Uplifting Message Passing Neural Network with Graph Original Information
Abstract
Message passing neural networks (MPNNs) learn the representation of graph-structured data based on graph original information, including node features and graph structures, and have shown astonishing improvement in node classification tasks. However, the expressive power of MPNNs is upper bounded by the first-order Weisfeiler-Leman test and its accuracy still has room for improvement. This work studies how to improve MPNNs’ expressiveness and generalizability by fully exploiting graph original information both theoretically and empirically. It further proposes a new GNN model called INGNN (INformation-enhanced Graph Neural Network) that leverages the insights to improve node classification performance. Extensive experiments on both synthetic and real datasets demonstrate the superiority (av-erage rank 1.78) of our INGNN compared with state-of-the-art methods.
Benchmark Results
Tested on 4 datasets 16 baseline values reported too low
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: Gophormer: Ego-Graph Transformer for Node Classification (2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 58 | BernNet | 0.7934
±0.0032 best reported | best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 75 | DAGNN | 0.7860 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 102 | GloGNN | 0.7740
±0.0170 best reported | best today: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 111 | H2GCN | 0.7711
±0.0157 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 126 | MixHop | 0.7626
±0.0295 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) |
| 176 | GPR-GNN | 0.7512
±0.0198 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 312 | LINKX | 0.7319
±0.0099 best reported | |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 579 | ACM-GCN | 0.7070
±0.0081 best reported | best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) |
| 630 | INGNN | 0.6982
±0.0108 | This paper |
| 801 | AdaGNN | 0.6344
±0.0194 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 16 | H2GCN | 0.9361
±0.0013 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 41 | ACM-GCN | 0.9096
±0.0062 best reported | best today: Language is All a Graph Needs (2023) |
| 70 | MixHop | 0.9004
±0.0141 best reported | best at pub: Power up! Robust Graph Convolutional Network via Graph Powering (AAAI 2019) best today: Language is All a Graph Needs (2023) |
| 85 | GloGNN | 0.8960
±0.0040 best reported | best today: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 93 | BernNet | 0.8933
±0.0007 best reported | best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 162 | LINKX | 0.8786
±0.0077 best reported | |
| 191 | GPR-GNN | 0.8738
±0.0063 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 226 | DAGNN | 0.8640 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 458 | INGNN | 0.7998
±0.0157 | This paper |
| 747 | AdaGNN | 0.7680
±0.0145 | This paper |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DC-GNN | 0.8669
±0.0022 | |
| 2 | M2M-GNN | 0.8594
±0.0040 | |
| 3 | GloGNN | 0.8560
±0.0027 | prev best: Finding Global Homophily in Graph Neural Networks When Meeting Heterophily (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 4 | INGNN | 0.8544
±0.0060 | This paper |
| 11 | LINKX | 0.8471
±0.0052 | This paper |
| 17 | MixHop | 0.8363
±0.0054 | This paper |
| 19 | AdaGNN | 0.8355
±0.0031 | This paper |
| 20 | GPR-GNN | 0.8354
±0.0032 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) |
| 23 | BernNet | 0.8326
±0.0029 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) Difference within reported uncertainty; not counted as underperformance. |
| 24 | H2GCN | 0.8320
±0.0055 best reported | best today: Clarify Confused Nodes via Separated Learning (2023) |
| 26 | ACM-GCN | 0.8298
±0.0063 best reported | best today: Clarify Confused Nodes via Separated Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 29 | GIN | 0.8268
±0.0032 | |
| 31 | GCN | 0.8247
±0.0027 | This paper |
| 36 | GAT | 0.8153
±0.0055 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 51 | MLP | 0.7534
±0.0064 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Clarify Confused Nodes via Separated Learning (2023) |
| 52 | DAGNN | 0.7484
±0.0052 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LargeScaleNet | 0.6582
±0.0036 | |
| 2 | S² DirGCN | 0.6495
±0.0033 | |
| 3 | FaberNet | 0.6462
±0.0101 | |
| 12 | INGNN | 0.5653
±0.0015 | This paper |
| 13 | LINKX | 0.5600
±0.0134 | This paper |
| 16 | GloGNN | 0.5480
±0.0030 best reported | best at pub: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 19 | MixHop | 0.5181
±0.0017 best reported | best at pub: Gradient Gating for Deep Multi-Rate Learning on Graphs (ICLR 2022) best today: Graph Neural Reaction Diffusion Models Submitted to the editors June 2023. Accepted in March 2024. (2024) Difference within reported uncertainty; not counted as underperformance. |
| 21 | AdaGNN | 0.4949
±0.0016 | This paper |
| 22 | GAT | 0.4937
±0.0020 | prev best: Gradient Gating for Deep Multi-Rate Learning on Graphs (ICLR 2022) |
| 23 | H2GCN | 0.4910
±0.0010 best reported | best at pub: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 25 | ACM-GCN | 0.4841
±0.0030 | prev best: Gradient Gating for Deep Multi-Rate Learning on Graphs (ICLR 2022) |
| 29 | BernNet | 0.4634
±0.0032 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 31 | GCN | 0.4602
±0.0026 | This paper |
| 32 | GPR-GNN | 0.4597
±0.0026 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 52 | DAGNN | 0.3849
±0.0028 | This paper |
| 56 | MLP | 0.3670
±0.0021 | This paper |
