Graph Attention Multi-Layer Perceptron
Abstract
Graph neural networks (GNNs) have achieved great success in many graph-based applications. However, the enormous size and high sparsity level of graphs hinder their applications under industrial scenarios. Although some scalable GNNs are proposed for large-scale graphs, they adopt a fixed $K$-hop neighborhood for each node, thus facing the over-smoothing issue when adopting large propagation depths for nodes within sparse regions. To tackle the above issue, we propose a new GNN architecture --- Graph Attention Multi-Layer Perceptron (GAMLP), which can capture the underlying correlations between different scales of graph knowledge. We have deployed GAMLP in Tencent with the Angel platform, and we further evaluate GAMLP on both real-world datasets and large-scale industrial datasets. Extensive experiments on these 14 graph datasets demonstrate that GAMLP achieves state-of-the-art performance while enjoying high scalability and efficiency. Specifically, it outperforms GAT by 1.3\ Besides, it ranks top-1 on both the leaderboards of the largest homogeneous and heterogeneous graph (i.e., ogbn-papers100M and ogbn-mag) of Open Graph Benchmark.
Benchmark Results
Tested on 9 datasets 23 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: Learning Graph Augmentations to Learn Graph Representations (2022) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 21 | APPNP | 0.9573
±0.0012 best reported | |
| 50 | SGC | 0.9511
±0.0009 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) |
| 242 | GAMLP(JK) | 0.9280
±0.0070 | This paper |
| 332 | AP-GCN | 0.9210
±0.0030 | This paper |
| 333 | GBP | 0.9210
±0.0080 | This paper |
| 349 | JK-Net | 0.9190
±0.0070 | This paper |
| 363 | SIGN | 0.9170
±0.0070 | This paper |
| 367 | S^2GC | 0.9160
±0.0060 | This paper |
| 388 | ResGCN | 0.9130
±0.0090 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Learning on Attribute-Missing Graphs (2020) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 308 | AP-GCN | 0.8518
±0.0023 best reported | best at pub: Adaptive Propagation Graph Convolutional Network (2020) |
| 320 | MLP | 0.8463 | |
| 325 | GAMLP(JK) | 0.8450
±0.0070 | This paper |
| 370 | GBP | 0.8350
±0.0080 | This paper |
| 378 | SIGN | 0.8310
±0.0080 | This paper |
| 379 | S^2GC | 0.8310
±0.0070 | This paper |
| 404 | JK-Net | 0.8200
±0.0060 | This paper |
| 418 | ResGCN | 0.8110
±0.0070 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | EnGCN | 0.9714
±0.0003 | |
| 2 | SAGN+SLE | 0.9710 | |
| 3 | GAMLP(JK) | 0.9704
±0.0001 | This paper |
| 4 | GraphSAINT | 0.9700 best reported | best at pub: SIGN: Scalable Inception Graph Neural Networks (2020) best today: LMC: Fast Training of GNNs via subgraph-wise sampling with Provable Convergence (ICLR 2023) |
| 12 | rf | 0.9662
±0.0100 | This paper |
| 14 | GraphSAGE | 0.9660 best reported | best at pub: Accelerating Large Scale Real-Time GNN Inference using Channel Pruning (2021) |
| 17 | Cluster-GCN | 0.9660 best reported | best at pub: Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks (KDD 2019) |
| 58 | GCN | 0.9530
±0.0010 | |
| 73 | SGC | 0.9490 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 42 | APPNP | 0.9654
±0.0007 best reported | best at pub: Towards Understanding Graph Neural Networks: An Algorithm Unrolling Perspective (2022) 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: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) |
| 208 | GAMLP(JK) | 0.9360
±0.0100 | This paper |
| 223 | GBP | 0.9330
±0.0070 | This paper |
| 236 | AP-GCN | 0.9310
±0.0090 | This paper |
| 237 | S^2GC | 0.9310
±0.0080 | This paper |
| 240 | SIGN | 0.9303
±0.0115 best reported | best at pub: Alternately Optimized Graph Neural Networks (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 254 | JK-Net | 0.9250
±0.0040 | This paper |
| 260 | ResGCN | 0.9220
±0.0150 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±0.0001 | This paper |
| 2 | GraphCON-GCN | 0.9960 | |
| 3 | GCNII | 0.9953
±0.0001 | |
| 4 | GraphSAINT | 0.9940
±0.0003 | prev best: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) Improvement within reported uncertainty; not highlighted. |
| 9 | Cluster-GCN | 0.9940 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) |
| 21 | GCN | 0.9850 | |
| 90 | SGC | 0.8920
±0.0150 best reported | best at pub: Scalable and Adaptive Graph Neural Networks with Self-Label-Enhanced Training (2021) |
| 101 | GraphSAGE | 0.7860 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 173 | MLP | 0.4620 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 25 | APPNP | 0.9400
±0.0030 best reported | best at pub: A Unified View on Graph Neural Networks as Graph Signal Denoising (2020) best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 31 | S^2GC | 0.9380
±0.0010 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) best today: Diffusion on Graph: Augmentation of Graph Structure for Node Classification (TMLR 2025) |
| 90 | GAMLP(R) | 0.9280
±0.0070 | This paper |
| 88 | MLP | 0.9280
±0.0020 | |
| 96 | SGC | 0.9270
±0.0010 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) |
| 106 | JK-Net | 0.9240
±0.0040 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) |
| 110 | GBP | 0.9230
±0.0040 | This paper |
| 128 | SIGN | 0.9190
±0.0030 | This paper |
| 136 | AP-GCN | 0.9160
±0.0070 | This paper |
| 174 | ResGCN | 0.8790
±0.0060 | This paper |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Jacobi | 0.8968 | |
| 2 | GPR | 0.8953 | |
| 3 | LEMP4HG | 0.8939 | |
| 4 | SAGE | 0.8933 | |
| 43 | SAGN+SLE | 0.8501
±0.0010 best reported | best at pub: Node Feature Extraction by Self-Supervised Multi-scale Neighborhood Prediction (ICLR 2021) |
| 71 | GAMLP(R) | 0.8359
±0.0009 | This paper |
| 72 | GBP | 0.8350
±0.0080 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 94 | SGC | 0.8220
±0.0090 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 351 | MLP | 0.6605
±0.0020 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | SGC | 0.7910 | |
| 2 | GAMLP | 0.7036
±0.0002 | |
| 3 | GLEM-GNN | 0.7036
±0.0002 | |
| 13 | GAMLP(JK) | 0.6807
±0.0010 | This paper |
| 14 | SAGN+SLE | 0.6800
±0.0015 best reported | best at pub: Scalable and Adaptive Graph Neural Networks with Self-Label-Enhanced Training (2021) best today: Graph Attention MLP with Reliable Label Utilization (2021) |
| 35 | SAGE | 0.6644
±0.0017 | |
| 95 | MLP | 0.4960
±0.0030 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LMSPS+LP+MS | 0.5784
±0.0022 | |
| 2 | SeHGNN+emb+ms | 0.5719
±0.0012 | |
| 3 | SeHGNN+ms | 0.5671
±0.0014 | |
| 18 | NARS-GAMLP | 0.5401
±0.0021 | prev best: Graph Attention MLP with Reliable Label Utilization (2021) Improvement within reported uncertainty; not highlighted. |
| 57 | GraphSAGE | 0.4646
±0.0060 | |
| 76 | MLP | 0.3243 |
