Relieving the Over-Aggregating Effect in Graph Transformers
Abstract
Graph attention has demonstrated superior performance in graph learning tasks. However, learning from global interactions can be challenging due to the large number of nodes. In this paper, we discover a new phenomenon termed over-aggregating. Over-aggregating arises when a large volume of messages is aggregated into a single node with less discrimination, leading to the dilution of the key messages and potential information loss. To address this, we propose Wideformer, a plug-and-play method for graph attention. Wideformer divides the aggregation of all nodes into parallel processes and guides the model to focus on specific subsets of these processes. The division can limit the input volume per aggregation, avoiding message dilution and reducing information loss. The guiding step sorts and weights the aggregation outputs, prioritizing the informative messages. Evaluations show that Wideformer can effectively mitigate over-aggregating. As a result, the backbone methods can focus on the informative messages, achieving superior performance compared to baseline methods.
Benchmark Results
Tested on 6 datasets 12 baseline values reported too low Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 61 | GraphSAGE | 0.7923
±0.0053 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 74 | GraphGPS + Wideformer | 0.7861
±0.0035 | This paper |
| 86 | GraphGPS+Entropy Reg | 0.7819
±0.0039 | This paper |
| 89 | SGFormer | 0.7798
±0.0091 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 91 | GraphGPS | 0.7796
±0.0037 | This paper |
| 259 | SAGE | 0.7361
±0.0190 | |
| 344 | Exphormer | 0.7290
±0.0040 best reported | best at pub: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 350 | MLP | 0.7289
±0.0010 | |
| 584 | SGFormer + Wideformer | 0.7063
±0.0078 | This paper |
| 615 | SGFormer + Entropy Reg | 0.7012
±0.0041 | This paper |
| 683 | Polynormer + Wideformer | 0.6810
±0.0042 | This paper |
| 713 | Polynormer + Entropy Reg | 0.6721
±0.0035 | This paper |
| 734 | Polynormer | 0.6643
±0.0150 | This paper |
Heterophily Benchmark
Roman-empire
Global leaderboard →Sorted by ROC-AUC. Highlighted rows are from other papers.
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Polynormer + Wideformer | 0.9216
±0.0024 | This paper |
| 2 | Polynormer | 0.9183
±0.0016 | This paper |
| 3 | Exphormer | 0.8903
±0.0037 | This paper |
| 4 | GAT | 0.8875
±0.0041 | This paper |
| 5 | GraphSAGE | 0.8574
±0.0067 | This paper |
| 6 | GraphGPS + Wideformer | 0.8212
±0.0039 | This paper |
| 7 | GraphGPS | 0.8146
±0.0040 | This paper |
| 8 | DIFFormer | 0.7910
±0.0032 | This paper |
| 9 | SGFormer + Wideformer | 0.7703
±0.0038 | This paper |
| 10 | SGFormer | 0.7520
±0.0089 | This paper |
| 11 | NAGphormer | 0.7434
±0.0077 | This paper |
| 12 | GCN | 0.7369
±0.0074 | This paper |
| 13 | GOAT | 0.7159
±0.0125 | This paper |
| 14 | GPRGNN | 0.6485
±0.0027 | This paper |
| 15 | NodeFormer | 0.6449
±0.0073 | This paper |
| # | 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 | |
| 14 | GAT | 0.5270
±0.0062 | prev best: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 15 | GraphSAGE | 0.5540
±0.0020 best reported | |
| 17 | Polynormer + Wideformer | 0.5505
±0.0008 | This paper |
| 18 | Polynormer | 0.5471
±0.0017 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 19 | Polynormer +ENACT | 0.5494 | This paper |
| 23 | SGFormer | 0.5414
±0.0062 best reported | |
| 24 | GCN | 0.5411
±0.0034 best reported | |
| 32 | Exphormer | 0.5351
±0.0046 | This paper |
| 35 | SGFormer + Wideformer | 0.5347
±0.0014 | This paper |
| 39 | SGFormer +ENACT | 0.5332 | This paper |
| 40 | GraphGPS | 0.5327
±0.0066 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 71 | NAGphormer | 0.5126
±0.0072 | This paper |
| 84 | MLP | 0.5058 | |
| 94 | GraphGPS + Wideformer | 0.4996
±0.0041 | This paper |
| 115 | GraphGPS +ENACT | 0.4852 | This paper |
| 125 | DIFFormer | 0.4784
±0.0065 | This paper |
| 149 | GPRGNN | 0.4488
±0.0034 | This paper |
| 152 | GOAT | 0.4461
±0.0050 | This paper |
| 160 | NodeFormer | 0.4386
