Graph Parsing Networks
Abstract
Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.
Benchmark Results
Tested on 3 datasets 12 baseline values reported too low Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 best reported | best at pub: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 184 | GPN | 0.8087
±0.0043 | This paper |
| 226 | GMT | 0.7990
±0.0040 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) |
| 229 | HoscPool | 0.7990
±0.0170 best reported | best at pub: Higher-order Clustering and Pooling for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 254 | SEP | 0.7935
±0.0033 best reported | best today: Scalable Graph Compressed Convolutions (2024) |
| 267 | EdgePool | 0.7893
±0.0222 | prev best: Embedding Graphs on Grassmann Manifold (2022) Improvement within reported uncertainty; not highlighted. |
| 269 | SPGP | 0.7890
±0.0027 | This paper |
| 299 | HGP-SL | 0.7845
±0.0077 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) |
| 308 | Attention | 0.7822
±0.0132 best reported | best at pub: Embedding Graphs on Grassmann Manifold (2022) |
| 368 | MINCUTPOOL | 0.7680
±0.0160 best reported | best at pub: Higher-order Clustering and Pooling for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 468 | GSAPool | 0.7133
±0.0092 best reported | best at pub: On Exploring Node-feature and Graph-structure Diversities for Node Drop Graph Pooling (2023) Difference within reported uncertainty; not counted as underperformance. |
OGB
ogbg-molpcba
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | StructPosGSSL-FA | 0.2745
±0.0195 | |
| 2 | StructPosGSSL-SA | 0.2710
±0.0165 | |
| 3 | GIN+VN | 0.2703
±0.0023 | |
| 4 | GPN | 0.2665
±0.0031 | This paper |
| 6 | SPGP | 0.2395
±0.0097 | This paper |
| 7 | GMT | 0.2370
±0.0050 | This paper |
| 8 | EdgePool | 0.2348
±0.0041 | This paper |
| 9 | GCN | 0.2020
±0.0024 | This paper |
| 10 | HGP-SL | 0.1864
±0.0028 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 38 | GCNII | 0.4082
±0.0179 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) |
| 52 | GPRGNN | 0.3992
±0.0067 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 62 | GGCN | 0.3929
±0.0048 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 86 | GPN | 0.3811
±0.0123 | This paper |
| 87 | Geom-GCN | 0.3810 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 100 | NSD | 0.3781
±0.0115 | prev best: Feature Transportation Improves Graph Neural Networks (AAAI 2023) Improvement within reported uncertainty; not highlighted. |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 162 | MixHop | 0.3648
±0.0120 best reported | best at pub: Towards Deep Attention in Graph Neural Networks: Problems and Remedies (ICML 2023) |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 266 | GIN | 0.3410
±0.0030 | |
| 408 | PairNorm | 0.2740
±0.0124 | This paper |
