Search to Capture Long-range Dependency with Stacking GNNs for Graph Classification
Abstract
In recent years, Graph Neural Networks (GNNs) have been popular in the graph classification task. Currently, shallow GNNs are more common due to the well-known over-smoothing problem facing deeper GNNs. However, they are sub-optimal without utilizing the information from distant nodes, i.e., the long-range dependencies. The mainstream methods in the graph classification task can extract the long-range dependencies either by designing the pooling operations or incorporating the higher-order neighbors, while they have evident drawbacks by modifying the original graph structure, which may result in information loss in graph structure learning. In this paper, by justifying the smaller influence of the over-smoothing problem in the graph classification task, we evoke the importance of stacking-based GNNs and then employ them to capture the long-range dependencies without modifying the original graph structure. To achieve this, two design needs are given for stacking-based GNNs, i.e., sufficient model depth and adaptive skip-connection schemes. By transforming the two design needs into designing data-specific inter-layer connections, we propose a novel approach with the help of neural architecture search (NAS), which is dubbed LRGNN (Long-Range Graph Neural Networks). Extensive experiments on five datasets show that the proposed LRGNN can achieve the best performance, and obtained data-specific GNNs with different depth and skip-connection schemes, which can better capture the long-range dependencies. 1
Benchmark Results
Tested on 3 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 | 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) |
| 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) |
| 100 | GraphTrans | 0.8260
±0.0120 best reported | best today: Dual-perspective Cross Contrastive Learning in Graph Transformers (2024) Difference within reported uncertainty; not counted as underperformance. |
| 103 | Full B12C1 | 0.8251
±0.0137 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 140 | Full B8C1 | 0.8182
±0.0174 | This paper |
| 158 | ResGCN | 0.8140
±0.0030 best reported | best at pub: SoftEdge: Regularizing Graph Classification with Random Soft Edges (2022) |
| 163 | Repeat B12C3 | 0.8131
±0.0168 | This paper |
| 180 | Diverse B12C3 | 0.8097
±0.0273 | This paper |
| 256 | GCNJK | 0.7924
±0.0211 | This paper |
| 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) |
| 378 | TwoHop(L4) | 0.7642
±0.0383 | This paper |
| 381 | GCNFA(L8) | 0.7639
±0.0372 | This paper |
| 391 | DGCNN(L8) | 0.7608
±0.0103 | This paper |
| 480 | GCNVIR(L8) | 0.7032
±0.0432 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 7 | DiffPool | 0.8161
±0.0232 best reported | best at pub: Memory-Based Graph Networks (ICLR 2020) |
| 32 | GIN | 0.7880
±0.0410 | |
| 148 | GCN | 0.7600
±0.0320 best reported | best at pub: CI-GNN: A Granger Causality-Inspired Graph Neural Network for Interpretable Brain Network-Based Psychiatric Diagnosis (2023) 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: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 207 | Full B8C1 | 0.7539
±0.0440 | This paper |
| 217 | TwoHop(L4) | 0.7530
±0.0427 | This paper |
| 218 | Repeat B12C3 | 0.7530
±0.0477 | This paper |
| 219 | Full B4C1 | 0.7530
±0.0467 | This paper |
| 220 | Full B12C1 | 0.7529
±0.0451 | This paper |
| 224 | GCNJK | 0.7524
±0.0415 | This paper |
| 231 | GraphTrans | 0.7518
±0.0336 best reported | best today: Dual-perspective Cross Contrastive Learning in Graph Transformers (2024) Difference within reported uncertainty; not counted as underperformance. |
| 233 | ResGCN | 0.7511
±0.0322 | prev best: SoftEdge: Regularizing Graph Classification with Random Soft Edges (2022) Improvement within reported uncertainty; not highlighted. |
| 257 | Diverse B12C3 | 0.7493
±0.0515 | This paper |
| 298 | GCNFA(L8) | 0.7431
±0.0416 | This paper |
| 318 | DGCNN(L8) | 0.7395
±0.0304 | This paper |
| 440 | GCNVIR(L8) | 0.7108
±0.0314 | 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) |
| 14 | GIN | 0.7810
±0.0350 | |
| 22 | Full B8C1 | 0.7620
±0.0518 | This paper |
| 41 | SAGPool | 0.7487
±0.0409 best reported | best at pub: Pooling Architecture Search for Graph Classification (2021) Difference within reported uncertainty; not counted as underperformance. |
| 46 | Full B12C1 | 0.7450
±0.0331 | This paper |
| 52 | GCNJK | 0.7420
±0.0376 | This paper |
| 53 | Repeat B12C3 | 0.7420
±0.0541 | This paper |
| 54 | Diverse B12C3 | 0.7420
±0.0335 | This paper |
| 58 | GraphTrans | 0.7400
±0.0574 | This paper |
| 62 | ResGCN | 0.7370
±0.0570 | This paper |
| 68 | GCNFA(L8) | 0.7360
±0.0562 | This paper |
| 78 | DiffPool | 0.7314
±0.0070 best reported | best at pub: Structural Entropy Guided Graph Hierarchical Pooling (ICML 2022) best today: Cluster-wise Graph Transformer with Dual-granularity Kernelized Attention (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 98 | TwoHop(L4) | 0.7240
±0.0561 | This paper |
| 113 | DGCNN(L8) | 0.7170
±0.0365 | This paper |
| 121 | GCNVIR(L8) | 0.7150
±0.0490 | This paper |