±0.0035 | This paper |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | BuNN | 0.9899
±0.0016 | |
| 2 | DC-GNN | 0.9850
±0.0021 | |
| 3 | Tango -GPS | 0.9839
±0.0054 | |
| 6 | Polynormer + Wideformer | 0.9726
±0.0001 | This paper |
| 7 | Polynormer + Entropy Reg | 0.9720
±0.0032 | This paper |
| 8 | Polynormer | 0.9713
±0.0017 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 36 | GAT | 0.9391
±0.0035 | prev best: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 42 | GraphSAGE | 0.9358
±0.0005 best reported | best at pub: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) Difference within reported uncertainty; not counted as underperformance. |
| 45 | GraphGPS + Wideformer | 0.9352
±0.0007 | This paper |
| 46 | SAGE | 0.9351
±0.0057 | |
| 48 | GraphGPS+Entropy Reg | 0.9335
±0.0023 | This paper |
| 49 | GraphGPS | 0.9326
±0.0010 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 59 | Exphormer | 0.9226
±0.0056 best reported | best at pub: Even Sparser Graph Transformers (NeurIPS 2024) |
| 68 | GCN | 0.9150
±0.0006 best reported | best at pub: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 75 | DIFFormer | 0.9089
±0.0058 | This paper |
| 97 | SGFormer + Wideformer | 0.8902
±0.0022 | This paper |
| 99 | SGFormer + Entropy Reg | 0.8887
±0.0033 | This paper |
| 102 | SGFormer | 0.8860
±0.0049 | |
| 108 | NodeFormer | 0.8671
±0.0088 | This paper |
| 109 | GPRGNN | 0.8624
±0.0061 | |
| 113 | NAGphormer | 0.8419
±0.0066 | This paper |
| 118 | GOAT | 0.8109
±0.0102 | This paper |
| 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 | |
| 7 | Polynormer + Wideformer | 0.8533
±0.0023 | This paper |
| 8 | Polynormer + Entropy Reg | 0.8521
±0.0033 | This paper |
| 12 | Polynormer | 0.8509
±0.0021 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 24 | GraphGPS + Wideformer | 0.8467
±0.0066 | This paper |
| 28 | GAT | 0.8443
±0.0100 best reported | best at pub: TopoBench: A Framework for Benchmarking Topological Deep Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 35 | GraphGPS+Entropy Reg | 0.8423
±0.0051 | This paper |
| 39 | GraphGPS | 0.8395
±0.0081 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 42 | Exphormer | 0.8377
±0.0078 | This paper |
| 50 | GCN | 0.8364
±0.0067 | This paper |
| 51 | DIFFormer | 0.8357
±0.0068 | This paper |
| 59 | SGFormer | 0.8333
±0.0068 best reported | best at pub: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 62 | GOAT | 0.8311
±0.0104 | This paper |
| 72 | SGFormer + Wideformer | 0.8255
±0.0003 | This paper |
| 77 | GraphSAGE | 0.8243
±0.0044 | This paper |
| 76 | SAGE | 0.8243
±0.0044 | |
| 78 | SGFormer + Entropy Reg | 0.8239
±0.0019 | This paper |
| 110 | NAGphormer | 0.7832
±0.0095 | This paper |
| 117 | NodeFormer | 0.7810
±0.0103 | This paper |
| 139 | MLP | 0.7362
±0.0020 | |
| 144 | GPRGNN | 0.7294
±0.0097 | This paper |
| # | 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 | |
| 17 | Polynormer + Wideformer | 0.7900
±0.0020 | This paper |
| 23 | Polynormer + Entropy Reg | 0.7869
±0.0024 | This paper |
| 24 | Polynormer | 0.7866
±0.0050 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 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 best reported | best at pub: UniGAP: A Universal and Adaptive Graph Upsampling Approach to Mitigate Over-Smoothing in Node Classification Tasks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 50 | SGFormer + Wideformer | 0.7694
±0.0005 | This paper |
| 52 | SGFormer + Entropy Reg | 0.7683
±0.0018 | This paper |
| 53 | SGFormer | 0.7681
±0.0009 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 58 | SAGE | 0.7644
±0.0062 | |
| 66 | GOAT | 0.7576
±0.0166 | This paper |
| 68 | GraphGPS + Wideformer | 0.7569
±0.0117 | This paper |
| 73 | GraphGPS | 0.7548
±0.0066 | prev best: SCNode: Spatial and Contextual Coordinates for Graph Representation Learning (TMLR 2024) |
| 82 | NodeFormer | 0.7427
±0.0146 | This paper |
| 83 | Exphormer | 0.7394
±0.0106 | This paper |
| 89 | DIFFormer | 0.7215
±0.0131 | This paper |
| 96 | MLP | 0.7082
±0.0010 | |
| 116 | NAGphormer | 0.6817
±0.0153 | This paper |
| 150 | GPRGNN | 0.5548
±0.0091 | This paper |
