ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting
Abstract
While Graph Neural Networks (GNNs) have achieved enormous success in multiple graph analytical tasks, modern variants mostly rely on the strong inductive bias of homophily. However, real-world networks typically exhibit both homophilic and heterophilic linking patterns, wherein adjacent nodes may share dissimilar attributes and distinct labels. Therefore, GNNs smoothing node proximity holistically may aggregate both task-relevant and irrelevant (even harmful) information, limiting their ability to generalize to heterophilic graphs and potentially causing non-robustness. In this work, we propose a novel Edge Splitting GNN (ES-GNN) framework to adaptively distinguish between graph edges either relevant or irrelevant to learning tasks. This essentially transfers the original graph into two subgraphs with the same node set but complementary edge sets dynamically. Given that, information propagation separately on these subgraphs and edge splitting are alternatively conducted, thus disentangling the task-relevant and irrelevant features. Theoretically, we show that our ES-GNN can be regarded as a solution to a disentangled graph denoising problem, which further illustrates our motivations and interprets the improved generalization beyond homophily. Extensive experiments over 11 benchmark and 1 synthetic datasets not only demonstrate the effective performance of ES-GNN but also highlight its robustness to adversarial graphs and mitigation of the over-smoothing problem.
Benchmark Results
Tested on 3 datasets 9 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 | |
| 5 | ACM-GCN | 0.9557
±0.0360 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 30 | GPR-GNN | 0.9291
±0.0132 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 34 | MLP | 0.9230
±0.0070 | |
| 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) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 104 | WRGAT | 0.8698 best reported | best today: Global-Local Graph Neural Networks for Node-Classification (2024) Difference within reported uncertainty; not counted as underperformance. |
| 141 | GloGNN | 0.8524
±0.0490 best reported | best at pub: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 175 | GOAL | 0.8362
±0.0670 best reported | best today: Sign is Not a Remedy: Multiset-to-Multiset Message Passing for Learning on Heterophilic Graphs (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 198 | ES-GNN | 0.8230
±0.0570 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Graph Pointer Neural Networks (AAAI 2021) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Graph Wave Networks (WWW 2025) |
| 273 | GEN | 0.7830
±0.0800 | This paper |
| 330 | SGC | 0.7440
±0.0600 best reported | best at pub: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 379 | DisenGCN | 0.7130
±0.0570 | This paper |
| 398 | FactorGCN | 0.6950
±0.0650 | This paper |
| 429 | NeuralSparse | 0.6640
±0.0570 | This paper |
| 489 | GCN-LPA | 0.6120
±0.0760 | This paper |
| 496 | DisGNN | 0.6060
±0.0390 | This paper |
| 562 | VEPM | 0.5580
±0.0430 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 best reported | best today: Heterophily-informed Message Passing (TMLR 2025) |
| 3 | RF-GCN | 0.9429 | |
| 11 | GPR-GNN | 0.9279
±0.0312 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Heterophily-Aware Graph Attention Network (2023) |
| 24 | MLP | 0.9136
±0.0070 | |
| 38 | FAGCN | 0.7940
±0.0550 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 74 | GloGNN | 0.8595
±0.0510 best reported | best at pub: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) best today: Aggregation-aware MLP: An Unsupervised Approach for Graph Message-passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 81 | GOAL | 0.8568
±0.0620 best reported | best today: Sign is Not a Remedy: Multiset-to-Multiset Message Passing for Learning on Heterophilic Graphs (ICML 2024) |
| 138 | SAGE | 0.8269 | |
| 150 | ES-GNN | 0.8220
±0.0400 | This paper |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 160 | WRGAT | 0.8162
±0.0390 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 168 | GEN | 0.8100
±0.0390 | This paper |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 211 | DisenGCN | 0.7740
±0.0440 | This paper |
| 252 | SGC | 0.7350
±0.0430 best reported | best at pub: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 324 | GCN-LPA | 0.6560
±0.0730 | This paper |
| 343 | NeuralSparse | 0.6410
±0.0550 | This paper |
| 467 | DisGNN | 0.5200
±0.0570 | This paper |
| 475 | VEPM | 0.5120
±0.0700 | This paper |
| 482 | FactorGCN | 0.5060
±0.0180 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 16 | ACM-GCN | 0.4198
±0.0089 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 42 | MLP | 0.4026
±0.0108 | |
| 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) |
| 56 | FAGCN | 0.3970 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 58 | GloGNN | 0.3820
±0.0120 | prev best: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 69 | ES-GNN | 0.3890
±0.0080 | This paper |
| 71 | H2GCN | 0.3840
±0.0100 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) |
| 75 | WRGAT | 0.3860
±0.0110 | prev best: Simplifying approach to Node Classification in Graph Neural Networks (2021) |
| 104 | GCN-LPA | 0.3780
±0.0090 | This paper |
| 119 | GEN | 0.3730
±0.0140 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 150 | DisenGCN | 0.3670
±0.0120 | This paper |
| 163 | GOAL | 0.3646
±0.0100 best reported | best today: Sign is Not a Remedy: Multiset-to-Multiset Message Passing for Learning on Heterophilic Graphs (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 182 | GAT | 0.3050
±0.0120 | prev best: Graph Pointer Neural Networks (AAAI 2021) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 212 | NeuralSparse | 0.3550
±0.0110 | This paper |
| 237 | SGC | 0.3090
±0.0060 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 346 | DisGNN | 0.3020
±0.0130 | This paper |
| 365 | VEPM | 0.2930
±0.0110 | This paper |
| 372 | FactorGCN | 0.2900
±0.0140 | This paper |
