SCNode: Spatial and Contextual Coordinates for Graph Representation Learning
Abstract
Effective node representation lies at the heart of Graph Neural Networks (GNNs), as it directly impacts their ability to perform downstream tasks such as node classification and link prediction. Most existing GNNs, particularly message passing graph neural networks, rely on neighborhood aggregation to iteratively compute node embeddings. While powerful, this paradigm suffers from well-known limitations of oversquashing, oversmoothing, and underreaching that degrade representation quality. More critically, MPGNNs often assume homophily, where connected nodes share similar features or labels, leading to poor generalization in heterophilic graphs where this assumption breaks down. To address these challenges, we propose SCNode, a Spatial-Contextual Node Embedding framework designed to perform consistently well in both homophilic and heterophilic settings. SCNode integrates spatial and contextual information, yielding node embeddings that are not only more discriminative but also structurally aware. Our approach introduces new homophily matrices for understanding class interactions and tendencies. Extensive experiments on benchmark datasets show that SCNode achieves superior performance over conventional GNN models, demonstrating its robustness and adaptability in diverse graph structures.
Benchmark Results
Tested on 11 datasets 18 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 58 | SCNode | 0.8865
±0.0125 | This paper |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 92 | SCNode | 0.7783
±0.0160 | This paper |
| 350 | MLP | 0.7289
±0.0010 |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GIANT-XRT | 0.7612
±0.0016 | |
| 2 | GEGCN | 0.7576
±0.0064 | |
| 3 | AGDN | 0.7522
±0.0007 | |
| 8 | RevGAT | 0.7426 | This paper |
| 11 | UniMP-v2 | 0.7392 | This paper |
| 14 | LEGNN | 0.7371 | This paper |
| 23 | GCN | 0.7300
±0.0017 | |
| 33 | DeepGCN | 0.7232 | This paper |
| 58 | SCNode | 0.7156 | This paper |
| 61 | GSAGE | 0.7149 | This paper |
| 66 | S3GCL | 0.7136 | This paper |
| 107 | MLP | 0.5765
±0.0012 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LMSPS+LP+MS | 0.5784
±0.0022 | |
| 2 | SeHGNN+emb+ms | 0.5719
±0.0012 | |
| 3 | SeHGNN+ms | 0.5671
±0.0014 | |
| 10 | LMSPS | 0.5483 | This paper |
| 23 | LEGNN | 0.5378 | |
| 33 | R-HGNN | 0.5204 | This paper |
| 42 | HGT | 0.5023
±0.0048 best reported | best at pub: Graph Attention MLP with Reliable Label Utilization (2021) |
| 43 | SCNode | 0.5003 | This paper |
| 47 | GAT | 0.4860
±0.0029 best reported | |
| 48 | RGCN | 0.4811
±0.0048 best reported | best at pub: Efficient Heterogeneous Graph Learning via Random Projection (2023) Difference within reported uncertainty; not counted as underperformance. |
| 57 | GraphSAGE | 0.4646
±0.0060 | |
| 60 | GCN | 0.4290
±0.0050 best reported | |
| 68 | GSAGE | 0.3704 | This paper |
| 76 | MLP | 0.3243 |
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 | |
| 10 | SCNode | 0.9459
±0.0525 | This paper |
| 34 | MLP | 0.9230
±0.0070 | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Global-Local Graph Neural Networks for Node-Classification (2024) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 415 | Geom-GCN | 0.6760 best reported | best at pub: Non-Local Graph Neural Networks (2020) 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 | |
| 43 | SCNode | 0.8809
±0.0191 | This paper |
| 138 | SAGE | 0.8269 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 best reported | best at pub: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) |
| 4 | SCNode | 0.8408
±0.0155 | This paper |
| 25 | FSGNN | 0.7827
±0.0128 best reported | best today: Directed Homophily-Aware Graph Neural Network (2025) |
| 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 | |
| 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) |
| 133 | H2GCN | 0.6030
