CPF, showing its superiority over other paradigms. Finally, benchmark node classification experiments, along with a real-world graph anomaly detection application, validate CPF's efficacy and practical utility. Code is available with the Github repository:.
Benchmark Results
Tested on 3 datasets 11 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 36 | CPF | 0.8928
±0.0070 | This paper |
| 39 | SAGE | 0.8911
±0.0012 | |
| 45 | GCNII | 0.8893
±0.0137 best reported | best at pub: Language is All a Graph Needs (2023) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 51 | H2GCN | 0.8882
±0.0011 best reported | |
| 64 | JacobiConv | 0.8853
±0.0080 | This paper |
| 72 | OptBasis | 0.8835
±0.0060 | This paper |
| 73 | UniFilter | 0.8831
±0.0070 | This paper |
| 76 | NIGCN | 0.8829
±0.0050 | This paper |
| 77 | GPRGNN | 0.8826
±0.0050 | This paper |
| 81 | AdaptKry | 0.8823
±0.0070 | This paper |
| 85 | Specformer | 0.8819
±0.0060 | This paper |
| 86 | ChebNetII | 0.8817
±0.0040 | This paper |
| 88 | GloGNN | 0.8812
±0.0040 | This paper |
| 91 | NFGNN | 0.8806
±0.0040 | This paper |
| 120 | OrderGNN | 0.8755
±0.0020 | This paper |
| 133 | ACMGCN | 0.8721
±0.0040 | This paper |
| 137 | Node-MoE | 0.8716
±0.0080 | This paper |
| 139 | ChebNet | 0.8712
±0.0060 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) Difference within reported uncertainty; not counted as underperformance. |
| 243 | LINKX | 0.8464
±0.0113 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Difference within reported uncertainty; not counted as underperformance. |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 16 | H2GCN | 0.9361
±0.0013 best reported | |
| 18 | GCN | 0.9296
±0.0015 best reported | |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 76 | CPF | 0.8993
±0.0050 | This paper |
| 85 | GloGNN | 0.8960
±0.0040 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 87 | JacobiConv | 0.8951
±0.0020 | This paper |
| 89 | Specformer | 0.8947
±0.0048 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 92 | OptBasis | 0.8938
±0.0030 | This paper |
| 94 | UniFilter | 0.8930
±0.0040 | This paper |
| 101 | GPRGNN | 0.8911
±0.0008 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 110 | ChebNetII | 0.8898
±0.0040 | This paper |
| 116 | SAGE | 0.8881
±0.0015 | |
| 123 | NIGCN | 0.8869
±0.0030 | This paper |
| 128 | Node-MoE | 0.8854
±0.0050 | This paper |
| 134 | NFGNN | 0.8843
±0.0040 | This paper |
| 137 | AdaptKry | 0.8838
±0.0060 | This paper |
| 143 | OrderGNN | 0.8831
±0.0030 | This paper |
| 162 | LINKX | 0.8786
±0.0077 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 192 | ACMGCN | 0.8737
±0.0040 | This paper |
| 199 | ChebNet | 0.8718
±0.0029 best reported | best at pub: Non-backtracking Graph Neural Networks (TMLR 2023) |
| 210 | MLP | 0.8690
±0.0074 |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | SGC | 0.7910 best reported | best at pub: Unifews: You Need Fewer Operations for Efficient Graph Neural Networks (ICML 2024) |
| 2 | GAMLP | 0.7036
±0.0002 | |
| 3 | GLEM-GNN | 0.7036
±0.0002 | |
| 6 | CPF | 0.6887
±0.0030 | This paper |
| 21 | ChebNetII | 0.6718
±0.0032 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Graph Neural Networks with Learnable and Optimal Polynomial Bases (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 23 | AdaptKry | 0.6707
±0.0020 | This paper |
| 25 | OptBasis | 0.6703
±0.0030 | This paper |
| 28 | UniFilter | 0.6679
±0.0030 | This paper |
| 31 | NIGCN | 0.6657
±0.0020 | This paper |
| 35 | SAGE | 0.6644
±0.0017 | |
| 37 | NFGNN | 0.6638
±0.0020 | This paper |
| 44 | PCConv | 0.6619
±0.0020 | This paper |
| 45 | GPRGNN | 0.6613
±0.0020 | This paper |
| 46 | Node-MoE | 0.6612
±0.0020 | This paper |
| 47 | BernNet | 0.6608
±0.0020 | This paper |
| 56 | JacobiConv | 0.6545
±0.0020 | This paper |
| 60 | FEGNN | 0.6519
±0.0030 | This paper |
| 80 | APPNP | 0.6288
±0.0010 | prev best: Unifews: You Need Fewer Operations for Efficient Graph Neural Networks (ICML 2024) |
| 95 | MLP | 0.4960
±0.0030 |
