Pooling Architecture Search for Graph Classification
Abstract
Graph classification is an important problem with applications across many domains, like chemistry and bioinformatics, for which graph neural networks (GNNs) have been state-of-the-art (SOTA) methods. GNNs are designed to learn node-level representation based on neighborhood aggregation schemes, and to obtain graph-level representation, pooling methods are applied after the aggregation operation in existing GNN models to generate coarse-grained graphs. However, due to highly diverse applications of graph classification, and the performance of existing pooling methods vary on different graphs. In other words, it is a challenging problem to design a universal pooling architecture to perform well in most cases, leading to a demand for data-specific pooling methods in real-world applications. To address this problem, we propose to use neural architecture search (NAS) to search for adaptive pooling architectures for graph classification. Firstly we designed a unified framework consisting of four modules: Aggregation, Pooling, Readout, and Merge, which can cover existing human-designed pooling methods for graph classification. Based on this framework, a novel search space is designed by incorporating popular operations in human-designed architectures. Then to enable efficient search, a coarsening strategy is proposed to continuously relax the search space, thus a differentiable search method can be adopted. Extensive experiments on six real-world datasets from three domains are conducted, and the results demonstrate the effectiveness and efficiency of the proposed framework.
Benchmark Results
Tested on 4 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 29 | ASAP | 0.7892
±0.0145 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 49 | GAT | 0.7800
±0.0300 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) Difference within reported uncertainty; not counted as underperformance. |
| 67 | SAGE | 0.7726
±0.0228 best reported | best at pub: Semi-Supervised Graph Classification: A Hierarchical Graph Perspective (WWW 2019) best today: Semi-Supervised Hierarchical Graph Classification (2022) Difference within reported uncertainty; not counted as underperformance. |
| 98 | PAS | 0.7664
±0.0329 | This paper |
| 132 | DGCNN | 0.7626 best reported | best at pub: Graph Convolutional Neural Networks with Node Transition Probability-based Message Passing and DropNode Regularization (2020) best today: Orthogonal Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 148 | GCN | 0.7600
±0.0320 best reported | best at pub: GraphiT: Encoding Graph Structure in Transformers (2021) best today: Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors (2025) Difference within reported uncertainty; not counted as underperformance. |
| 149 | MLP | 0.7600
±0.0320 | |
| 154 | SAGPool | 0.7595
±0.0452 best reported | best at pub: How Framelets Enhance Graph Neural Networks (ICML 2021) best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 155 | GraphSAGE | 0.7590
±0.0320 | |
| 172 | MINCUTPOOL | 0.7575
±0.0380 | This paper |
| 206 | GCN-JK | 0.7539
±0.0517 | This paper |
| 228 | GraphNAS-WS | 0.7520
±0.0251 | This paper |
| 255 | SAGE-JK | 0.7494
±0.0355 | This paper |
| 288 | GAT-JK | 0.7457
±0.0405 | This paper |
| 320 | Random | 0.7394
±0.0423 | This paper |
| 346 | EA | 0.7341
±0.0298 | This paper |
| 358 | Bayesian | 0.7314
±0.0239 | This paper |
| 360 | GIN-JK | 0.7312
±0.0451 | This paper |
| 386 | GraphNAS | 0.7251
±0.0336 | This paper |
| 395 | MLP-Baseline | 0.7239
±0.0353 | This paper |
| 396 | SNAG-WS | 0.7233
±0.0244 | This paper |
| 450 | SNAG | 0.7053
±0.0311 | This paper |
| # | 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 best reported | best at pub: Semi-Supervised Graph Classification: A Hierarchical Graph Perspective (WWW 2019) best today: Semi-Supervised Hierarchical Graph Classification (2022) Difference within reported uncertainty; not counted as underperformance. |
| 18 | DiffPool | 0.8064 best reported | best at pub: Graph U-Nets (2019) best today: Orthogonal Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 32 | ASAP | 0.7950
±0.0180 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 43 | GCN | 0.7912
±0.0307 best reported | best at pub: Hierarchical Graph Capsule Network (AAAI 2020) Difference within reported uncertainty; not counted as underperformance. |
| 46 | PAS | 0.7896
±0.0368 | This paper |
| 56 | SAGPool | 0.7870
