The Impact of Global Structural Information in Graph Neural Networks Applications

Davide Buffelli, Fabio Vandin

Main figure for The Impact of Global Structural Information in Graph Neural Networks Applications

Abstract

Graph Neural Networks (GNNs) rely on the graph structure to define an aggregation strategy where each node updates its representation by combining information from its neighbours. A known limitation of GNNs is that, as the number of layers increases, information gets smoothed and squashed and node embeddings become indistinguishable, negatively affecting performance. Therefore, practical GNN models employ few layers and only leverage the graph structure in terms of limited, small neighbourhoods around each node. Inevitably, practical GNNs do not capture information depending on the global structure of the graph. While there have been several works studying the limitations and expressivity of GNNs, the question of whether practical applications on graph structured data require global structural knowledge or not remains unanswered. In this work, we empirically address this question by giving access to global information to several GNN models, and observing the impact it has on downstream performance. Our results show that global information can in fact provide significant benefits for common graph-related tasks. We further identify a novel regularization strategy that leads to an average accuracy improvement of more than 5% on all considered tasks.

Benchmark Results

Tested on 4 datasets 1 baseline value reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
actual #21 vs paper #184 163 places worse
0.9004
best reported
actual #21 vs paper #184 163 places worse
paper 0.8610 ±0.0250

Difference within reported uncertainty; not counted as underperformance.

paper 0.8610 ±0.0250 Δ at pub 0.0107 Δ today 0.0394
39
SAGE
0.8911 ±0.0012
44
GAT
actual #44 vs paper #472 428 places worse
0.8897 ±0.0014
best reported
actual #44 vs paper #472 428 places worse
paper 0.8240 ±0.0220
paper 0.8240 ±0.0220 Δ at pub 0.0060 Δ today 0.0657
141
GraphSAGE
actual #141 vs paper #289 148 places worse
0.8410 ±0.0160
actual #141 vs paper #289 148 places worse
paper 0.8410 ±0.0160
paper 0.8410 ±0.0160 Δ at pub 0.0960 Δ today 0.0298
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
35
GAT
actual #35 vs paper #610 575 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #610 575 places worse
paper 0.7020 ±0.0130
paper 0.7020 ±0.0130 Δ at pub 0.0230 Δ today 0.1060
44
GCN
actual #44 vs paper #668 624 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #668 624 places worse
paper 0.6860 ±0.0960

Difference within reported uncertainty; not counted as underperformance.

paper 0.6860 ±0.0960 Δ at pub 0.0260 Δ today 0.1173
61
GraphSAGE
actual #61 vs paper #446 385 places worse
0.7210 ±0.0210
actual #61 vs paper #446 385 places worse
paper 0.7210 ±0.0210
paper 0.7210 ±0.0210 Δ at pub 0.0490 Δ today 0.0713
259
SAGE
0.7361 ±0.0190
350
MLP
0.7289 ±0.0010
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
actual #18 vs paper #707 689 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #707 689 places worse
paper 0.7760 ±0.0220
paper 0.7760 ±0.0220 Δ at pub 0.0190 Δ today 0.1536
20
GAT
actual #20 vs paper #410 390 places worse
0.8040 ±0.0110
actual #20 vs paper #410 390 places worse
paper 0.8040 ±0.0110

Improvement within reported uncertainty; not highlighted.

paper 0.8040 ±0.0110 Δ at pub 0.0140 Δ today 0.1193
116
SAGE
0.8881 ±0.0015
125
GraphSAGE
actual #125 vs paper #393 268 places worse
0.8070 ±0.0160
actual #125 vs paper #393 268 places worse
paper 0.8070 ±0.0160

Improvement within reported uncertainty; not highlighted.

paper 0.8070 ±0.0160 Δ at pub 0.0220 Δ today 0.0794
210
MLP
0.8690 ±0.0074

TU Dortmund

#ModelAccuracy ↑Paper
1
GC-GNN (GCN)
0.9210 ±0.0810
2
SUGAR
0.8403 ±0.0133
3
Ortho-g-U-Nets
0.8387
15
SAGE
0.8088 ±0.0233
38
DiffPool
0.7930 ±0.0220
This paper
127
k-GNN
0.7560 ±0.0210
This paper
129
GCN
0.7550 ±0.0280
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere