Graph Learning with Distributional Edge Layouts
Abstract
Graph Neural Networks (GNNs) learn from graph-structured data by passing local messages between neighboring nodes along edges on certain topological layouts. Typically, these topological layouts in modern GNNs are deterministically computed (e.g., attention-based GNNs) or locally sampled (e.g., GraphSage) under heuristic assumptions. In this paper, we for the first time pose that these layouts can be globally sampled via Langevin dynamics following Boltzmann distribution equipped with explicit physical energy, leading to higher feasibility in the physical world. We argue that such a collection of sampled/optimized layouts can capture the wide energy distribution and bring extra expressivity on top of WL-test, therefore easing downstream tasks. As such, we propose Distributional Edge Layouts (DELs) to serve as a complement to a variety of GNNs. DEL is a pre-processing strategy independent of subsequent GNN variants, thus being highly flexible. Experimental results demonstrate that DELs consistently and substantially improve a series of GNN baselines, achieving state-of-the-art performance on multiple datasets.
Benchmark Results
Tested on 7 datasets 8 baseline values 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 | |
| 38 | DEL-F | 0.9334
±0.0068 | This paper |
| 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. |
| 63 | GCN | 0.9220
±0.0440 | |
| 75 | GPS(RWSE) | 0.9194
±0.0150 | This paper |
| 159 | WL | 0.9040
±0.0570 best reported | best at pub: How Powerful are $K$-hop Message Passing Graph Neural Networks (NeurIPS 2022) Difference within reported uncertainty; not counted as underperformance. |
| 183 | GAT | 0.9010
±0.0580 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: The Expressive Power of Graph Neural Networks: A Survey (2023) |
| 202 | GMT | 0.8990
±0.0420 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) |
| 258 | GraphMAE | 0.8930
±0.0110 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 350 | Graph Transformer + DEL-K | 0.8777
±0.0012 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 404 | GAT + DEL-K | 0.8652
±0.0042 | This paper |
| 437 | SEP-G | 0.8556
±0.0109 | This paper |
| 479 | GAT + MPNN | 0.8430
±0.0121 | This paper |
| 484 | Graphtransformer | 0.8402
±0.0100 | This paper |
| 499 | Graph Transformer + MPNN | 0.8375
±0.0120 | This paper |
| 631 | Graph Transformer + Random distance | 0.7972
±0.0082 | This paper |
| 644 | GAT + Random distance | 0.7916
±0.0177 | This paper |
| # | 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 | |
| 4 | GAT | 0.9623 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 12 | WL | 0.8590
±0.0010 best reported | best at pub: Propagation Kernels (2014) |
| 34 | GPS(DEL-F) | 0.8436
±0.0015 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 188 | Graph Transformer +DEL-F | 0.8062
±0.0036 | This paper |
| 200 | GraphMAE | 0.8042
±0.0035 best reported | best at pub: GraphMAE: Self-Supervised Masked Graph Autoencoders (KDD 2022) best today: Self-Supervised Graph Learning via Spectral Bootstrapping and Laplacian-Based Augmentations (2025) Difference within reported uncertainty; not counted as underperformance. |
| 226 | GMT | 0.7990
±0.0040 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 281 | GAT +DEL-F | 0.7868
±0.0028 | This paper |
| 282 | Graph Transformer + DEL-K | 0.7867
±0.0032 | This paper |
| 286 | Graph Transformer + MPNN | 0.7862
±0.0023 | This paper |
| 304 | SEP-G | 0.7835
±0.0033 | This paper |
| 314 | Graphtransformer | 0.7816
±0.0038 | This paper |
| 349 | GAT + MPNN | 0.7728
±0.0027 | This paper |
| 350 | GAT + DEL-K | 0.7722
±0.0015 | This paper |
| 466 | GAT + Random distance | 0.7146
±0.0076 | This paper |
| 489 | Graph Transformer + Random distance | 0.6971
±0.0012 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 35 | Graph Transformer +DEL-F | 0.7876
±0.0040 | This paper |
| 36 | Graph Transformer + DEL-K | 0.7862
±0.0068 | This paper |
| 40 | GPS(DEL-K) | 0.7842
±0.0059 | This paper |
| 45 | GAT +DEL-F | 0.7819
±0.0058 | This paper |
| 49 | GAT | 0.7800
±0.0300 best reported | best at pub: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) Difference within reported uncertainty; not counted as underperformance. |
| 64 | GAT + DEL-K | 0.7734
±0.0035 | This paper |
| 66 | Graph Transformer + MPNN | 0.7729
±0.0068 | This paper |
| 67 | SAGE | 0.7726
±0.0228 | |
| 76 | GAT + MPNN | 0.7718
±0.0041 | This paper |
| 83 | Graphtransformer | 0.7704
±0.0024 | This paper |
| 114 | SEP-G | 0.7642
±0.0039 | This paper |
| 116 | GAT + Random distance | 0.7641
±0.0054 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 190 | WL | 0.7560
±0.0040 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 213 | GraphMAE | 0.7530
±0.0039 | This paper |
| 221 | Graph Transformer + Random distance | 0.7527
±0.0013 | This paper |
| 236 | GMT | 0.7510
±0.0060 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) best today: Multi-Scale Harmonic Encoding for Feature-Wise Graph Message Passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GC-GNN (GCN) | 0.9210
±0.0810 | |
| 2 | SUGAR | 0.8403
±0.0133 | |
| 3 | Ortho-g-U-Nets | 0.8387 | |
| 11 | GPS(DEL-F) [Final] | 0.8140
±0.0046 | This paper |
| 12 | GPS(RWSE, DEL-K) | 0.8121
±0.0078 | This paper |
| 15 | SAGE | 0.8088
±0.0233 | |
| 25 | WL | 0.7978
±0.0036 | This paper |
| 33 | Graph Transformer +DEL-F | 0.7950
±0.0015 | This paper |
| 36 | GraphMAE | 0.7942
±0.0042 | This paper |
| 39 | Graph Transformer + DEL-K | 0.7925
±0.0011 | This paper |
| 48 | GAT +DEL-F | 0.7889
±0.0034 | This paper |
| 53 | GAT + DEL-K | 0.7878
±0.0035 | This paper |
| 55 | GMT | 0.7872
±0.0059 | This paper |
| 74 | GIN | 0.7805
±0.0189 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 77 | SEP-G | 0.7798
±0.0057 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | ID-GNN+BEC | 0.8150
±0.0240 | |
| 2 | GIN+BEC | 0.8080
±0.0330 | |
| 3 | GCN+BEC | 0.7990
±0.0340 | |
| 4 | GCN | 0.7980
±0.0230 | |
| 8 | GAT +DEL-F | 0.7863
±0.0054 | This paper |
| 13 | Graph Transformer +DEL-F | 0.7828
±0.0027 | This paper |
| 14 | GIN | 0.7641
±0.0093 | prev best: Graph Homomorphism Convolution (ICML 2020) Improvement within reported uncertainty; not highlighted. |
| 15 | Graph Transformer + DEL-K | 0.7765
±0.0049 | This paper |
| 16 | GPS(DEL-F) | 0.7750
±0.0065 | This paper |
| 18 | GAT + DEL-K | 0.7686
±0.0058 | This paper |
| 20 | Graph Transformer + MPNN | 0.7651
±0.0039 | This paper |
| 24 | GAT + Random distance | 0.7608
±0.0048 | This paper |
| 26 | GAT + MPNN | 0.7585
±0.0048 | This paper |
| 31 | GraphMAE | 0.7552
±0.0066 | This paper |
| 33 | Graph Transformer + Random distance | 0.7527
±0.0065 | This paper |
| 55 | SEP-G | 0.7412
±0.0056 | This paper |
| 70 | GMT | 0.7348
±0.0076 | This paper |
| 72 | WL | 0.7340
±0.0463 | prev best: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSNN | 0.7790
±0.0360 | |
| 2 | SIN | 0.7560
±0.0320 | |
| 3 | CIN | 0.7560
±0.0370 | |
| 5 | GIN | 0.7510
±0.0510 best reported | best at pub: Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm (TMLR 2022) |
| 20 | Graph Transformer + DEL-K | 0.5354
±0.0027 | This paper |
| 21 | Graph Transformer +DEL-F | 0.5339
±0.0033 | This paper |
| 22 | GAT +DEL-F | 0.5327
±0.0099 | This paper |
| 23 | GPS(DEL-F) | 0.5295
±0.0064 | This paper |
| 24 | GAT + DEL-K | 0.5286
±0.0033 | This paper |
| 25 | GAT + MPNN | 0.5286
±0.0029 | This paper |
| 27 | Graph Transformer + MPNN | 0.5281
±0.0025 | This paper |
| 29 | GAT + Random distance | 0.5260
±0.0058 | This paper |
| 31 | Graph Transformer + Random distance | 0.5231
±0.0045 | This paper |
| 38 | GCN | 0.5190 | |
| 39 | GraphMAE | 0.5163
±0.0052 | This paper |
| 41 | SEP-G | 0.5153
±0.0065 | This paper |
| 50 | GMT | 0.5066
±0.0082 | This paper |
| 72 | WL | 0.4933
±0.0475 | prev best: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) Improvement within reported uncertainty; not highlighted. |
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 | |
| 69 | GPS | 0.7880
±0.0101 best reported | best at pub: On the Connection Between MPNN and Graph Transformer (ICML 2023) |
| 109 | GIN | 0.7780
±0.0182 | |
| 111 | GPS + DEL-K | 0.7773
±0.0161 | This paper |
| 132 | GPS + DEL-F | 0.7735
±0.0097 | This paper |
| 140 | GAT | 0.7717
±0.0137 best reported | best at pub: Do We Need Anisotropic Graph Neural Networks? (ICLR 2021) |
| 143 | GT + DEL-K | 0.7713
±0.0141 | This paper |
| 156 | GT + DEL-F | 0.7702
±0.0075 | This paper |
| 174 | GT | 0.7651
±0.0093 | This paper |
| 226 | GAT +DEL-F | 0.7547
±0.0105 | This paper |
| 233 | GAT + DEL-K | 0.7524
±0.0124 | This paper |
