Graph Convolutional Networks with EigenPooling
Abstract
Graph neural networks, which generalize deep neural network models to graph structured data, have attracted increasing attention in recent years. They usually learn node representations by transforming, propagating and aggregating node features and have been proven to improve the performance of many graph related tasks such as node classification and link prediction. To apply graph neural networks for the graph classification task, approaches to generate the graph representation from node representations are demanded. A common way is to globally combine the node representations. However, rich structural information is overlooked. Thus a hierarchical pooling procedure is desired to preserve the graph structure during the graph representation learning. There are some recent works on hierarchically learning graph representation analogous to the pooling step in conventional convolutional neural (CNN) networks. However, the local structural information is still largely neglected during the pooling process. In this paper, we introduce a pooling operator $ $ based on graph Fourier transform, which can utilize the node features and local structures during the pooling process. We then design pooling layers based on the pooling operator, which are further combined with traditional GCN convolutional layers to form a graph neural network framework $ $ for graph classification. Theoretical analysis is provided to understand $ $ from both local and global perspectives. Experimental results of the graph classification task on $6$ commonly used benchmarks demonstrate the effectiveness of the proposed framework.
Benchmark Results
Tested on 5 datasets 4 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 158 | GraphSAGE | 0.9040
±0.0780 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Asynchronous Neural Networks for Learning in Graphs (2022) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 425 | DGCNN | 0.8583
±0.0116 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: Graph Structure Refinement with Energy-based Contrastive Learning (AAAI 2024) |
| 593 | Set2Set | 0.7640 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 598 | Diff-pool | 0.8060 | This paper |
| 613 | EigenPooling-1 | 0.8010 | This paper |
| 637 | EigenPooling-3 | 0.7950 | This paper |
| 650 | EigenPooling-2 | 0.7890 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 best reported | best today: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 best reported | best today: Weisfeiler and Leman Go Infinite: Spectral and Combinatorial Pre-Colorings (TMLR 2022) |
| 365 | EigenPooling-3 | 0.7700 | This paper |
| 371 | EigenPooling-2 | 0.7670 | This paper |
| 373 | DGCNN | 0.7650
±0.0190 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: GraphCrop: Subgraph Cropping for Graph Classification (2020) |
| 396 | EigenPooling-1 | 0.7600 | This paper |
| 393 | Diff-pool | 0.7600 | This paper |
| 463 | Set2Set | 0.7170
±0.0073 best reported | best today: On Exploring Node-feature and Graph-structure Diversities for Node Drop Graph Pooling (2023) Difference within reported uncertainty; not counted as underperformance. |
| # | 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 | |
| 104 | EigenPooling-3 | 0.7660 | This paper |
| 132 | DGCNN | 0.7626 best reported | best today: Orthogonal Graph Neural Networks (AAAI 2021) |
| 148 | GCN | 0.7400 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) Improvement within reported uncertainty; not highlighted. |
| 149 | MLP | 0.7600
±0.0320 | |
| 155 | GraphSAGE | 0.7460 | prev best: Graph Neural Networks With Convolutional ARMA Filters (2019) Improvement within reported uncertainty; not highlighted. |
| 160 | Diff-pool | 0.7590 | This paper |
| 205 | EigenPooling-2 | 0.7540 | This paper |
| 239 | EigenPooling-1 | 0.7510 | This paper |
| 301 | Set2Set | 0.7429 best reported | best at pub: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: Memory-Based Graph Networks (ICLR 2020) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GMN | 0.7866 | |
| 2 | MemGNN | 0.7550 | |
| 3 | TFGW SP | 0.7510
±0.0500 | |
| 17 | GatedGCN | 0.7000
±0.0494 | |
| 26 | GraphSAGE | 0.6817
±0.0545 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: GNNBenchmark (JMLR 2023) |
| 32 | GIN | 0.6767
±0.0583 | |
| 36 | GCN | 0.6650
±0.0691 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Hierarchical Graph Capsule Network (AAAI 2020) |
| 50 | EigenPooling-1 | 0.6500 | This paper |
| 55 | EigenPooling-2 | 0.6450 | This paper |
| 56 | EigenPooling-3 | 0.6450 | This paper |
| 61 | Diff-pool | 0.6360 | This paper |
| 93 | Set2Set | 0.6015 best reported | best today: Memory-Based Graph Networks (ICLR 2020) |
| 119 | DGCNN | 0.5712 best reported | |
| 124 | MLP | 0.5583
±0.0352 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GC-GNN (GCN) | 0.9210
±0.0810 | |
| 2 | SUGAR | 0.8403
±0.0133 | |
| 3 | Ortho-g-U-Nets | 0.8387 | |
| 15 | SAGE | 0.8088
±0.0233 | |
| 37 | DGCNN | 0.7937 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: Orthogonal Graph Neural Networks (AAAI 2021) |
| 43 | GCN | 0.7590 | prev best: Graph Neural Networks With Convolutional ARMA Filters (2019) Improvement within reported uncertainty; not highlighted. |
| 59 | EigenPooling-3 | 0.7860 | This paper |
| 75 | Diff-pool | 0.7800 | This paper |
| 91 | EigenPooling-1 | 0.7750 | This paper |
| 105 | EigenPooling-2 | 0.7700 | This paper |
| 109 | GraphSAGE | 0.7660 | prev best: Graph Neural Networks With Convolutional ARMA Filters (2019) Improvement within reported uncertainty; not highlighted. |
| 146 | Set2Set | 0.7450 | This paper |
