Graph Convolutional Neural Networks with Node Transition Probability-based Message Passing and DropNode Regularization
Abstract
Graph convolutional neural networks (GCNNs) have received much attention recently, owing to their capability in handling graph-structured data. Among the existing GCNNs, many methods can be viewed as instances of a neural message passing motif; features of nodes are passed around their neighbors, aggregated and transformed to produce better nodes' representations. Nevertheless, these methods seldom use node transition probabilities, a measure that has been found useful in exploring graphs. Furthermore, when the transition probabilities are used, their transition direction is often improperly considered in the feature aggregation step, resulting in an inefficient weighting scheme. In addition, although a great number of GCNN models with increasing level of complexity have been introduced, the GCNNs often suffer from over-fitting when being trained on small graphs. Another issue of the GCNNs is over-smoothing, which tends to make nodes' representations indistinguishable. This work presents a new method to improve the message passing process based on node transition probabilities by properly considering the transition direction, leading to a better weighting scheme in nodes' features aggregation compared to the existing counterpart. Moreover, we propose a novel regularization method termed DropNode to address the over-fitting and over-smoothing issues simultaneously. DropNode randomly discards part of a graph, thus it creates multiple deformed versions of the graph, leading to data augmentation regularization effect. Additionally, DropNode lessens the connectivity of the graph, mitigating the effect of over-smoothing in deep GCNNs. Extensive experiments on eight benchmark datasets for node and graph classification tasks demonstrate the effectiveness of the proposed methods in comparison with the state of the art.
Benchmark Results
Tested on 4 datasets 5 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 177 | DGI | 0.8630
±0.0020 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 192 | PGCN + DropNode (RW-dropping) | 0.8590
±0.0040 | This paper |
| 249 | GCN + DropNode | 0.8460
±0.0100 | This paper |
| 262 | Graph U-Net | 0.8440
±0.0060 | This paper |
| 327 | GMNN | 0.8370 | This paper |
| 441 | GCN + DropEdge | 0.8280 | This paper |
| 561 | GPCONV | 0.8170
±0.0050 | This paper |
| 579 | DGCNN | 0.8140
±0.0050 | This paper |
| 724 | MLP | 0.7768 |
| # | 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: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 66 | DGI | 0.7890
±0.0020 best reported | best at pub: Deep Learning on Graphs: A Survey (2018) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 183 | PGCN_n + DropNode (RW-dropping) | 0.7490
±0.0050 | This paper |
| 210 | GCN_n + DropNode | 0.7430
±0.0050 | This paper |
| 304 | Graph U-Net | 0.7320
±0.0050 | This paper |
| 339 | GMNN | 0.7290 | This paper |
| 350 | MLP | 0.7289
±0.0010 | |
| 429 | GCN + DropEdge | 0.7230 | This paper |
| 586 | PGCN_n | 0.7060
±0.0070 | This paper |
| 631 | DGCNN | 0.6980
±0.0070 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 57 | Graph U-Net | 0.7768 | This paper |
| 69 | PGCN_g+DropNode | 0.7721 | This paper |
| 106 | GCN_g+DropNode | 0.7658 | This paper |
| 126 | CapsGNN | 0.7630
±0.0360 best reported | best at pub: Wasserstein Embedding for Graph Learning (ICLR 2020) Difference within reported uncertainty; not counted as underperformance. |
| 132 | DGCNN | 0.7554 | prev best: Graph Convolutional Networks with EigenPooling (KDD 2019) best today: Orthogonal Graph Neural Networks (AAAI 2021) |
| 133 | Diff-Pool (Soft Assign) | 0.7625 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 232 | PGCN_g+2FC | 0.7513 | This paper |
| 267 | GCN + 2FC | 0.7486 | This paper |
| 278 | FCN | 0.7468 | This paper |
| 417 | SAGPool_h | 0.7186 | This paper |
| 459 | SAGPool_g | 0.7004 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GMN | 0.7866 | |
| 2 | MemGNN | 0.7550 | |
| 3 | TFGW SP | 0.7510
±0.0500 | |
| 14 | PGCN_g+DropNode | 0.7050 | This paper |
| 17 | GatedGCN | 0.7000
±0.0494 | |
| 19 | GCN_g+DropNode | 0.6900 | This paper |
| 26 | GraphSAGE | 0.6817
±0.0545 | |
| 37 | GCN + 2FC | 0.6645 | This paper |
| 39 | FCN (2FC) | 0.6617 | This paper |
| 40 | PGCN_g+2FC | 0.6617 | This paper |
| 69 | Diff-Pool (Soft Assign) | 0.6253 | This paper |
| 119 | DGCNN | 0.5712 best reported | |
| 124 | MLP | 0.5583
±0.0352 | |
| 127 | CapsGNN | 0.5531
±0.0423 best reported | best at pub: Wasserstein Embedding for Graph Learning (ICLR 2020) best today: Contrastive Graph Few-Shot Learning (2022) Difference within reported uncertainty; not counted as underperformance. |
| 161 | Graph U-Net | 0.4833 | This paper |