±0.0229 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) Difference within reported uncertainty; not counted as underperformance. |
| 69 | MINCUTPOOL | 0.7822
±0.0054 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 73 | GAT-JK | 0.7809
±0.0618 | This paper |
| 74 | GIN | 0.7805
±0.0189 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 79 | Random | 0.7792
±0.0482 | This paper |
| 84 | GCN-JK | 0.7769
±0.0235 | This paper |
| 89 | MLP-Baseline | 0.7752
±0.0390 | This paper |
| 96 | SAGE-JK | 0.7735
±0.0420 | This paper |
| 99 | GAT | 0.7730
±0.0368 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) Difference within reported uncertainty; not counted as underperformance. |
| 103 | Graph U-Net | 0.7710
±0.0517 | This paper |
| 107 | GraphNAS-WS | 0.7674
±0.0455 | This paper |
| 109 | GraphSAGE | 0.7660 | |
| 128 | Bayesian | 0.7555
±0.0321 | This paper |
| 135 | EA | 0.7514
±0.0301 | This paper |
| 136 | GIN-JK | 0.7513
±0.0395 | This paper |
| 154 | SNAG-WS | 0.7351
±0.0303 | This paper |
| 159 | SNAG | 0.7223
±0.0386 | This paper |
| 161 | GraphNAS | 0.7198
±0.0454 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | ID-GNN+BEC | 0.8150
±0.0240 | |
| 2 | GIN+BEC | 0.8080
±0.0330 | |
| 3 | GCN+BEC | 0.7990
±0.0340 | |
| 4 | GCN | 0.7980
±0.0230 best reported | best at pub: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 14 | GIN | 0.7810
±0.0350 best reported | best at pub: Graph Homomorphism Convolution (ICML 2020) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 38 | PAS | 0.7510
±0.0532 | This paper |
| 41 | SAGPool | 0.7487
±0.0409 | This paper |
| 49 | ASAP | 0.7427
±0.0397 | This paper |
| 56 | GAT | 0.7407
±0.0453 | prev best: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) Improvement within reported uncertainty; not highlighted. |
| 57 | EA | 0.7400
±0.0412 | This paper |
| 63 | DGCNN | 0.7367
±0.0570 | This paper |
| 65 | GraphNAS-WS | 0.7360
±0.0463 | This paper |
| 66 | SNAG-WS | 0.7360
±0.0516 | This paper |
| 71 | GCN-JK | 0.7347
±0.0445 | This paper |
| 75 | GAT-JK | 0.7327
±0.0468 | This paper |
| 77 | Graph U-Net | 0.7317
±0.0484 | This paper |
| 78 | DiffPool | 0.7186
±0.0563 | prev best: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) Improvement within reported uncertainty; not highlighted. |
| 87 | SAGE-JK | 0.7287
±0.0618 | This paper |
| 88 | MLP-Baseline | 0.7287
±0.0520 | This paper |
| 93 | Bayesian | 0.7270
±0.0335 | This paper |
| 94 | MINCUTPOOL | 0.7265
±0.0075 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 96 | SNAG | 0.7250
±0.0461 | This paper |
| 99 | GraphSAGE | 0.7230
±0.0530 | |
| 103 | SAGE | 0.7217
±0.0529 | This paper |
| 106 | Random | 0.7210
±0.0554 | This paper |
| 107 | GIN-JK | 0.7207
±0.0486 | This paper |
| 126 | GraphNAS | 0.7110
±0.0230 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSNN | 0.7790
±0.0360 | |
| 2 | SIN | 0.7560
±0.0320 | |
| 3 | CIN | 0.7560
±0.0370 | |
| 5 | GIN | 0.7510
±0.0510 best reported | best at pub: Graph Homomorphism Convolution (ICML 2020) best today: Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm (TMLR 2022) |
| 33 | PAS | 0.5220
±0.0373 | This paper |
| 38 | GCN | 0.5190 best reported | best at pub: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) best today: AutoGEL: An Automated Graph Neural Network with Explicit Link Information (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 43 | DiffPool | 0.5131
±0.0072 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 45 | MINCUTPOOL | 0.5104
±0.0070 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 46 | GraphSAGE | 0.5090 | |
| 47 | GIN-JK | 0.5080
±0.0302 | This paper |
| 48 | ASAP | 0.5078
±0.0075 best reported | best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 58 | SNAG-WS | 0.5000
±0.0248 | This paper |
| 60 | MLP-Baseline | 0.4980
±0.0428 | This paper |
| 61 | Random | 0.4980
±0.0398 | This paper |
| 62 | Bayesian | 0.4980
±0.0397 | This paper |
| 65 | SAGE-JK | 0.4973
±0.0340 | This paper |
| 69 | GAT | 0.4967
±0.0430 | prev best: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) Improvement within reported uncertainty; not highlighted. |
| 70 | GAT-JK | 0.4953
±0.0384 | This paper |
| 73 | SAGPool | 0.4933
±0.0490 | This paper |
| 74 | SNAG | 0.4933
±0.0289 | This paper |
| 78 | DGCNN | 0.4900
±0.0356 | This paper |
| 80 | GCN-JK | 0.4886
±0.0496 | This paper |
| 82 | Graph U-Net | 0.4880
±0.0319 | This paper |
| 83 | EA | 0.4860
±0.0405 | This paper |
| 86 | SAGE | 0.4853
±0.0543 | This paper |
| 89 | GraphNAS-WS | 0.4827
±0.0350 | This paper |
| 95 | GraphNAS | 0.4693
±0.0364 | This paper |
