Node-wise Filtering in Graph Neural Networks: A Mixture of Experts Approach
Abstract
Graph Neural Networks (GNNs) have proven to be highly effective for node classification tasks across diverse graph structural patterns. Traditionally, GNNs employ a uniform global filter—typically a low-pass filter for homophilic graphs and a high-pass filter for heterophilic graphs. However, real-world graphs often exhibit a complex mix of homophilic and heterophilic patterns, rendering a single global filter approach suboptimal. In this work, we theoretically demonstrate that a global filter optimized for one pattern can adversely affect performance on nodes with differing patterns. To address this, we introduce a novel GNN framework Node-MoE that utilizes a mixture of experts to adaptively select the appropriate filters for different nodes. Extensive experiments demonstrate the effectiveness of Node-MoE on both homophilic and heterophilic graphs.
Benchmark Results
Tested on 1 dataset 8 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 | |
| 22 | ChebNetII | 0.4175
±0.0107 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) |
| 38 | GCNII | 0.4082
±0.0179 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 41 | APPNP | 0.4046
±0.0064 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 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) |
| 58 | GloGNN | 0.3959
±0.0029 best reported | |
| 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) |
| 174 | Node-MoE | 0.3628
±0.0101 | This paper |
| 180 | LINKX | 0.3610
±0.0155 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 197 | GMoE | 0.3575
±0.0131 | This paper |
| 238 | WRGCN | 0.3489
±0.0111 | This paper |
| 439 | LP | 0.2462
±0.0051 | prev best: Simplifying Node Classification on Heterophilous Graphs with Compatible Label Propagation (TMLR 2022) |
