On The Expressive Power of GNN Derivatives

Yam Eitan, Moshe Eliasof, Yoav Gelberg, Fabrizio Frasca, Guy Bar-Shalom, Haggai Maron

Main figure for On The Expressive Power of GNN Derivatives

Abstract

Despite significant advances in Graph Neural Networks (GNNs), their limited expressivity remains a fundamental challenge. Research on GNN expressivity has produced many expressive architectures, leading to architecture hierarchies with models of increasing expressive power. Separately, derivatives of GNNs with respect to node features have been widely studied in the context of the oversquashing and over-smoothing phenomena, GNN explainability, and more. To date, these derivatives remain unexplored as a means to enhance GNN expressivity. In this paper, we show that these derivatives provide a natural way to enhance the expressivity of GNNs. We introduce High-Order Derivative GNN (HOD-GNN), a novel method that enhances the expressivity of Message Passing Neural Networks (MPNNs) by leveraging high-order node derivatives of the base model. These derivatives generate expressive structure-aware node embeddings processed by a second GNN in an end-to-end trainable architecture. Theoretically, we show that the resulting architecture family's expressive power aligns with the WL hierarchy. We also draw deep connections between HOD-GNN, Subgraph GNNs, and popular structural encoding schemes. For computational efficiency, we develop a message-passing algorithm for computing high-order derivatives of MPNNs that exploits graph sparsity and parallelism. Evaluations on popular graph learning benchmarks demonstrate HOD-GNN's strong performance on popular graph learning tasks.

Proposed method: HOD-GNN

Benchmark Results

Tested on 3 datasets 9 baseline values reported too low

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

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
actual #14 vs paper #216 202 places worse
0.8400 ±0.0040
best reported
actual #14 vs paper #216 202 places worse
paper 0.7529 ±0.0069
paper 0.7529 ±0.0069 Δ at pub 0.0871
24
GIN
actual #24 vs paper #234 210 places worse
0.8290 ±0.0069
best reported
actual #24 vs paper #234 210 places worse
paper 0.7491 ±0.0051
paper 0.7491 ±0.0051 Δ at pub 0.0799
83
PNA
actual #83 vs paper #279 196 places worse
0.7930 ±0.0150
best reported
actual #83 vs paper #279 196 places worse
paper 0.7330 ±0.0110
paper 0.7330 ±0.0110 Δ at pub 0.0600
104
Graph ViT
0.7851 ±0.0077
This paper
122
HOD-GNN
0.7799 ±0.0071
This paper
124
HyMN
0.7782 ±0.0059
This paper
135
GraphSAGE
0.7744 ±0.0038
140
GPSE
0.7740 ±0.0080
This paper
142
Policy-Learn
0.7736 ±0.0060
This paper
168
Random
0.7662 ±0.0063
This paper
170
GIN + Laplacian PE
0.7660 ±0.0030
This paper
177
GIN + RWSE
0.7630 ±0.0050
This paper
178
Full
0.7625 ±0.0112
This paper
181
GSN
0.7608 ±0.0079
This paper
194
GPS
0.7570 ±0.0040
This paper
226
Reconstr. GNN
0.7515 ±0.0140
This paper

LRGB

#ModelMAE ↓Paper
1
GCN
actual #1 vs paper #183 182 places worse
0.2421 ±0.0016
best reported
actual #1 vs paper #183 182 places worse
paper 0.3496 ±0.0013
2
IPR-MPNN
0.2422 ±0.0007
3
TANGO-GPS
0.2422 ±0.0014
5
GIN
0.2429 ±0.0019
7
GatedGCN
actual #7 vs paper #182 175 places worse
0.2431 ±0.0020
best reported
actual #7 vs paper #182 175 places worse
paper 0.3420 ±0.0013
19
Graph ViT
actual #19 vs paper #51 32 places worse
0.2449 ±0.0016
best reported
actual #19 vs paper #51 32 places worse
paper 0.2474 ±0.0016

Difference within reported uncertainty; not counted as underperformance.

