KDD 2024

Understanding Oversmoothing in Diffusion-Based GNNs From the Perspective of Operator Semigroup Theory

Weichen Zhao, Chenguang Wang, Xinyan Wang, Congying Han, Tiande Guo, Tianshu Yu

Main figure for Understanding Oversmoothing in Diffusion-Based GNNs From the Perspective of Operator Semigroup Theory

Abstract

This paper presents an analytical study of the oversmoothing issue in diffusion-based Graph Neural Networks (GNNs). Generalizing beyond extant approaches grounded in random walk analysis or particle systems, we approach this problem through operator semigroup theory. This theoretical framework allows us to rigorously prove that oversmoothing is intrinsically linked to the ergodicity of the diffusion operator. Relying on semigroup method, we can quantitatively analyze the dynamic of graph diffusion and give a specific mathematical form of the smoothing feature by ergodicity and invariant measure of operator, which improves previous works only show existence of oversmoothing. This finding further poses a general and mild ergodicity-breaking condition, encompassing the various specific solutions previously offered, thereby presenting a more universal and theoretically grounded approach to relieve oversmoothing in diffusion-based GNNs. Additionally, we offer a probabilistic interpretation of our theory, forging a link with prior works and broadening the theoretical horizon. Our experimental results reveal that this ergodicity-breaking term effectively mitigates oversmoothing measured by Dirichlet energy, and simultaneously enhances performance in node classification tasks.

Benchmark Results

Tested on 3 datasets 8 baseline values reported too low

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

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
34
MLP
0.9230 ±0.0070
53
GraphSAGE
actual #53 vs paper #193 140 places worse
0.9000 ±0.0365
best reported
actual #53 vs paper #193 140 places worse
paper 0.8243 ±0.0614

Difference within reported uncertainty; not counted as underperformance.

paper 0.8243 ±0.0614 Δ at pub 0.0757 Δ today 0.0757
57
GREAD
actual #57 vs paper #160 103 places worse
0.8973 ±0.0449
best reported
actual #57 vs paper #160 103 places worse
paper 0.8459 ±0.0453

Difference within reported uncertainty; not counted as underperformance.

paper 0.8459 ±0.0453 Δ today 0.0514
79
Ours-Expn
0.8865 ±0.0264
This paper
82
GRAFF
actual #82 vs paper #164 82 places worse
0.8838 ±0.0353
best reported
actual #82 vs paper #164 82 places worse
paper 0.8432 ±0.0551

Difference within reported uncertainty; not counted as underperformance.

paper 0.8432 ±0.0551 Δ at pub 0.0406 Δ today 0.0406
102
Ours-Log
0.8703 ±0.0524
This paper
167
Ours-Exp
0.8406 ±0.0459
This paper
189
SAGE
0.8269
211
GAT
actual #211 vs paper #576 365 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #576 365 places worse
paper 0.5216 ±0.0663
paper 0.5216 ±0.0663 Δ at pub 0.2784 Δ today 0.2946
217
GRAND
actual #217 vs paper #308 91 places worse
0.8140 ±0.0350
best reported
actual #217 vs paper #308 91 places worse
paper 0.7568 ±0.0725

Difference within reported uncertainty; not counted as underperformance.

paper 0.7568 ±0.0725 Δ at pub 0.0452 Δ today 0.0572
257
GCN
actual #257 vs paper #568 311 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #568 311 places worse
paper 0.5514 ±0.0516
best today: Graph Wave Networks (WWW 2025)
paper 0.5514 ±0.0516 Δ at pub 0.2326 Δ today 0.2419
376
CGNN
actual #376 vs paper #378 2 places worse
0.7140 ±0.0410
best reported
actual #376 vs paper #378 2 places worse
paper 0.7135 ±0.0405

Difference within reported uncertainty; not counted as underperformance.

