Long Range Graph Benchmark

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

PDF Abstract

Results from the Paper


Task Dataset Model Metric Name Metric Value Global Rank Result Benchmark
Node Classification COCO-SP SAN+RWSE macro F1 0.2434±0.0156 # 9
Node Classification COCO-SP SAN+LapPE macro F1 0.2592±0.0158 # 7
Node Classification COCO-SP Transformer+LapPE macro F1 0.2618±0.0031 # 6
Node Classification COCO-SP GCN macro F1 0.0841±0.0010 # 14
Node Classification COCO-SP GatedGCN+LapPE macro F1 0.2574±0.0034 # 8
Node Classification COCO-SP GatedGCN macro F1 0.2641±0.0045 # 5
Node Classification COCO-SP GINE macro F1 0.1339±0.0044 # 12
Node Classification PascalVOC-SP Transformer+LapPE macro F1 0.2694±0.0098 # 12
Node Classification PascalVOC-SP SAN+LapPE macro F1 0.3230±0.0039 # 6
Node Classification PascalVOC-SP GCN macro F1 0.1268±0.0060 # 15
Node Classification PascalVOC-SP GINE macro F1 0.1265±0.0076 # 16
Node Classification PascalVOC-SP GatedGCN macro F1 0.2873±0.0219 # 9
Node Classification PascalVOC-SP GatedGCN+LapPE macro F1 0.2860±0.0085 # 10
Node Classification PascalVOC-SP SAN+RWSE macro F1 0.3216±0.0027 # 7
Link Prediction PCQM-Contact GatedGCN+RWSE Hits@1 0.1288±0.0013 # 8
Hits@3 0.3808±0.0006 # 5
Hits@10 0.8517±0.0005 # 4
MRR 0.3242±0.0008 # 12
Link Prediction PCQM-Contact GINE Hits@1 0.1337±0.0013 # 4
Hits@3 0.3642±0.0043 # 9
Hits@10 0.8147±0.0062 # 9
MRR 0.3180±0.0027 # 15
Link Prediction PCQM-Contact GCN Hits@1 0.1321±0.0007 # 6
Hits@3 0.3791±0.0004 # 6
Hits@10 0.8256±0.0006 # 8
MRR 0.3234±0.0006 # 13
Link Prediction PCQM-Contact SAN+LapPE Hits@1 0.1355±0.0017 # 3
Hits@3 0.4004±0.0021 # 4
Hits@10 0.8478±0.0044 # 6
MRR 0.3350±0.0003 # 9
Link Prediction PCQM-Contact SAN+RWSE Hits@1 0.1312±0.0016 # 7
Hits@3 0.4030±0.0008 # 3
Hits@10 0.8550±0.0024 # 3
MRR 0.3341±0.0006 # 10
Link Prediction PCQM-Contact Transformer+LapPE Hits@1 0.1221±0.0011 # 10
Hits@3 0.3679±0.0033 # 8
Hits@10 0.8517±0.0039 # 4
MRR 0.3174±0.0020 # 16
Link Prediction PCQM-Contact GatedGCN Hits@1 0.1279±0.0018 # 9
Hits@3 0.3783±0.0004 # 7
Hits@10 0.8433±0.0011 # 7
MRR 0.3218±0.0011 # 14
Graph Classification Peptides-func SAN+LapPE AP 0.6384±0.0121 # 19
Graph Classification Peptides-func SAN+RWSE AP 0.6439±0.0075 # 18
Graph Classification Peptides-func GINE AP 0.5498±0.0079 # 26
Graph Classification Peptides-func Transformer+LapPE AP 0.6326±0.0126 # 20
Graph Classification Peptides-func GatedGCN+RWSE AP 0.6069±0.0035 # 21
Graph Classification Peptides-func GatedGCN AP 0.5864±0.0077 # 24
Graph Classification Peptides-func GCN AP 0.5930±0.0023 # 23
Graph Regression Peptides-struct GCN MAE 0.3496±0.0013 # 25
Graph Regression Peptides-struct GINE MAE 0.3547±0.0045 # 26
Graph Regression Peptides-struct GatedGCN MAE 0.3420±0.0013 # 23
Graph Regression Peptides-struct GatedGCN+RWSE MAE 0.3357±0.0006 # 22
Graph Regression Peptides-struct Transformer+LapPE MAE 0.2529±0.0016 # 15
Graph Regression Peptides-struct SAN+LapPE MAE 0.2683±0.0043 # 21
Graph Regression Peptides-struct SAN+RWSE MAE 0.2545±0.0012 # 17

Methods