Breaking the Entanglement of Homophily and Heterophily in Semi-supervised Node Classification
Abstract
Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for daptively odeling the natural directed graphs as the ndirected or irected graph to maximize the benefits from subsequent graph learning. Furthermore, we propose daptive irected attern ggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 16 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\
Benchmark Results
Tested on 4 datasets 30 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 32 | GPRGNN | 0.8102
±0.0071 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 36 | GCNII | 0.8076
±0.0030 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 102 | GloGNN | 0.7740
±0.0170 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 122 | GRAND | 0.7657 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 312 | LINKX | 0.7319
±0.0099 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 350 | MLP | 0.7289
±0.0010 | |
| 375 | DGCN | 0.7260 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) |
| 507 | DirGNN | 0.7150
±0.0088 best reported | best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) |
| 656 | MagNet | 0.6890
±0.0067 best reported | best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) |
| 755 | AMUD | 0.6600
±0.0040 | This paper |
| 773 | NSTE | 0.6490
±0.0070 | This paper |
| 774 | JacobiConv | 0.6480
±0.0090 | This paper |
| 775 | DIMPA | 0.6480
±0.0090 | This paper |
| 776 | A2DUG | 0.6480
±0.0080 | This paper |
| 783 | DiGCN | 0.6470
±0.0060 | This paper |
| 785 | BerNet | 0.6450
±0.0060 | This paper |
| 806 | AERO-GNN | 0.6300
±0.0060 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 10 | JacobiConv | 0.9295
±0.0246 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Simplified PCNet with Robustness (2024) |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Simplified PCNet with Robustness (2024) |
| 24 | MLP | 0.9136
±0.0070 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 74 | GloGNN | 0.8595
±0.0510 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Aggregation-aware MLP: An Unsupervised Approach for Graph Message-passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 98 | AERO-GNN | 0.8480
±0.0330 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. |
| 106 | MagNet | 0.8430
±0.0700 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. |
| 123 | LINKX | 0.8346
±0.0061 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Differentiable Cluster Graph Neural Network (2024) Difference within reported uncertainty; not counted as underperformance. |
| 136 | AMUD | 0.8290
±0.0300 | This paper |
| 138 | SAGE | 0.8269 | |
| 142 | GRAND | 0.8246
±0.0709 best reported | best at pub: Dirichlet Energy Enhancement of Graph Neural Networks by Framelet Augmentation (2023) best today: Graph Navier–Stokes Networks (2026) |
| 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) |
| 173 | A2DUG | 0.8050
±0.0430 | This paper |
| 180 | DirGNN | 0.8000
±0.0360 | This paper |
| 185 | DIMPA | 0.7930
±0.0310 | This paper |
| 190 | NSTE | 0.7860
±0.0230 | This paper |
| 191 | BerNet | 0.7850
±0.0230 | This paper |
| 203 | DGCN | 0.7790
±0.0310 | This paper |
| 205 | DiGCN | 0.7780
±0.0490 | This paper |
| 252 | SGC | 0.7350
±0.0430 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 15 | DirGNN | 0.7974
±0.0140 best reported | best today: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 31 | JacobiConv | 0.7420
±0.0103 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 40 | AERO-GNN | 0.7158
±0.0240 best reported | best today: Scalable Graph Compressed Convolutions (2024) |
| 45 | GloGNN | 0.7133
±0.0242 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 52 | GCN | 0.7033 best reported | best at pub: Spectral-Aware Augmentation for Enhanced Graph Representation Learning (2023) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 64 | LINKX | 0.6842
±0.0132 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 72 | GPRGNN | 0.6748
±0.0040 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 76 | SGC | 0.6710
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 103 | GCNII | 0.6386
±0.0304 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Scalable Graph Compressed Convolutions (2024) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 147 | MagNet | 0.5832
±0.0287 best reported | best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 151 | GRAND | 0.5772
±0.0186 best reported | best at pub: TIDE: Time Derivative Diffusion for Deep Learning on Graphs (ICML 2022) |
| 169 | MLP | 0.5429 | |
| 218 | AMUD | 0.4620
±0.0130 | This paper |
| 231 | DIMPA | 0.4380
±0.0160 | This paper |
| 232 | A2DUG | 0.4380
±0.0280 | This paper |
| 235 | DiGCN | 0.4340
±0.0180 | This paper |
| 243 | DGCN | 0.4230
±0.0230 | This paper |
| 244 | NSTE | 0.4220
±0.0260 | This paper |
| 262 | BerNet | 0.3860
±0.0180 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 9 | DirGNN | 0.7513
±0.0195 best reported | best today: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 19 | GloGNN | 0.7121
±0.0184 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 40 | LINKX | 0.6181
±0.0180 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 41 | AERO-GNN | 0.6176
±0.0240 best reported | best today: Scalable Graph Compressed Convolutions (2024) |
| 46 | GCN | 0.6067 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 60 | JacobiConv | 0.5738
±0.0125 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) |
| 76 | GPRGNN | 0.5435
±0.0087 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 81 | SGC | 0.5230
±0.0230 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 116 | AMUD | 0.4520
±0.0130 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 134 | A2DUG | 0.4280
±0.0110 | This paper |
| 136 | MagNet | 0.4270
±0.0150 | This paper |
| 145 | DiGCN | 0.4200
±0.0170 | This paper |
| 148 | NSTE | 0.4190
±0.0090 | This paper |
| 153 | DIMPA | 0.4120
±0.0100 | This paper |
| 158 | DGCN | 0.4060
±0.0100 | This paper |
| 164 | GRAND | 0.4005
±0.0150 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 172 | MLP | 0.3930
±0.0079 | |
| 176 | GCNII | 0.3881
±0.0197 best reported | best at pub: GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 188 | BerNet | 0.3790
±0.0080 | This paper |
