Scale-aware Message Passing For Graph Node Classification
Abstract
Most Graph Neural Networks (GNNs) operate at the first-order scale, even though multi-scale representations are known to be crucial in domains such as image classification. In this work, we investigate whether GNNs can similarly benefit from multi-scale learning, rather than being limited to a fixed depth of $k$-hop aggregation. We begin by formalizing scale invariance in graph learning, providing theoretical guarantees and empirical evidence for its effectiveness. Building on this principle, we introduce ScaleNet, a scale-aware message-passing architecture that combines directed multi-scale feature aggregation with an adaptive self-loop mechanism. ScaleNet achieves state-of-the-art performance on six benchmark datasets, covering both homophilic and heterophilic graphs. To handle scalability, we further propose LargeScaleNet, which extends multi-scale learning to large graphs and sets new state-of-the-art results on three large-scale benchmarks. We also show that FaberNet’s strength largely arises from multi-scale feature integration. Together with these state-of-the-art results, our findings suggest that scale invariance may serve as a valuable principle for improving the performance of single-order GNNs. The code for all experiments is available at this link.
Benchmark Results
Tested on 6 datasets 19 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 best reported | best at pub: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 12 | APPNP | 0.8754 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 54 | GIN | 0.8303
±0.0021 | |
| 57 | SGFormer | 0.8271
±0.0056 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 90 | Polynormer | 0.8026
±0.0092 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 109 | ScaleNet | 0.7960
±0.0070 | This paper |
| 110 | MagNet | 0.7959
±0.0039 best reported | |
| 120 | GraphGPS | 0.7926
±0.0057 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 127 | 1iGi2 | 0.7920
±0.0050 | This paper |
| 137 | LargeScaleNet | 0.7900
±0.0050 | This paper |
| 167 | DiGib | 0.7830
±0.0070 | This paper |
| 195 | 1iG | 0.7740
±0.0060 | This paper |
| 202 | Dir-GNN | 0.7720
±0.0080 | This paper |
| 207 | DiG | 0.7710
±0.0100 | This paper |
| 210 | ChebNet | 0.7690
±0.0090 | This paper |
| 223 | 1iGu2 | 0.7560
±0.0090 | This paper |
| 227 | 1ym | 0.7540
±0.0040 | This paper |
| 237 | MLP | 0.7340
±0.0060 | prev best: Fully-inductive Node Classification on Arbitrary Graphs (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 262 | SigMaNet | 0.7140
±0.0070 | This paper |
| 312 | QuaNet | 0.5520
±0.0190 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 7 | Dir-GNN | 0.8048
±0.0146 best reported | best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 11 | ScaleNet | 0.8010
±0.0150 | This paper |
| 13 | LargeScaleNet | 0.7990
±0.0160 | This paper |
| 52 | GCN | 0.7033 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 53 | 1iG | 0.7020
±0.0160 | This paper |
| 79 | APPNP | 0.6670
±0.0270 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 108 | SAGE | 0.6340
±0.0300 | This paper |
| 115 | GraphSAGE | 0.6215
±0.0042 | |
| 132 | 1iGu2 | 0.6040
±0.0240 | This paper |
| 138 | Polynormer | 0.6000
±0.0180 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 140 | ChebNet | 0.5928
±0.0125 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) Difference within reported uncertainty; not counted as underperformance. |
| 146 | 1iGi2 | 0.5840
±0.0250 | This paper |
| 147 | MagNet | 0.5820
±0.0290 | |
| 150 | Sym | 0.5780
±0.0300 | This paper |
| 159 | GraphGPS | 0.5620
±0.0380 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 166 | 1ym | 0.5490
±0.0270 | This paper |
| 169 | MLP | 0.5429 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 180 | DiGib | 0.5220
±0.0370 | This paper |
| 188 | SGFormer | 0.5140
±0.0170 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 193 | DiG | 0.5040
±0.0210 | This paper |
| 260 | QuaNet | 0.3880
±0.0290 | 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 | |
| 5 | ScaleNet | 0.7600
±0.0200 | This paper |
| 6 | LargeScaleNet | 0.7590
±0.0200 | This paper |
| 7 | Dir-GNN | 0.7560
±0.0190 | This paper |
| 46 | GCN | 0.6067 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 61 | GraphGPS | 0.5690
±0.0300 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 68 | APPNP | 0.5590
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 87 | 1iG | 0.5070
±0.0580 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | This paper |
| 125 | ChebNet | 0.4386
±0.0164 best reported | best at pub: Scalable Graph Compressed Convolutions (2024) |
| 128 | GraphSAGE | 0.4378
±0.0190 | |
| 136 | MagNet | 0.4270
±0.0150 best reported | |
| 137 | 1iGi2 | 0.4270
±0.0250 | This paper |
| 138 | SGFormer | 0.4265
±0.0241 best reported | best at pub: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 146 | Polynormer | 0.4197
±0.0214 best reported | |
| 161 | 1iGu2 | 0.4040
±0.0180 | This paper |
| 172 | MLP | 0.3930
±0.0079 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 173 | DiG | 0.3920
±0.0180 | This paper |
| 183 | Sym | 0.3810
±0.0140 | This paper |
| 190 | DiGib | 0.3770
±0.0150 | This paper |
| 213 | 1ym | 0.3550
±0.0110 | This paper |
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 | This paper |
| 7 | Polynormer | 0.9266
±0.0060 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 9 | FaberNet | 0.9232
±0.0030 | prev best: HoloNets: Spectral Convolutions do extend to Directed Graphs (ICLR 2023) Improvement within reported uncertainty; not highlighted. |
| 22 | DirGNN | 0.9130
±0.0046 | This paper |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 47 | MagNet | 0.8807
±0.0027 | This paper |
| 77 | GCN | 0.8272
±0.0082 best reported | best at pub: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 78 | GraphGPS | 0.8272
±0.0068 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 92 | FSGNN | 0.7992
±0.0056 | This paper |
| 135 | MLP | 0.6665
±0.0047 best reported | best at pub: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 144 | SGphormer | 0.6507
±0.0051 | This paper |
| 184 | DiGCN | 0.5271
±0.0032 | This paper |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LargeScaleNet | 0.6582
±0.0036 | This paper |
| 2 | S² DirGCN | 0.6495
±0.0033 | |
| 3 | FaberNet | 0.6462
±0.0101 | This paper |
| 5 | DirGNN | 0.6397
±0.0030 | This paper |
| 9 | MagNet | 0.6029
±0.0027 | This paper |
| 18 | Polynormer | 0.5250
±0.0077 | This paper |
| 20 | FSGNN | 0.5047
±0.0021 | This paper |
| 31 | GCN | 0.4602
±0.0026 | This paper |
| 56 | MLP | 0.3670
±0.0021 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | FaberNet | 0.7510
±0.0003 best reported | best at pub: HoloNets: Spectral Convolutions do extend to Directed Graphs (ICLR 2023) |
| 2 | LargeScaleNet | 0.7505
±0.0005 | This paper |
| 3 | DirGNN | 0.7395
±0.0005 | This paper |
| 9 | FSGNN | 0.6507
±0.0003 | This paper |
| 16 | GCN | 0.5102
±0.0006 | prev best: Non-Local Graph Neural Networks (2020) |
| 32 | MLP | 0.3150 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