paper 0.7135 ±0.0405 Δ today 0.0005
499
PairNorm
actual #499 vs paper #499
0.6030 ±0.0430
best reported
actual #499 vs paper #499
paper 0.6027 ±0.0434
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.6027 ±0.0434 Δ at pub 0.0003 Δ today 0.0003
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
24
MLP
0.9136 ±0.0070
52
GREAD
actual #52 vs paper #249 197 places worse
0.8703 ±0.0495
best reported
actual #52 vs paper #249 197 places worse
paper 0.7378 ±0.0453
paper 0.7378 ±0.0453 Δ today 0.1325
112
GRAFF
actual #112 vs paper #277 165 places worse
0.8405 ±0.0610
best reported
actual #112 vs paper #277 165 places worse
paper 0.7108 ±0.0364
paper 0.7108 ±0.0364 Δ at pub 0.1297 Δ today 0.1297
138
SAGE
0.8269
142
GRAND
actual #142 vs paper #237 95 places worse
0.8246 ±0.0709
best reported
actual #142 vs paper #237 95 places worse
paper 0.7459 ±0.0404

Difference within reported uncertainty; not counted as underperformance.

paper 0.7459 ±0.0404 Δ at pub 0.0761 Δ today 0.0787
157
GraphSAGE
actual #157 vs paper #222 65 places worse
0.8196 ±0.0739
best reported
actual #157 vs paper #222 65 places worse
paper 0.7595 ±0.0501

Difference within reported uncertainty; not counted as underperformance.

paper 0.7595 ±0.0501 Δ at pub 0.0601
158
GAT
actual #158 vs paper #358 200 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #358 200 places worse
paper 0.6189 ±0.0505
paper 0.6189 ±0.0505 Δ at pub 0.2001
170
GCN
actual #170 vs paper #372 202 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #372 202 places worse
paper 0.6054 ±0.0530
paper 0.6054 ±0.0530 Δ at pub 0.1866 Δ today 0.2028
199
Ours-Log
0.7811 ±0.0390
This paper
209
Ours-Exp
0.7757 ±0.0383
This paper
221
Ours-Expn
0.7648 ±0.0271
This paper
319
CGNN
0.6622 ±0.0769
This paper
389
PairNorm
0.5892 ±0.0315
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
0.4026 ±0.0108
68
GraphSAGE
actual #68 vs paper #258 190 places worse
0.3899 ±0.0085
best reported
actual #68 vs paper #258 190 places worse
paper 0.3423 ±0.0099
paper 0.3423 ±0.0099 Δ at pub 0.0476
96
GREAD
actual #96 vs paper #111 15 places worse
0.3790 ±0.0117
best reported
actual #96 vs paper #111 15 places worse
paper 0.3759 ±0.0106

Difference within reported uncertainty; not counted as underperformance.

paper 0.3759 ±0.0106 Δ today 0.0031
106
Ours-Expn
0.3779 ±0.0086
This paper
113
Ours-Log
0.3755 ±0.0080
This paper
115
Ours-Exp
0.3737 ±0.0117
This paper
129
GRAFF
actual #129 vs paper #209 80 places worse
0.3711 ±0.0108
best reported
actual #129 vs paper #209 80 places worse
paper 0.3555 ±0.0120

Difference within reported uncertainty; not counted as underperformance.

paper 0.3555 ±0.0120 Δ at pub 0.0156 Δ today 0.0156
135
GCN
actual #135 vs paper #408 273 places worse
0.3690
best reported
actual #135 vs paper #408 273 places worse
paper 0.2732 ±0.0110
paper 0.2732 ±0.0110 Δ at pub 0.0958
182
GAT
actual #182 vs paper #406 224 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #406 224 places worse
paper 0.2744 ±0.0089
paper 0.2744 ±0.0089 Δ at pub 0.0861
189
CGNN
0.3595 ±0.0086
This paper
203
GRAND
0.3562 ±0.0101
This paper
266
GIN
0.3410 ±0.0030
408
PairNorm
0.2740 ±0.0124
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) Best today — OK at publication; today's leaderboard best is elsewhere