NeurIPS 2022

LRGB

Vijay Prakash Dwivedi, Ladislav Rampášek, Mikhail Galkin, Alipanah Parviz, Guy Wolf, A. Luu, D. Beaini

Main figure for LRGB

Abstract

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) and deposited at Zenodo. 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.

Benchmark Results

Tested on 5 datasets Non-standard metric on 2 datasets

Tables show presented results in global context (best 3 papers + GCN + MLP).

LRGB

#ModelMAE ↓Paper
1
GCN
actual #1 vs paper #183 182 places worse
0.2421 ±0.0016
best reported
actual #1 vs paper #183 182 places worse
paper 0.3496 ±0.0013
paper 0.3496 ±0.0013 Δ today 0.1075
2
IPR-MPNN
0.2422 ±0.0007
3
TANGO-GPS
0.2422 ±0.0014
5
GIN
0.2429 ±0.0019
7
GatedGCN
actual #7 vs paper #182 175 places worse
0.2431 ±0.0020
best reported
actual #7 vs paper #182 175 places worse
paper 0.3420 ±0.0013
paper 0.3420 ±0.0013 Δ today 0.0989
49
GINE
actual #49 vs paper #184 135 places worse
0.2473 ±0.0017
best reported
actual #49 vs paper #184 135 places worse
paper 0.3547 ±0.0045
paper 0.3547 ±0.0045 Δ today 0.1074
69
GatedGCN+RWSE
actual #69 vs paper #179 110 places worse
0.2485 ±0.0022
best reported
actual #69 vs paper #179 110 places worse
paper 0.3357 ±0.0006
paper 0.3357 ±0.0006 Δ today 0.0872
113
Transformer+LapPE
0.2529 ±0.0016
This paper
123
SAN+RWSE
0.2545 ±0.0012
This paper
155
SAN+LapPE
actual #155 vs paper #155
0.2680 ±0.0040
best reported
actual #155 vs paper #155
paper 0.2683 ±0.0043

Difference within reported uncertainty; not counted as underperformance.

paper 0.2683 ±0.0043 Δ today 0.0003
183
GCNII
0.3471 ±0.0010
This paper
201
MLP
0.4351 ±0.0008
#ModelAP ↑Paper
1
S^2GCN
0.7311 ±0.0066
2
S4G
0.7293 ±0.0004
3
BuNN
0.7276 ±0.0065
4
GCN
actual #4 vs paper #142 138 places worse
0.7261 ±0.0011
best reported
actual #4 vs paper #142 138 places worse
paper 0.5930 ±0.0023
paper 0.5930 ±0.0023 Δ today 0.1331
26
GIN
0.7059 ±0.0089
34
GatedGCN
actual #34 vs paper #149 115 places worse
0.7006 ±0.0033
best reported
actual #34 vs paper #149 115 places worse
paper 0.5864 ±0.0077
paper 0.5864 ±0.0077 Δ today 0.1142
35
GCNII
actual #35 vs paper #159 124 places worse
0.6990 ±0.0030
best reported
actual #35 vs paper #159 124 places worse
paper 0.5543 ±0.0078
73
GatedGCN+RWSE
actual #73 vs paper #134 61 places worse
0.6685 ±0.0062
best reported
actual #73 vs paper #134 61 places worse
paper 0.6069 ±0.0035
paper 0.6069 ±0.0035 Δ today 0.0616
78
GINE
actual #78 vs paper #162 84 places worse
0.6621 ±0.0067
best reported
actual #78 vs paper #162 84 places worse
paper 0.5498 ±0.0079
paper 0.5498 ±0.0079 Δ today 0.1123
89
SAN+RWSE
actual #89 vs paper #111 22 places worse
0.6562 ±0.0075
best reported
actual #89 vs paper #111 22 places worse
paper 0.6439 ±0.0075

Difference within reported uncertainty; not counted as underperformance.

paper 0.6439 ±0.0075 Δ today 0.0123
116
SAN+LapPE
0.6384 ±0.0121
This paper
118
Transformer+LapPE
0.6326 ±0.0126
This paper
181
MLP
0.4060 ±0.0021

PascalVOC-SP

Global leaderboard →
Non-default metric. This paper reports F1-macro; the dataset default is F1. Values below use F1-macro only.

Sorted by F1-macro. Highlighted rows are from other papers.

#ModelF1-macro ↑Paper
1
SAN+LapPE
0.3230 ±0.0039
This paper
2
SAN+RWSE
0.3216 ±0.0027
This paper
3
GatedGCN
0.2873 ±0.0219
This paper
4
GatedGCN+LapPE
0.2860 ±0.0085
This paper
5
Transformer+LapPE
0.2694 ±0.0098
This paper
9
GCNII
0.1698 ±0.0080
This paper
10
GCN
0.1268 ±0.0060
This paper
11
GINE
0.1265 ±0.0076
This paper
#ModelMRR ↑Paper
1
FloydNet
0.6143
2
Exphormer
0.4737 ±0.0024
3
Exphormer + LapPE
0.4737 ±0.0024
8
GatedGCN
actual #8 vs paper #77 69 places worse
0.4670 ±0.0004
best reported
actual #8 vs paper #77 69 places worse
paper 0.3218 ±0.0011
paper 0.3218 ±0.0011 Δ today 0.1452
15
GINE
actual #15 vs paper #78 63 places worse
0.4617 ±0.0005
best reported
actual #15 vs paper #78 63 places worse
paper 0.3180 ±0.0027
paper 0.3180 ±0.0027 Δ today 0.1437
16
GIN
0.4617 ±0.0005
28
GCN
actual #28 vs paper #76 48 places worse
0.4526 ±0.0006
best reported
actual #28 vs paper #76 48 places worse
paper 0.3234 ±0.0006
paper 0.3234 ±0.0006 Δ today 0.1292
61
SAN+LapPE
0.3350 ±0.0003
This paper
62
SAN+RWSE
0.3341 ±0.0006
This paper
75
GatedGCN+RWSE
0.3242 ±0.0008
This paper
80
Transformer+LapPE
0.3174 ±0.0020
This paper
82
GCNII
0.3161 ±0.0004
This paper

COCO-SP

Global leaderboard →
Non-default metric. This paper reports F1-macro; the dataset default is F1. Values below use F1-macro only.

Sorted by F1-macro. Highlighted rows are from other papers.

#ModelF1-macro ↑Paper
1
GatedGCN
0.2641 ±0.0045
This paper
2
Transformer+LapPE
0.2618 ±0.0031
This paper
3
SAN+LapPE
0.2592 ±0.0158
This paper
4
GatedGCN+LapPE
0.2574 ±0.0034
This paper
5
SAN+RWSE
0.2434 ±0.0156
This paper
6
GINE
0.1339 ±0.0044
This paper
7
GCN
0.0841 ±0.0010
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers) Best today — OK at publication; today's leaderboard best is elsewhere