Graph Neural Networks for Graphs with Heterophily: A Survey
Abstract
Recent years have witnessed fast developments of graph neural networks (GNNs) that have benefited myriad graph analytic tasks and applications. Most GNNs rely on the homophily assumption that nodes belonging to the same class are more likely to be connected. However, as a ubiquitous graph property in numerous real-world scenarios, heterophily,, nodes with different labels tend to be linked, significantly limits the performance of tailor-made homophilic GNNs. Hence, GNNs for heterophilic graphs are gaining increasing research attention to enhance graph learning with heterophily. In this paper, we provide a comprehensive review of GNNs for heterophilic graphs. Specifically, we propose a systematic taxonomy that governs existing heterophilic GNN models, along with general summaries and detailed analyses. Furthermore, we discuss the relationship between heterophily and various graph research domains, aiming to facilitate the development of more effective GNNs across a spectrum of practical applications and learning tasks in the graph research community. In the end, we point out potential directions to advance and inspire future research and applications on heterophilic graph learning with GNNs.
Benchmark Results
Tested on 5 datasets Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
Heterophily Benchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Dir-Poly | 0.9451
±0.0022 | |
| 2 | D-CDE | 0.9387
±0.0041 | |
| 3 | LargeScaleNet | 0.9358
±0.0024 | |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 35 | PD-GNN | 0.8923
±0.0056 | This paper |
| 64 | SAGE | 0.8574
±0.0067 | This paper |
| 77 | GCN | 0.8272
±0.0082 best reported | best today: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 83 | GAT | 0.8145
±0.0009 best reported | best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 87 | AGS-GNN | 0.8049
±0.0048 | This paper |
| 115 | ACM-GCN | 0.7189
±0.0061 best reported | best today: ATLAS: Adaptive Topology-based Learning at Scale for Homophilic and Heterophilic Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 129 | H2GCN | 0.6809
±0.0029 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 135 | MLP | 0.6665
±0.0047 | |
| 154 | GloGNN | 0.6385
±0.0049 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 168 | LINKX | 0.5914
±0.0045 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | UniGAP | 0.6375
±0.0110 | |
| 2 | H2GCN + HalfHop | 0.5961
±0.0100 | |
| 3 | GraphSAGE + HalfHop | 0.5897
±0.0150 | |
| 7 | H2GCN | 0.5681
±0.0090 best reported | |
| 12 | SAGE | 0.5569
±0.0023 best reported | |
| 14 | GAT | 0.5559
±0.0027 best reported | |
| 15 | GraphSAGE | 0.5540
±0.0020 | |
| 24 | GCN | 0.5411
±0.0034 best reported | |
| 43 | AGS-GNN | 0.5321
±0.0046 | This paper |
| 47 | ACM-GCN | 0.5294
±0.0023 | This paper |
| 53 | LINKX | 0.5268
±0.0026 | This paper |
| 79 | PD-GNN | 0.5096
±0.0043 | This paper |
| 84 | MLP | 0.5058 | |
| 196 | GloGNN | 0.3728
±0.0066 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | BuNN | 0.9899
±0.0016 | |
| 2 | DC-GNN | 0.9850
±0.0021 | |
| 3 | Tango -GPS | 0.9839
±0.0054 | |
| 32 | PD-GNN | 0.9403
±0.0045 | This paper |
| 36 | GAT | 0.9391
±0.0035 best reported | best today: Relieving the Over-Aggregating Effect in Graph Transformers (NeurIPS 2025) |
| 42 | GraphSAGE | 0.9358
±0.0005 | |
| 46 | SAGE | 0.9351
±0.0057 | This paper |
| 68 | GCN | 0.9150
±0.0006 best reported | best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 81 | ACM-GCN | 0.9047
±0.0057 | This paper |
| 85 | H2GCN | 0.8995
±0.0038 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 111 | AGS-GNN | 0.8556
±0.0028 | This paper |
| 120 | LINKX | 0.8002
±0.0003 | This paper |
| 148 | GloGNN | 0.6253
±0.0134 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 156 | MLP | 0.5099
±0.0147 |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Polynormer-r | 0.8591
±0.0074 | |
| 2 | DC-GNN | 0.8588
±0.0081 | |
| 3 | TANGO-GPS | 0.8566
±0.0101 | |
| 15 | PD-GNN | 0.8483
±0.0040 | This paper |
| 28 | GAT | 0.8443
±0.0100 best reported | best today: TopoBench: A Framework for Benchmarking Topological Deep Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 50 | GCN | 0.8364
±0.0067 | This paper |
| 76 | SAGE | 0.8243
±0.0044 | This paper |
| 77 | GraphSAGE | 0.8243
±0.0044 | |
| 84 | LINKX | 0.8115
±0.0123 best reported | best today: ATLAS: Adaptive Topology-based Learning at Scale for Homophilic and Heterophilic Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 91 | AGS-GNN | 0.8052
±0.0041 | This paper |
| 92 | ACM-GCN | 0.8045
±0.0054 | This paper |
| 113 | H2GCN | 0.7815 best reported | |
| 139 | MLP | 0.7362
±0.0020 | |
| 140 | GloGNN | 0.7339
±0.0117 | This paper |
Questions
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MLP | 0.9733
±0.0006 | |
| 2 | AGS-GNN | 0.9727 | This paper |
| 3 | MeanGNN | 0.9716
±0.0006 | |
| 4 | GCN | 0.9715
±0.0004 best reported | best today: Learning Posterior Predictive Distributions for Node Classification from Synthetic Graph Priors (ICLR 2026) |
| 5 | GAT | 0.9713
±0.0005 best reported | best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 8 | LINKX | 0.9706 | This paper |
| 11 | ACM-GCN | 0.9702 | This paper |
| 28 | PD-GNN | 0.7888 | This paper |
| 33 | SAGE | 0.7644 | This paper |
| 50 | GloGNN | 0.6574 | This paper |
| 51 | H2GCN | 0.6359 | This paper |
