Towards Deep Attention in Graph Neural Networks: Problems and Remedies
Abstract
Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.
Benchmark Results
Tested on 5 datasets 33 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 66 | FAGCN | 0.9489
±0.0048 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 90 | GT | 0.9420
±0.0016 best reported | |
| 134 | MixHop | 0.9360
±0.0137 best reported | best today: Graph Navier–Stokes Networks (2026) |
| 354 | GCN-II | 0.9181
±0.0090 | This paper |
| 390 | MLP | 0.9128
±0.0063 | |
| 426 | A-DGN | 0.9053
±0.0130 | This paper |
| 454 | GATv2 | 0.8987
±0.0120 | This paper |
| 480 | GATv2^R | 0.8871
±0.0170 | This paper |
| 524 | DMP | 0.8263
±0.0410 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 72 | GPRGNN | 0.9050
±0.0091 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 126 | FAGCN | 0.8968
±0.0097 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 199 | GATv2 | 0.8825
±0.0771 best reported | best today: Automatic Graph Topology-Aware Transformer (2024) Difference within reported uncertainty; not counted as underperformance. |
| 320 | MLP | 0.8463 | |
| 337 | GT | 0.8438
±0.0130 | This paper |
| 340 | GCN-II | 0.8424
±0.0120 | This paper |
| 358 | A-DGN | 0.8370
±0.0150 | This paper |
| 409 | GATv2R | 0.8173
±0.0220 | This paper |
| 432 | MixHop | 0.7952
±0.0210 | This paper |
| 472 | DMP | 0.7058
±0.1130 | This paper |
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 | |
| 28 | GPRGNN | 0.9295
±0.0131 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 | |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8961
±0.0152 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 68 | DMP | 0.8919 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 166 | GT | 0.8408
±0.0560 | This paper |
| 201 | A-DGN | 0.8222
±0.0480 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) 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) |
| 258 | GATv2 | 0.7929
±0.0403 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 267 | GCN-II | 0.7859
±0.0660 | This paper |
| 276 | MixHop | 0.7784
±0.0773 best reported | best at pub: Graph Pointer Neural Networks (AAAI 2021) best today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 386 | DAGNN | 0.7027
±0.0493 best reported | best at pub: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Difference within reported uncertainty; not counted as underperformance. |
| 494 | GATv2^R | 0.6068
±0.0660 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: Simplified PCNet with Robustness (2024) |
| 24 | MLP | 0.9136
±0.0070 | |
| 31 | DMP | 0.8919 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 38 | FAGCN | 0.8852
±0.0133 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 133 | A-DGN | 0.8314
±0.0670 | This paper |
| 138 | SAGE | 0.8269 | |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 177 | GATv2 | 0.8033
±0.0333 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 179 | GT | 0.8000
±0.0490 | This paper |
| 183 | MixHop | 0.7950
±0.0630 best reported | best at pub: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 188 | GCN-II | 0.7884
±0.0660 | This paper |
| 250 | DAGNN | 0.7351
±0.0718 best reported | |
| 414 | GATv2R | 0.5732
±0.0450 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 41 | APPNP | 0.4046
±0.0064 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 42 | MLP | 0.4026
±0.0108 | |
| 45 | GT | 0.4010 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 52 | GPRGNN | 0.3992
±0.0067 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 56 | FAGCN | 0.3970 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 122 | DMP | 0.3726
±0.0179 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 162 | MixHop | 0.3648
±0.0120 | prev best: Deformable Graph Transformer (2022) |
| 166 | A-DGN | 0.3641
±0.0100 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 195 | GCN-II | 0.3577
±0.0100 | This paper |
| 211 | DAGNN | 0.3551
±0.0110 best reported | |
| 230 | GATv2 | 0.3510
±0.0020 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) best today: What Can We Learn From MIMO Graph Convolutions? (IJCAI 2025) |
| 275 | GATv2^R | 0.3373
±0.0090 | This paper |
