Heterophily-Aware Graph Attention Network
Abstract
Graph Neural Networks (GNNs) have shown remarkable success in graph representation learning. Unfortunately, current weight assignment schemes in standard GNNs, such as the calculation based on node degrees or pair-wise representations, can hardly be effective in processing the networks with heterophily, in which the connected nodes usually possess different labels or features. Existing heterophilic GNNs tend to ignore the modeling of heterophily of each edge, which is also a vital part in tackling the heterophily problem. In this paper, we first propose a heterophily-aware attention scheme and reveal the benefits of modeling the edge heterophily, i.e., if a GNN assigns different weights to edges according to different heterophilic types, it can learn effective local attention patterns, enabling nodes to acquire appropriate information from distinct neighbors. Then, we propose a novel Heterophily-Aware Graph Attention Network (HA-GAT) by fully exploring and utilizing the local distribution as the underlying heterophily, to handle the networks with different homophily ratios. To demonstrate the effectiveness of the proposed HA-GAT, we analyze the proposed heterophily-aware attention scheme and local distribution exploration, by seeking an interpretation from their mechanism. Extensive results demonstrate that our HA-GAT achieves state-of-the-art performances on eight datasets with different homophily ratios in both the supervised and semi-supervised node classification tasks.
Benchmark Results
Tested on 3 datasets 5 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 | |
| 30 | GPR-GNN | 0.9291
±0.0132 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Difference within reported uncertainty; not counted as underperformance. |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: Design your own universe: a physics-informed agnostic method for enhancing graph neural networks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 44 | HA-GAT | 0.9175
±0.0352 | This paper |
| 53 | GraphSAGE | 0.8420
±0.0492 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) Improvement within reported uncertainty; not highlighted. |
| 68 | DMP | 0.8919 best reported | 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. |
| 113 | ChebyNet | 0.8622
±0.0245 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 144 | BM-GCN | 0.8513
±0.0464 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) Difference within reported uncertainty; not counted as underperformance. |
| 251 | JKNet-GCN | 0.7962
±0.0394 | This paper |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 258 | GATv2 | 0.7929
±0.0403 | This paper |
| 415 | Geom-GCN | 0.6760 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 8 | HA-GAT | 0.9344
±0.0284 | This paper |
| 11 | GPR-GNN | 0.9279
±0.0312 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 31 | DMP | 0.8919 best reported | 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. |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 101 | ChebyNet | 0.8459
±0.0449 | This paper |
| 138 | SAGE | 0.8269 | |
| 156 | BM-GCN | 0.8197
±0.0613 | This paper |
| 157 | GraphSAGE | 0.8196
±0.0739 | prev best: Graph-Coupled Oscillator Networks (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 177 | GATv2 | 0.8033
±0.0333 | This paper |
| 216 | JKNet-GCN | 0.7716
±0.0421 | 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) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 13 | HA-GAT(M) | 0.4216
±0.0114 | This paper |
| 42 | MLP | 0.4026
±0.0108 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 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. |
| 59 | BM-GCN | 0.3956
±0.0143 | This paper |
| 64 | ChebyNet | 0.3917
±0.0143 | This paper |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 87 | Geom-GCN | 0.3810 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 122 | DMP | 0.3726
±0.0179 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) Difference within reported uncertainty; not counted as underperformance. |
| 230 | GATv2 | 0.3494
±0.0121 | prev best: Deformable Graph Transformer (2022) |
| 254 | JKNet-GCN | 0.3441
±0.0130 | This paper |
| 266 | GIN | 0.3410
±0.0030 |
