Higher-order Clustering and Pooling for Graph Neural Networks
Abstract
Graph Neural Networks achieve state-of-the-art performance on a plethora of graph classification tasks, especially due to pooling operators, which aggregate learned node embeddings hierarchically into a final graph representation. However, they are not only questioned by recent work showing on par performance with random pooling, but also ignore completely higher-order connectivity patterns. To tackle this issue, we propose HoscPool, a clustering-based graph pooling operator that captures higher-order information hierarchically, leading to richer graph representations. In fact, we learn a probabilistic cluster assignment matrix end-to-end by minimising relaxed formulations of motif spectral clustering in our objective function, and we then extend it to a pooling operator. We evaluate HoscPool on graph classification tasks and its clustering component on graphs with ground-truth community structure, achieving best performance. Lastly, we provide a deep empirical analysis of pooling operators' inner functioning. The code is available here.
Benchmark Results
Tested on 2 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 | |
| 141 | MINCUTPOOL | 0.9060
±0.0460 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) |
| 202 | GMT | 0.8990
±0.0420 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) |
| 239 | DiffPool | 0.8940
±0.0460 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) |
| 367 | ASAP | 0.8740
±0.0570 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) |
| 403 | MLP | 0.8660
±0.0495 | |
| 535 | Random | 0.8270
±0.0680 best reported | best at pub: AutoGL: A Library for Automated Graph Learning (ICLR 2021) Difference within reported uncertainty; not counted as underperformance. |
| 561 | HoscPool | 0.8230
±0.0130 | This paper |
| 576 | HP-2 | 0.8170
±0.0210 | This paper |
| 623 | SAGPool | 0.7986
±0.0236 best reported | best at pub: Embedding Graphs on Grassmann Manifold (2022) |
| 625 | HP-1 | 0.7980
±0.0160 | This paper |
| 659 | No pool | 0.7810
±0.0130 | This paper |
| 710 | EigPool | 0.7520
±0.0270 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 5 | DiffPool | 0.9210
±0.0260 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) best today: Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders (IJCAI 2024) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 212 | HP-2 | 0.8030
±0.0200 | This paper |
| 229 | HoscPool | 0.7990
±0.0170 | 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) Difference within reported uncertainty; not counted as underperformance. |
| 259 | SAGPool | 0.7910
±0.0300 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) best today: The expressive power of pooling in Graph Neural Networks (NeurIPS 2023) Difference within reported uncertainty; not counted as underperformance. |
| 309 | ASAP | 0.7821
±0.0175 best reported | best at pub: Multi-grained Semantics-aware Graph Neural Networks (2020) |
| 346 | HP-1 | 0.7730
±0.0160 | This paper |
| 354 | No pool | 0.7710
±0.0190 | This paper |
| 358 | Random | 0.7700
±0.0170 | This paper |
| 368 | MINCUTPOOL | 0.7680
±0.0160 | prev best: Rethinking pooling in graph neural networks (NeurIPS 2020) Improvement within reported uncertainty; not highlighted. |
| 412 | EigPool | 0.7500
±0.0220 | This paper |
