NeurIPS 2021

Reconstruction for Powerful Graph Representations

Leonardo Cotta, Christopher Morris, Bruno Ribeiro

Main figure for Reconstruction for Powerful Graph Representations

Abstract

Graph neural networks (GNNs) have limited expressive power, failing to represent many graph classes correctly. While more expressive graph representation learning (GRL) alternatives can distinguish some of these classes, they are significantly harder to implement, may not scale well, and have not been shown to outperform well-tuned GNNs in real-world tasks. Thus, devising simple, scalable, and expressive GRL architectures that also achieve real-world improvements remains an open challenge. In this work, we show the extent to which graph reconstruction---reconstructing a graph from its subgraphs---can mitigate the theoretical and practical problems currently faced by GRL architectures. First, we leverage graph reconstruction to build two new classes of expressive graph representations. Secondly, we show how graph reconstruction boosts the expressive power of any GNN architecture while being a (provably) powerful inductive bias for invariances to vertex removals. Empirically, we show how reconstruction can boost GNN's expressive power---while maintaining its invariance to permutations of the vertices---by solving seven graph property tasks not solvable by the original GNN. Further, we demonstrate how it boosts state-of-the-art GNN's performance across nine real-world benchmark datasets.

Benchmark Results

Tested on 4 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
67
PNA (n-3)
0.7885 ±0.0048
This paper
109
GIN
0.7780 ±0.0182
119
GIN (n-2)
0.7753 ±0.0159
This paper
164
GCN (n-1)
0.7683 ±0.0188
This paper
179
PNA (ceil(n/2))
0.7648 ±0.0035
This paper
283
GCN (ceil(n/2))
0.7216 ±0.0196
This paper
294
GIN (ceil(n/2))
0.6843 ±0.0123
This paper
#ModelAP ↑Paper
1
GRPE-Large
0.3150 ±0.0010
2
Graphormer
0.3140
3
Graphormer-FLAG
0.3139 ±0.0032
31
GIN
0.2902 ±0.0017
73
PNA (orig.)
0.2545 ±0.0004
This paper
83
Reconstr. (n-1) [GIN]
0.2360 ±0.0002
This paper
85
Reconstr. (n-3) [GIN]
0.2333 ±0.0009
This paper
87
Reconstr. (n-2) [GIN]
0.2325
This paper
88
Reconstr. (n-1) [PNA]
0.2311 ±0.0005
This paper
92
Reconstr. (n-2) [PNA]
0.2210 ±0.0003
This paper
95
Reconstr. (n-1) [GCN]
0.2125 ±0.0025
This paper
97
GIN (orig.)
0.2116 ±0.0028
This paper
99
GCN (orig.)
0.2020 ±0.0024
This paper
100
Reconstr. (n-2) [GCN]
0.2010 ±0.0008
This paper
101
Reconstr. (n-3) [PNA]
0.2005 ±0.0015
This paper
102
Reconstr. (n-3) [GCN]
0.1904 ±0.0003
This paper
110
Reconstr. (ceil(n/2)) [GIN]
0.1350 ±0.0032
This paper
111
Reconstr. (ceil(n/2)) [PNA]
0.1233 ±0.0120
This paper
112
Reconstr. (ceil(n/2)) [GCN]
0.1169 ±0.0141
This paper

MoleculeNet

#ModelROC-AUC ↑Paper
1
HIMP
0.8740 ±0.0050
2
GINE w/ VN
0.8720 ±0.0030
3
NaiveGINe+ K=3 w/ VN
0.8700 ±0.0040
14
GCN
0.8400 ±0.0040
159
Reconstr. (n-2) [GIN]
0.7684 ±0.0062
This paper
162
Reconstr. (n-3) [GIN]
0.7678 ±0.0064
This paper
173
Reconstr. (n-1) [GCN]
0.7646 ±0.0077
This paper
188
Reconstr. (n-3) [GCN]
0.7588 ±0.0073
This paper
199
Reconstr. (n-2) [GCN]
0.7558 ±0.0099
This paper
217
GCN (orig.)
0.7529 ±0.0069
This paper
225
Reconstr. (n-1) [GIN]
0.7515 ±0.0140
This paper
235
GIN (orig.)
0.7491 ±0.0051
This paper
248
Reconstr. (ceil(n/2)) [GIN]
0.7440 ±0.0075
This paper
263
Reconstr. (ceil(n/2)) [GCN]
0.7403 ±0.0063
This paper
269
Reconstr. (ceil(n/2)) [PNA]
0.7371 ±0.0061
This paper
320
Reconstr. (n-2) [PNA]
0.6522 ±0.0047
This paper
322
Reconstr. (n-3) [PNA]
0.6503 ±0.0058
This paper
325
Reconstr. (n-1) [PNA]
0.6414 ±0.0076
This paper
331
PNA (orig.)
0.6269 ±0.0063
This paper

GNNBenchmark

#ModelAccuracy ↑Paper
7
Reconstr. (n-1)
1.0000
This paper
1
PPGN
1.0000
2
RW-AgentNet
1.0000
3
AgentNet
1.0000
8
GCN
1.0000
41
Positional GIN
0.9933 ±0.0133
This paper
45
PPGN (3-WL)
0.9780 ±0.1091
This paper
59
Reconstr. (ceil(n/2))
0.4933 ±0.0742
This paper
75
PNA (orig.)
0.1000 ±0.0298
This paper
91
GCN (orig.)
0.0666 ±0.0210
This paper
92
GIN (orig.)
0.0466 ±0.0400
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers)