Label-Wise Graph Convolutional Network for Heterophilic Graphs
Abstract
Graph Neural Networks (GNNs) have achieved remarkable performance in modeling graphs for various applications. However, most existing GNNs assume the graphs exhibit strong homophily in node labels, i.e., nodes with similar labels are connected in the graphs. They fail to generalize to heterophilic graphs where linked nodes may have dissimilar labels and attributes. Therefore, we investigate a novel framework that performs well on graphs with either homophily or heterophily. Specifically, we propose a label-wise message passing mechanism to avoid the negative effects caused by aggregating dissimilar node representations and preserve the heterophilic contexts for representation learning. We further propose a bi-level optimization method to automatically select the model for graphs with homophily/heterophily. Theoretical analysis and extensive experiments demonstrate the effectiveness of our proposed framework for node classification on both homophilic and heterophilic graphs.
Benchmark Results
Tested on 3 datasets 1 baseline value 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 | |
| 28 | GPRGNN | 0.7700
±0.0640 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 117 | GCNs | 0.8620
±0.0580 | This paper |
| 130 | ASGC | 0.8590
±0.0470 | This paper |
| 141 | GloGNN | 0.8524
±0.0490 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 144 | BM-GCN | 0.8513
±0.0464 best reported | best today: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 213 | SimP-GCN | 0.8160 best reported | best at pub: Non-Local Graph Neural Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Graph Wave Networks (WWW 2025) |
| 276 | MixHop | 0.7784
±0.0773 best reported | best at pub: Graph Pointer Neural Networks (AAAI 2021) best today: Graph Navier–Stokes Networks (2026) |
| 325 | LINKX | 0.7460
±0.0840 | This paper |
| 490 | SuperGAT | 0.6108
±0.0497 best reported | best today: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (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 | |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 35 | GCNII | 0.8030
±0.0530 | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Improvement within reported uncertainty; not highlighted. |
| 131 | GCNs | 0.8320
±0.0550 | This paper |
| 138 | SAGE | 0.8269 | |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 183 | MixHop | 0.7950
±0.0630 | prev best: Graph Pointer Neural Networks (AAAI 2021) Improvement within reported uncertainty; not highlighted. |
| 416 | SuperGAT | 0.5730
±0.0430 | This paper |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LargeScaleNet | 0.6582
±0.0036 | |
| 2 | S² DirGCN | 0.6495
±0.0033 | |
| 3 | FaberNet | 0.6462
±0.0101 | |
| 13 | LINKX | 0.5600
±0.0130 | This paper |
| 14 | GCNs | 0.5580
±0.0020 | This paper |
| 16 | GloGNN | 0.5480
±0.0030 | This paper |
| 19 | MixHop | 0.5181
±0.0017 best reported | |
| 23 | H2GCN | 0.4910
±0.0010 | This paper |
| 26 | GCNII | 0.4721
±0.0028 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. |
| 31 | GCN | 0.4602
±0.0026 best reported | best today: Scale-aware Message Passing For Graph Node Classification (2024) Difference within reported uncertainty; not counted as underperformance. |
| 34 | GPRGNN | 0.4510
±0.0020 | This paper |
| 44 | FAGCN | 0.4060
±0.0040 | This paper |
| 49 | ASGC | 0.3920
±0.0010 | This paper |
| 54 | SuperGAT | 0.3810
±0.0010 | This paper |
| 56 | MLP | 0.3670
±0.0020 | This paper |