paper 0.2474 ±0.0016 Δ at pub 0.0025 Δ today 0.0025
23
HOD-GNN
0.2450 ±0.0011
This paper
39
HyMN
0.2464 ±0.0013
This paper
40
GPSE + GPS
0.2464 ±0.0025
This paper
49
GINE
actual #49 vs paper #184 135 places worse
0.2473 ±0.0017
best reported
actual #49 vs paper #184 135 places worse
paper 0.3547 ±0.0045
paper 0.3547 ±0.0045 Δ at pub 0.1074 Δ today 0.1074
57
Policy-Learn
0.2475 ±0.0011
This paper
66
Exphormer
0.2481 ±0.0007
This paper
74
GPSE + GCN
0.2487 ±0.0011
This paper
79
GCN + Laplacian PE
0.2492 ±0.0019
This paper
81
Subgraphormer 30%
0.2494 ±0.0020
This paper
88
GraphGPS+LapPE
actual #88 vs paper #88
0.2500 ±0.0005
actual #88 vs paper #88
paper 0.2500 ±0.0005
paper 0.2500 ±0.0005 Δ at pub 0.2703
104
DRew-GCN+LapPE
actual #104 vs paper #114 10 places worse
0.2517 ±0.0011
best reported
actual #104 vs paper #114 10 places worse
paper 0.2536 ±0.0015

Difference within reported uncertainty; not counted as underperformance.

paper 0.2536 ±0.0015 Δ today 0.0019
133
GCN + RWSE
0.2574 ±0.0020
This paper
149
MixHop-GCN+LapPE
0.2614 ±0.0023
This paper
150
DIGL+MPNN+LapPE
0.2616 ±0.0018
This paper
155
SAN+LapPE
actual #155 vs paper #155
0.2680 ±0.0040
best reported
actual #155 vs paper #155
paper 0.2683 ±0.0043

Difference within reported uncertainty; not counted as underperformance.

paper 0.2683 ±0.0043 Δ at pub 0.0003
175
MOSE
0.3180 ±0.0100
This paper
183
GCNII
0.3471 ±0.0010
This paper
201
MLP
0.4351 ±0.0008
#ModelAP ↑Paper
1
S^2GCN
0.7311 ±0.0066
2
S4G
0.7293 ±0.0004
3
BuNN
0.7276 ±0.0065
4
GCN
actual #4 vs paper #142 138 places worse
0.7261 ±0.0011
best reported
actual #4 vs paper #142 138 places worse
paper 0.5930 ±0.0023
paper 0.5930 ±0.0023 Δ at pub 0.0930 Δ today 0.1331
12
DRew-GCN+LapPE
0.7150 ±0.0044
This paper
26
GIN
0.7059 ±0.0089
34
GatedGCN
actual #34 vs paper #149 115 places worse
0.7006 ±0.0033
best reported
actual #34 vs paper #149 115 places worse
paper 0.5864 ±0.0077
paper 0.5864 ±0.0077 Δ at pub 0.0901 Δ today 0.1142
35
GCNII
actual #35 vs paper #159 124 places worse
0.6990 ±0.0030
best reported
actual #35 vs paper #159 124 places worse
paper 0.5543 ±0.0078
best at pub: LRGB (NeurIPS 2022)
paper 0.5543 ±0.0078 Δ today 0.1447
42
HOD-GNN
0.6968 ±0.0056
This paper
44
Graph ViT
actual #44 vs paper #47 3 places worse
0.6942 ±0.0075
best reported
actual #44 vs paper #47 3 places worse
paper 0.6919 ±0.0085

Difference within reported uncertainty; not counted as underperformance.

paper 0.6919 ±0.0085 Δ at pub 0.0023
50
HyMN
0.6857 ±0.0055
This paper
51
MixHop-GCN+LapPE
0.6843 ±0.0049
This paper
52
DIGL+MPNN+LapPE
0.6830 ±0.0026
This paper
71
GPSE + GPS
0.6688 ±0.0151
This paper
78
GINE
actual #78 vs paper #162 84 places worse
0.6621 ±0.0067
best reported
actual #78 vs paper #162 84 places worse
paper 0.5498 ±0.0079
paper 0.5498 ±0.0079 Δ at pub 0.1123 Δ today 0.1123
92
GraphGPS+LapPE
actual #92 vs paper #92
0.6535 ±0.0041
actual #92 vs paper #92
paper 0.6535 ±0.0041

Improvement within reported uncertainty; not highlighted.

paper 0.6535 ±0.0041 Δ at pub 0.0684
95
Exphormer
0.6527 ±0.0043
This paper
110
Policy-Learn
0.6459 ±0.0018
This paper
115
Subgraphormer 30%
0.6415 ±0.0052
This paper
116
SAN+LapPE
0.6384 ±0.0121
This paper
117
MOSE
0.6350 ±0.0110
This paper
122
GPSE + GCN
0.6316 ±0.0085
This paper
123
SignNet
0.6314 ±0.0059
This paper
128
GCN + Laplacian PE
0.6218 ±0.0055
This paper
135
GCN + RWSE
0.6067 ±0.0069
This paper
181
MLP
0.4060 ±0.0021
SOTA performance (not significantly different from the best) Proposed method (this paper) 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 at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere