Graph convolutions that can finally model local structure

R'emy Brossard, Oriel Frigo, David Dehaene

Main figure for Graph convolutions that can finally model local structure

Abstract

Despite quick progress in the last few years, recent studies have shown that modern graph neural networks can still fail at very simple tasks, like detecting small cycles. This hints at the fact that current networks fail to catch information about the local structure, which is problematic if the downstream task heavily relies on graph substructure analysis, as in the context of chemistry. We propose a very simple correction to the now standard GIN convolution that enables the network to detect small cycles with nearly no cost in terms of computation time and number of parameters. Tested on real life molecule property datasets, our model consistently improves performance on large multi-tasked datasets over all baselines, both globally and on a per-task setting.

Benchmark Results

Tested on 3 datasets

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

OGB

#ModelROC-AUC ↑Paper
1
Multi-RF Fusion with Multi-GNN Blending
0.8476 ±0.0002
2
HyperFusion
0.8475 ±0.0003
3
PAS+FPs
0.8420 ±0.0015
9
GatedGCN
0.8090 ±0.0160
70
HIMP
0.7880 ±0.0080
This paper
78
DeeperGCN
0.7860 ±0.0120
This paper
109
GIN
0.7780 ±0.0182
148
GINE w/ VN
0.7710 ±0.0150
This paper
171
GINe+ K=1 w/ VN
0.7660 ±0.0140
This paper
184
GCN
actual #184 vs paper #193 9 places worse
0.7610 ±0.0100
actual #184 vs paper #193 9 places worse
paper 0.7610 ±0.0100

Improvement within reported uncertainty; not highlighted.

paper 0.7610 ±0.0100 Δ at pub 0.0002
203
GCN w/ VN
0.7600 ±0.0120
This paper
213
NaiveGINe+ K=3 w/ VN
0.7580 ±0.0130
This paper
220
GINE
0.7560 ±0.0140
This paper

MoleculeNet

Tox21

Global leaderboard →

Default metric is ROC-AUC. The paper reports 8 values on ROC-AUC and 8 values on Accuracy .

#ModelROC-AUC ↑ defaultAccuracy ↑Paper
1
HIMP
0.8740 ± 0.0050
0.8740 ± 0.0050
Accuracy 0.8740 ± 0.0050
This paper
2
GINE w/ VN
0.8720 ± 0.0030
0.8720 ± 0.0030
Accuracy 0.8720 ± 0.0030
This paper
3
NaiveGINe+ K=3 w/ VN
0.8700 ± 0.0040
0.8700 ± 0.0040
Accuracy 0.8700 ± 0.0040
This paper
4
GINe+ K=1 w/ VN
0.8670 ± 0.0040
0.8670 ± 0.0040
Accuracy 0.8670 ± 0.0040
This paper
5
GINE
0.8668 ±0.0077
best reported
0.8500 ± 0.0090
Accuracy 0.8500 ± 0.0090
paper 0.8500 ±0.0090
6
GCN w/ VN
0.8590 ± 0.0050
0.8590 ± 0.0050
Accuracy 0.8590 ± 0.0050
This paper
14
GCN
0.8400 ±0.0040
0.8400 ± 0.0040
Accuracy 0.8400 ± 0.0040
paper 0.8400 ±0.0040
prev best: Memory-Based Graph Networks (ICLR 2020)
paper 0.8400 ±0.0040 Δ at pub 0.0110
23
DeeperGCN
0.8310 ± 0.0040
0.8310 ± 0.0040
Accuracy 0.8310 ± 0.0040
This paper
24
GIN
0.8290 ± 0.0069
—

ToxCast

Global leaderboard →

Default metric is ROC-AUC. The paper reports 8 values on ROC-AUC and 8 values on Accuracy .

#ModelROC-AUC ↑ defaultAccuracy ↑Paper
1
GeomGCL
0.7630
—
2
LiGhT DeepGPT
0.7570 ± 0.0110
—
3
CoMPT
0.7550
—
4
GINE w/ VN
0.7490 ± 0.0020
0.7490 ± 0.0020
Accuracy 0.7490 ± 0.0020
This paper
5
GINe+ K=1 w/ VN
0.7490 ± 0.0080
0.7490 ± 0.0080
Accuracy 0.7490 ± 0.0080
This paper
9
GCN w/ VN
0.7430 ± 0.0030
0.7430 ± 0.0030
Accuracy 0.7430 ± 0.0030
This paper
12
GINE
0.7410 ± 0.0040
0.7410 ± 0.0040
Accuracy 0.7410 ± 0.0040
This paper
13
NaiveGINe+ K=3 w/ VN
0.7370 ± 0.0070
0.7370 ± 0.0070
Accuracy 0.7370 ± 0.0070
This paper
14
GCN
0.7350 ±0.0020
0.7350 ± 0.0020
Accuracy 0.7350 ± 0.0020
paper 0.7350 ±0.0020
paper 0.7350 ±0.0020 Δ at pub 0.0611
21
HIMP
0.7210 ± 0.0040
0.7210 ± 0.0040
Accuracy 0.7210 ± 0.0040
This paper
29
DeeperGCN
0.7140 ± 0.0050
0.7140 ± 0.0050
Accuracy 0.7140 ± 0.0050
This paper
32
GIN
0.7095 ± 0.0027
—
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere