Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study
Abstract
Training deep graph neural networks (GNNs) is notoriously hard. Besides the standard plights in training deep architectures such as vanishing gradients and overfitting, it also uniquely suffers from over-smoothing, information squashing, and so on, which limits their potential power for encoding the high-order neighbor structure in large-scale graphs. Although numerous efforts are proposed to address these limitations, such as various forms of skip connections, graph normalization, and random dropping, it is difficult to disentangle the advantages brought by a deep GNN architecture from those ``tricks" necessary to train such an architecture. Moreover, the lack of a standardized benchmark with fair and consistent experimental settings poses an almost insurmountable obstacle to gauge the effectiveness of new mechanisms. In view of those, we present the first fair and reproducible benchmark dedicated to assessing the ``tricks" of training deep GNNs. We categorize existing approaches, investigate their hyperparameter sensitivity, and unify the basic configuration. Comprehensive evaluations are then conducted on tens of representative graph datasets including the recent large-scale Open Graph Benchmark, with diverse deep GNN backbones. We demonstrate that an organic combo of initial connection, identity mapping, group and batch normalization attains the new state-of-the-art results for deep GNNs on large datasets. Codes are available:.
Benchmark Results
Tested on 6 datasets 9 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 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 21 | APPNP | 0.9573
±0.0012 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) Difference within reported uncertainty; not counted as underperformance. |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | |
| 50 | SGC | 0.9511
±0.0009 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) |
| 87 | GCNII | 0.9430
±0.0020 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 260 | DAGNN | 0.9269 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) |
| 364 | JKNet | 0.9169 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) best today: Structure-Aware DropEdge Towards Deep Graph Convolutional Networks (2023) |
| 390 | MLP | 0.9128
±0.0063 | |
| 488 | OGB | 0.8829
±0.0173 | This paper |
| 576 | DGMLP | 0.2531 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 | |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 52 | GCNII | 0.9104
±0.0041 best reported | best at pub: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 72 | GPRGNN | 0.9050
±0.0091 best reported | |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 230 | JKNet | 0.8760 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 320 | MLP | 0.8463 | |
| 324 | DAGNN | 0.8450
±0.0120 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 451 | OGB | 0.7540
±0.0188 | This paper |
| 501 | DGMLP | 0.3740 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 7 | GPRGNN | 0.9777
±0.0015 best reported | best today: Clarify Confused Nodes via Separated Learning (2023) |
| 9 | GCN | 0.9774
±0.0035 | |
| 42 | APPNP | 0.9375
±0.0061 | prev best: Elastic Graph Neural Networks (ICML 2021) best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 59 | GCNII | 0.9597
±0.0011 best reported | best today: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 58 | MLP | 0.9597
±0.0007 | |
| 70 | SGC | 0.9580
±0.0010 best reported | best at pub: Elastic Graph Neural Networks (ICML 2021) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 192 | OGB | 0.9412
±0.0056 | This paper |
| 197 | DAGNN | 0.9401
±0.0060 best reported | best today: Building Shortcuts between Distant Nodes with Biaffine Mapping for Graph Convolutional Networks (2023) Difference within reported uncertainty; not counted as underperformance. |
| 227 | JKNet | 0.9325
±0.0082 best reported | Difference within reported uncertainty; not counted as underperformance. |
| 261 | DGMLP | 0.9207
±0.0031 | 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 today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 | |
| 46 | APPNP | 0.9131
±0.0197 best reported | best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 250 | OGB | 0.7968
±0.0377 | This paper |
| 330 | SGC | 0.7440
±0.0600 best reported | best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 386 | DAGNN | 0.7027
±0.0493 best reported | |
| 392 | JKNet | 0.7000
±0.0549 best reported | best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 441 | DGMLP | 0.6486 | 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 today: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best today: Simplified PCNet with Robustness (2024) |
| 24 | MLP | 0.9136
±0.0070 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 138 | SAGE | 0.8269 | |
| 164 | OGB | 0.8124
±0.0577 | This paper |
| 241 | JKNet | 0.7443
±0.0830 best reported | best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 250 | DAGNN | 0.7351
±0.0718 best reported | |
| 252 | SGC | 0.7350
±0.0430 best reported | best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 439 | DGMLP | 0.5405 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 38 | GCNII | 0.3428
±0.0112 | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Improvement within reported uncertainty; not highlighted. |
| 41 | APPNP | 0.4046
±0.0064 best reported | best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 42 | MLP | 0.4026
±0.0108 | |
| 52 | GPRGNN | 0.3992
±0.0067 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 139 | OGB | 0.3684
±0.0070 | This paper |
| 211 | DAGNN | 0.3551
±0.0110 best reported | |
| 237 | SGC | 0.3490
±0.0070 best reported | best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 281 | JKNet | 0.3342
±0.0028 best reported | best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 426 | DGMLP | 0.2545
±0.0015 | This paper |
