Is Homophily a Necessity for Graph Neural Networks?
Abstract
Graph neural networks (GNNs) have shown great prowess in learning representations suitable for numerous graph-based machine learning tasks. When applied to semi-supervised node classification, GNNs are widely believed to work well due to the homophily assumption (``like attracts like''), and fail to generalize to heterophilous graphs where dissimilar nodes connect. Recent works have designed new architectures to overcome such heterophily-related limitations. However, we empirically find that standard graph convolutional networks (GCNs) can actually achieve strong performance on some commonly used heterophilous graphs. This motivates us to reconsider whether homophily is truly necessary for good GNN performance. We find that this claim is not quite accurate, and certain types of ``good'' heterophily exist, under which GCNs can achieve strong performance. Our work carefully characterizes the implications of different heterophily conditions, and provides supporting theoretical understanding and empirical observations. Finally, we examine existing heterophilous graphs benchmarks and reconcile how the GCN (under)performs on them based on this understanding.
Benchmark Results
Tested on 4 datasets
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 today: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 34 | MLP | 0.8330
±0.0454 | best today: Design your own universe: a physics-informed agnostic method for enhancing graph neural networks (2024) Improvement within reported uncertainty; not highlighted. |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 150 | H2GCN-1 | 0.8486
±0.0677 | This paper |
| 176 | MLP + GCN | 0.8360
±0.0604 | This paper |
| 191 | CPGNN-MLP | 0.8262
±0.0688 | This paper |
| 203 | H2GCN-2 | 0.8216
±0.0528 | This paper |
| 257 | GCN | 0.6381
±0.0527 | prev best: Non-Local Graph Neural Networks (2020) best today: Graph Wave Networks (WWW 2025) Improvement within reported uncertainty; not highlighted. |
| 289 | CPGNN-Cheby | 0.7703
±0.0583 best reported | best today: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 11 | GPR-GNN | 0.9279
±0.0312 best reported | best today: Heterophily-Aware Graph Attention Network (2023) |
| 24 | MLP | 0.8486
±0.0604 | prev best: Non-Local Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 97 | MLP + GCN | 0.8482
±0.0487 | This paper |
| 138 | SAGE | 0.8269 | |
| 153 | H2GCN-1 | 0.8216
±0.0600 | This paper |
| 154 | H2GCN-2 | 0.8216
±0.0600 | This paper |
| 170 | GCN | 0.5935
±0.0419 | best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Improvement within reported uncertainty; not highlighted. |
| 182 | CPGNN-MLP | 0.7993
±0.0612 | This paper |
| 233 | CPGNN-Cheby | 0.7508
±0.0751 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.3617
±0.0109 | best today: Heterophily-Aware Graph Attention Network (2023) Improvement within reported uncertainty; not highlighted. |
| 53 | GPR-GNN | 0.3992
±0.0067 best reported | best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 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) |
| 175 | MLP + GCN | 0.3624
±0.0109 | This paper |
| 190 | H2GCN-1 | 0.3594
±0.0130 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Steering Graph Neural Networks with Pinning Control (2023) Difference within reported uncertainty; not counted as underperformance. |
| 196 | CPGNN-MLP | 0.3576
±0.0092 | This paper |
| 204 | H2GCN-2 | 0.3562
±0.0130 | This paper |
| 258 | CPGNN-Cheby | 0.3428
±0.0077 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 | |
| 35 | H2GCN-1 | 0.8667
±0.0469 | This paper |
| 36 | MLP + GCN | 0.8643
±0.0400 | This paper |
| 37 | MLP | 0.8629
±0.0450 | prev best: Non-Local Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 39 | H2GCN-2 | 0.8588
±0.0422 | This paper |
| 47 | CPGNN-MLP | 0.8458
±0.0272 | This paper |
| 56 | GPR-GNN | 0.8412 best reported | best today: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 63 | GCN | 0.6176
±0.0615 | prev best: Non-Local Graph Neural Networks (2020) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 69 | GraphSAGE | 0.8118
±0.0556 | |
| 83 | CPGNN-Cheby | 0.7919
±0.0280 | This paper |
