TMLR 2022

Understanding convolution on graphs via energies

Francesco Di Giovanni, J. Rowbottom, B. Chamberlain, Thomas Markovich, Michael M. Bronstein

Main figure for Understanding convolution on graphs via energies

Abstract

Graph Neural Networks (GNNs) typically operate by message-passing, where the state of a node is updated based on the information received from its neighbours. Most message-passing models act as graph convolutions, where features are mixed by a shared, linear transformation before being propagated over the edges. On node-classification tasks, graph convolutions have been shown to suffer from two limitations: poor performance on heterophilic graphs, and over-smoothing. It is common belief that both phenomena occur because such models behave as low-pass filters, meaning that the Dirichlet energy of the features decreases along the layers incurring a smoothing effect that ultimately makes features no longer distinguishable. In this work, we rigorously prove that simple graph-convolutional models can actually enhance high frequencies and even lead to an asymptotic behaviour we refer to as over-sharpening, opposite to over-smoothing. We do so by showing that linear graph convolutions with symmetric weights minimize a multi-particle energy that generalizes the Dirichlet energy; in this setting, the weight matrices induce edge-wise attraction (repulsion) through their positive (negative) eigenvalues, thereby controlling whether the features are being smoothed or sharpened. We also extend the analysis to non-linear GNNs, and demonstrate that some existing time-continuous GNNs are instead always dominated by the low frequencies. Finally, we validate our theoretical findings through ablations and real-world experiments.

Benchmark Results

Tested on 3 datasets 9 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
39
GGCN
actual #39 vs paper #148 109 places worse
0.9213 ±0.0305
best reported
actual #39 vs paper #148 109 places worse
paper 0.8486 ±0.0455
best today: Graph Wave Networks (WWW 2025)
paper 0.8486 ±0.0455 Δ today 0.0727
53
GraphSAGE
0.9000 ±0.0365
82
GRAFF
0.8838 ±0.0453
This paper
106
GRAFF_NL
0.8649 ±0.0484
This paper
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 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
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
15
GGCN
actual #15 vs paper #79 64 places worse
0.9230 ±0.0367
best reported
actual #15 vs paper #79 64 places worse
paper 0.8568 ±0.0663

Difference within reported uncertainty; not counted as underperformance.

paper 0.8568 ±0.0663 Δ today 0.0662
22
GPRGNN
actual #22 vs paper #177 155 places worse
0.9157 ±0.0196
best reported
actual #22 vs paper #177 155 places worse
paper 0.8027 ±0.0811

Difference within reported uncertainty; not counted as underperformance.

paper 0.8027 ±0.0811 Δ at pub 0.0162 Δ today 0.1130
24
MLP
actual #24 vs paper #158 134 places worse
0.9136 ±0.0070
best reported
actual #24 vs paper #158 134 places worse
paper 0.8189 ±0.0640

Difference within reported uncertainty; not counted as underperformance.

paper 0.8189 ±0.0640 Δ at pub 0.0297 Δ today 0.0947
35
GCNII
actual #35 vs paper #203 168 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #203 168 places worse
paper 0.7786 ±0.0379
paper 0.7786 ±0.0379 Δ at pub 0.0640 Δ today 0.1132
68
H2GCN
actual #68 vs paper #136 68 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #136 68 places worse
paper 0.8270 ±0.0528
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.8270 ±0.0528 Δ today 0.0353
93
Sheaf(max)
0.8486 ±0.0471
This paper
112
GRAFF
0.8405 ±0.0610
This paper
138
SAGE
0.8269
142
GRAND
actual #142 vs paper #151 9 places worse
0.8246 ±0.0709
best reported
actual #142 vs paper #151 9 places worse
paper 0.8216 ±0.0709

Difference within reported uncertainty; not counted as underperformance.

paper 0.8216 ±0.0709 Δ today 0.0030
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
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7595 ±0.0501 Δ at pub 0.0005 Δ today 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
213
GRAFF_NL
0.7730 ±0.0324
This paper
319
CGNN
0.6622 ±0.0769
This paper
342
Geom-GCN
actual #342 vs paper #372 30 places worse
0.6412
best reported
actual #342 vs paper #372 30 places worse
paper 0.6054 ±0.0367

Difference within reported uncertainty; not counted as underperformance.

paper 0.6054 ±0.0367 Δ at pub 0.0027 Δ today 0.0358
389
PairNorm
actual #389 vs paper #389
0.5892 ±0.0315
actual #389 vs paper #389
paper 0.5892 ±0.0315
prev best: Graph-Coupled Oscillator Networks (ICML 2022)

Improvement within reported uncertainty; not highlighted.

paper 0.5892 ±0.0315 Δ at pub 0.0002
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
38
GCNII
actual #38 vs paper #114 76 places worse
0.3744 ±0.0130
actual #38 vs paper #114 76 places worse
paper 0.3744 ±0.0130

Improvement within reported uncertainty; not highlighted.

paper 0.3744 ±0.0130 Δ at pub 0.0055 Δ today 0.0338
42
MLP
actual #42 vs paper #158 116 places worse
0.4026 ±0.0108
best reported
actual #42 vs paper #158 116 places worse
paper 0.3653 ±0.0070
paper 0.3653 ±0.0070 Δ at pub 0.0365 Δ today 0.0373
52
GPRGNN
actual #52 vs paper #247 195 places worse
0.3992 ±0.0067
best reported
actual #52 vs paper #247 195 places worse
paper 0.3463 ±0.0122
paper 0.3463 ±0.0122 Δ at pub 0.0141 Δ today 0.0529
62
GGCN
actual #62 vs paper #113 51 places worse
0.3929 ±0.0048
best reported
actual #62 vs paper #113 51 places worse
paper 0.3754 ±0.0156

Difference within reported uncertainty; not counted as underperformance.

paper 0.3754 ±0.0156 Δ today 0.0175
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 today 0.0476
71
H2GCN
actual #71 vs paper #198 127 places worse
0.3885 ±0.0117
best reported
actual #71 vs paper #198 127 places worse
paper 0.3570 ±0.0100
paper 0.3570 ±0.0100 Δ at pub 0.0270 Δ today 0.0315
87
Geom-GCN
actual #87 vs paper #308 221 places worse
0.3810
best reported
actual #87 vs paper #308 221 places worse
paper 0.3159 ±0.0115
paper 0.3159 ±0.0115 Δ at pub 0.0651
101
Sheaf(max)
0.3781 ±0.0115
This paper
129
GRAFF
0.3711 ±0.0108
This paper
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 0.0816 Δ today 0.0861
188
GRAFF_NL
0.3596 ±0.0095
This paper
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