±0.0231 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 138 | Polynormer | 0.6000
±0.0180 best reported | best today: Scale-aware Message Passing For Graph Node Classification (2024) |
| 159 | GraphGPS | 0.5620
±0.0380 best reported | best today: Scale-aware Message Passing For Graph Node Classification (2024) |
| 169 | MLP | 0.5429 | |
| 188 | SGFormer | 0.5140
±0.0170 best reported | best today: Scale-aware Message Passing For Graph Node Classification (2024) |
| 249 | LRGNN | 0.4124
±0.0295 | This paper |
| 267 | NodeFormer | 0.3638
±0.0385 best reported | best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Difference within reported uncertainty; not counted as underperformance. |
| 270 | CPGNN | 0.3300
±0.0315 | 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 | |
| 11 | FSGNN | 0.7416 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) |
| 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) |
| 39 | H2GCN | 0.6190
±0.0140 best reported | |
| 46 | GCN | 0.6067 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 61 | GraphGPS | 0.5690
±0.0300 best reported | best today: Scale-aware Message Passing For Graph Node Classification (2024) |
| 67 | GAT | 0.5630
±0.0220 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 111 | SCNode | 0.4585
±0.0236 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 138 | SGFormer | 0.4265
±0.0241 best reported | |
| 170 | LRGNN | 0.3951
±0.0212 | This paper |
| 172 | MLP | 0.3930
±0.0079 | |
| 175 | NodeFormer | 0.3889
±0.0267 best reported | best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Difference within reported uncertainty; not counted as underperformance. |
| 241 | CPGNN | 0.3004
±0.0203 | This paper |
Heterophily Benchmark
| # | 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 | |
| 28 | GAT | 0.8443
±0.0100 best reported | best at pub: TopoBench: A Framework for Benchmarking Topological Deep Learning (2024) |
| 50 | GCN | 0.8364
±0.0067 | |
| 59 | SGFormer | 0.8333
±0.0068 | This paper |
| 96 | SCNode | 0.7999
±0.0041 | This paper |
| 139 | MLP | 0.7362
±0.0020 |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | NID_GAT | 0.9703
±0.0002 | |
| 2 | NID_GCN | 0.9685
±0.0010 | |
| 3 | UniGAP | 0.8421
±0.0080 | |
| 16 | GCN | 0.7902
±0.0060 best reported | |
| 26 | GAT | 0.7835
±0.0116 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 46 | GraphSAGE | 0.7721
±0.0130 | |
| 53 | SGFormer | 0.7681
±0.0009 best reported | best today: Relieving the Over-Aggregating Effect in Graph Transformers (NeurIPS 2025) |
| 63 | SCNode | 0.7604
±0.0162 | This paper |
| 73 | GraphGPS | 0.7215
±0.0116 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: Relieving the Over-Aggregating Effect in Graph Transformers (NeurIPS 2025) Improvement within reported uncertainty; not highlighted. |
| 82 | NodeFormer | 0.7427
±0.0114 | This paper |
| 96 | MLP | 0.7082
±0.0010 | |
| 121 | LRGNN | 0.6641
±0.0175 | This paper |
Other Graph Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MA-GCL | 0.8883
±0.0030 | |
| 2 | CCA-SSG | 0.8842
±0.0030 | |
| 3 | ARIEL | 0.8827
±0.0020 | |
| 9 | GAT | 0.8693
±0.0030 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) |
| 10 | GCN | 0.8651
±0.0050 best reported | best at pub: MA-GCL: Model Augmentation Tricks for Graph Contrastive Learning (AAAI 2022) |
| 22 | SGFormer | 0.7422
±0.0036 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 24 | NodeFormer | 0.7156
±0.0042 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 27 | Polynormer | 0.5481
±0.0049 | This paper |
| 28 | FSGNN | 0.5274
±0.0083 | This paper |
| 29 | SCNode | 0.5257
±0.0042 | This paper |
| 33 | GIN | 0.4916
±0.0102 | |
| 47 | GraphGPS | 0.4494
±0.0077 | This paper |
| 48 | GPRGNN | 0.4488
±0.0082 | This paper |
| 59 | LRGNN | 0.4223
±0.0485 | This paper |
| 61 | H2GCN | 0.4071 best reported | |
| 64 | CPGNN | 0.3979
±0.0077 | This paper |
| 65 | GloGNN | 0.3689
±0.0014 | This paper |
