Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm
Abstract
Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or involve operations that incur high time and space complexities. In this work, we propose a general and provably powerful GNN framework that preserves the scalability of the message passing scheme. In particular, we first propose to empower 1-WL for graph isomorphism test by considering edges among neighbors, giving rise to NC-1-WL. The expressiveness of NC-1-WL is shown to be strictly above 1-WL and below 3-WL theoretically. Further, we propose the NC-GNN framework as a differentiable neural version of NC-1-WL. Our simple implementation of NC-GNN is provably as powerful as NC-1-WL. Experiments demonstrate that our NC-GNN performs effectively and efficiently on various benchmarks.
Benchmark Results
Tested on 7 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 48 | NC-GNN | 0.9280
±0.0500 best reported | best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 63 | GCN | 0.9220
±0.0440 | |
| 403 | MLP | 0.8660
±0.0495 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 3 | GCN | 0.9727 | |
| 108 | NC-GNN | 0.8250
±0.0190 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 23 | GCN | 0.8260
±0.0220 | |
| 24 | Empowering GNNs | 0.8250
±0.0120 | This paper |
| 30 | GIN | 0.8220
±0.0210 best reported | best at pub: On the Equivalence between Graph Isomorphism Testing and Function Approximation with GNNs (NeurIPS 2019) best today: Scalable Expressiveness through Preprocessed Graph Perturbations (2024) Difference within reported uncertainty; not counted as underperformance. |
| 59 | CIN | 0.8140
±0.0140 | This paper |
| 151 | MLP | 0.7920
±0.0240 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSNN | 0.7790
±0.0360 | This paper |
| 2 | SIN | 0.7560
±0.0320 | This paper |
| 3 | CIN | 0.7560
±0.0370 | This paper |
| 4 | Empowering GNNs | 0.7520
±0.0450 | This paper |
| 5 | GIN | 0.7510
±0.0510 | prev best: Graph Homomorphism Convolution (ICML 2020) |
| 6 | GNN-AK+ | 0.7500
±0.0420 | This paper |
| 7 | PPGN | 0.7300
±0.0580 | This paper |
| 38 | GCN | 0.5190 |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | A-NLSF | 0.8149
±0.0067 | |
| 2 | differential encoding | 0.8096
±0.0029 | |
| 3 | MPNN + VN + NoPE | 0.8055
±0.0038 | |
| 16 | GatedGCN | 0.7531
±0.0083 | |
| 26 | NC-GNN | 0.7194
±0.0043 | This paper |
| 31 | GraphSNN | 0.7066
±0.0165 | This paper |
| 32 | GIN + 3-cycle count feature | 0.7058
±0.0064 | This paper |
| 33 | GIN | 0.7037
±0.0107 best reported | best at pub: Parameterized Hypercomplex Graph Neural Networks for Graph Classification (2021) best today: Adaptive Canonicalization with Application to Invariant Anisotropic Geometric Networks (2025) Difference within reported uncertainty; not counted as underperformance. |
| 38 | GCN | 0.6857
±0.0061 |
GNNBenchmark
| # | 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 | |
| 69 | NC-GNN | 0.6933
±0.0036 | This paper |
| 70 | GCN | 0.6903
±0.0137 | |
| 79 | GIN | 0.6472
±0.0155 | This paper |
| 91 | PPGN | 0.5713
±0.0654 | This paper |
| 104 | RingGNN | 0.4242
±0.2006 | 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 | |
| 55 | NC-GNN | 0.8663
±0.0002 | This paper |
| 66 | GatedGCN | 0.8651
±0.0008 | |
| 72 | RingGNN | 0.8625
±0.0001 | This paper |
| 86 | PPGN | 0.8566
±0.0035 | This paper |
| 88 | GCN | 0.8561
±0.0003 | |
| 89 | GIN | 0.8559
±0.0001 | This paper |
| 123 | MLP | 0.5052 |
