Contextualized Messages Boost Graph Representations
Abstract
Graph neural networks (GNNs) have gained significant attention in recent years for their ability to process data that may be represented as graphs. This has prompted several studies to explore their representational capability based on the graph isomorphism task. Notably, these works inherently assume a countable node feature representation, potentially limiting their applicability. Interestingly, only a few study GNNs with uncountable node feature representation. In the paper, a new perspective on the representational capability of GNNs is investigated across all levels---node-level, neighborhood-level, and graph-level---when the space of node feature representation is uncountable. Specifically, the injective and metric requirements of previous works are softly relaxed by employing a pseudometric distance on the space of input to create a soft-injective function such that distinct inputs may produce similar outputs if and only if the pseudometric deems the inputs to be sufficiently similar on some representation. As a consequence, a simple and computationally efficient soft-isomorphic relational graph convolution network (SIR-GCN) that emphasizes the contextualized transformation of neighborhood feature representations via anisotropic and dynamic message functions is proposed. Furthermore, a mathematical discussion on the relationship between SIR-GCN and key GNNs in literature is laid out to put the contribution into context, establishing SIR-GCN as a generalization of classical GNN methodologies. To close, experiments on synthetic and benchmark datasets demonstrate the relative superiority of SIR-GCN, outperforming comparable models in node and graph property prediction tasks.
Benchmark Results
Tested on 11 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 | |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 173 | SIR-GCN | 0.7806
±0.0066 | This paper |
| 237 | MLP | 0.7469
±0.0085 |
OGB
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Multi-RF Fusion with Multi-GNN Blending | 0.8476
±0.0002 | |
| 2 | HyperFusion | 0.8475
±0.0003 | |
| 3 | PAS+FPs | 0.8420
±0.0015 | |
| 9 | GatedGCN | 0.8090
±0.0160 | |
| 109 | GIN | 0.7780
±0.0182 | |
| 114 | SIR-GCN | 0.7763
±0.0084 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GIANT-XRT | 0.7612
±0.0016 | |
| 2 | GEGCN | 0.7576
±0.0064 | |
| 3 | AGDN | 0.7522
±0.0007 | |
| 23 | GCN | 0.7300
±0.0017 | |
| 29 | SIR-GCN | 0.7252
±0.0016 | This paper |
| 107 | MLP | 0.5765
±0.0012 |
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 | |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 52 | SIR-GCN | 0.8767
±0.0028 | This paper |
| 135 | MLP | 0.6665
±0.0047 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | UniGAP | 0.6375
±0.0110 | |
| 2 | H2GCN + HalfHop | 0.5961
±0.0100 | |
| 3 | GraphSAGE + HalfHop | 0.5897
±0.0150 | |
| 12 | SAGE | 0.5569
±0.0023 | |
| 50 | FSGNN | 0.5274
±0.0083 | This paper |
| 84 | MLP | 0.5058 | |
| 103 | GPR-GNN | 0.4937
±0.0071 best reported | best at pub: Evolving Computation Graphs (ICML 2023) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 114 | JacobiConv | 0.4853
±0.0096 best reported | best at pub: Evolving Computation Graphs (ICML 2023) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 133 | SIR-GCN | 0.4673
±0.0061 | This paper |
| 137 | FAGCN | 0.4632
±0.0250 best reported | best at pub: Evolving Computation Graphs (ICML 2023) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 140 | GBK-GNN | 0.4598
±0.0071 | This paper |
| 196 | GloGNN | 0.3728
±0.0066 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | BuNN | 0.9899
±0.0016 | |
| 2 | DC-GNN | 0.9850
±0.0021 | |
| 3 | Tango -GPS | 0.9839
±0.0054 | |
| 28 | SIR-GCN | 0.9412
±0.0042 | This paper |
| 36 | GAT | 0.9391
±0.0035 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Relieving the Over-Aggregating Effect in Graph Transformers (NeurIPS 2025) |
| 42 | GraphSAGE | 0.9358
±0.0005 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) Difference within reported uncertainty; not counted as underperformance. |
| 46 | SAGE | 0.9351
±0.0057 | |
| 62 | Graphtransformer | 0.9185
±0.0076 | This paper |
| 68 | GCN | 0.9150
±0.0006 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 83 | FSGNN | 0.9008
±0.0070 | This paper |
| 89 | H_2GCN | 0.8971
±0.0031 | This paper |
| 110 | GPR-GNN | 0.8624
±0.0061 | This paper |
| 137 | CPGNN | 0.7127
±0.0114 best reported | best at pub: Evolving Computation Graphs (ICML 2023) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 156 | MLP | 0.5099
±0.0147 |
| # | 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 | |
| 50 | GCN | 0.8364
±0.0067 | |
| 65 | SIR-GCN | 0.8285
±0.0072 | This paper |
| 139 | MLP | 0.7362
±0.0020 |
GNNBenchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Schrödinger | 0.9913
±0.0004 | |
| 2 | CNN | 0.9907
±0.0007 | |
| 3 | MPNN | 0.9895
±0.0006 | |
| 11 | GatedGCN | 0.9855
±0.0002 | |
| 32 | GIN | 0.9833
±0.0011 | |
| 78 | SIR-GCN | 0.9790
±0.0008 | This paper |
| 126 | MLP | 0.9534
±0.0014 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | RandAlign | 0.7942
±0.0007 | |
| 2 | differential encoding | 0.7907
±0.0027 | |
| 3 | PPGT | 0.7856
±0.0070 | |
| 55 | SIR-GCN | 0.7198
±0.0040 | This paper |
| 62 | GatedGCN | 0.7133
±0.0039 | |
| 92 | GraphSAGE | 0.6690
±0.0020 | |
| 126 | MLP | 0.5634
±0.0018 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GRPE-Small | 0.8159
±0.0019 | |
| 2 | TANGO-GPS | 0.8011
±0.0014 | |
| 3 | GRIT | 0.8003
±0.0028 | |
| 54 | GatedGCN | 0.7608
±0.0020 | |
| 70 | GCN | 0.6903
±0.0137 | |
| 81 | SIR-GCN | 0.6335
±0.0019 | This paper |
| 114 | MLP | 0.2097
±0.0000 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DeepGraph (48) | 0.9066
±0.0006 | |
| 2 | GRIT (our run) | 0.9041
±0.0023 | |
| 3 | GRIT 2-QiQRW | 0.9016
±0.0045 | |
| 66 | GatedGCN | 0.8651
±0.0008 | |
| 80 | SIR-GCN | 0.8575
±0.0003 | This paper |
| 88 | GCN | 0.8561
±0.0003 | |
| 123 | MLP | 0.5052 |
