Adaptive Canonicalization with Application to Invariant Anisotropic Geometric Networks

Y. Lin, Ron Levie

Main figure for Adaptive Canonicalization with Application to Invariant Anisotropic Geometric Networks

Abstract

Canonicalization is a widely used strategy in equivariant machine learning, enforcing symmetry in neural networks by mapping each input to a standard form. Yet, it often introduces discontinuities that can affect stability during training, limit generalization, and complicate universal approximation theorems. In this paper, we address this by introducing adaptive canonicalization, a general framework in which the canonicalization depends both on the input and the network. Specifically, we present the adaptive canonicalization based on prior maximization, where the standard form of the input is chosen to maximize the predictive confidence of the network. We prove that this construction yields continuous and symmetry-respecting models that admit universal approximation properties. We propose two applications of our setting: (i) resolving eigenbasis ambiguities in spectral graph neural networks, and (ii) handling rotational symmetries in point clouds. We empirically validate our methods on molecular and protein classification, as well as point cloud classification tasks. Our adaptive canonicalization outperforms the three other common solutions to equivariant machine learning: data augmentation, standard canonicalization, and equivariant architectures.

Benchmark Results

Tested on 6 datasets 12 baseline values reported too low

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

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
actual #39 vs paper #515 476 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #515 476 places worse
paper 0.8329 ±0.0360
paper 0.8329 ±0.0360 Δ at pub 0.1001
63
GCN
actual #63 vs paper #577 514 places worse
0.9220 ±0.0440
best reported
actual #63 vs paper #577 514 places worse
paper 0.8163 ±0.0310
paper 0.8163 ±0.0310 Δ at pub 0.1057
158
GraphSAGE
0.9040 ±0.0780
183
GAT
actual #183 vs paper #517 334 places worse
0.9010 ±0.0580
best reported
actual #183 vs paper #517 334 places worse
paper 0.8317 ±0.0440
paper 0.8317 ±0.0440 Δ at pub 0.0693 Δ today 0.0693
217
ChebNet
actual #217 vs paper #563 346 places worse
0.8970 ±0.0641
best reported
actual #217 vs paper #563 346 places worse
paper 0.8215 ±0.0160
paper 0.8215 ±0.0160 Δ at pub 0.0755
333
A-NLSF
0.8794 ±0.0090
This paper
403
MLP
actual #403 vs paper #638 235 places worse
0.8660 ±0.0495
best reported
actual #403 vs paper #638 235 places worse
paper 0.7931 ±0.0350
paper 0.7931 ±0.0350 Δ at pub 0.0729
453
OAP+GIN
0.8495 ±0.0200
This paper
481
NLSF
0.8413 ±0.0150
This paper
482
FA+GIN
0.8407 ±0.0240
This paper
536
S^2GNN
0.8270 ±0.0210
This paper
#ModelAccuracy ↑Paper
1
GMN
0.7866
2
MemGNN
0.7550
3
TFGW SP
0.7510 ±0.0500
8
A-NLSF
0.7301 ±0.0080
This paper
17
GatedGCN
0.7000 ±0.0494
20
GAT
actual #20 vs paper #188 168 places worse
0.6850 ±0.0524
best reported
actual #20 vs paper #188 168 places worse
paper 0.3983 ±0.0370
best at pub: GNNBenchmark (JMLR 2023)
paper 0.3983 ±0.0370 Δ at pub 0.2867
26
GraphSAGE
0.6817 ±0.0545
32
GIN
actual #32 vs paper #168 136 places worse
0.6767 ±0.0583
best reported
actual #32 vs paper #168 136 places worse
paper 0.4569 ±0.0260
best at pub: GNNBenchmark (JMLR 2023)
paper 0.4569 ±0.0260 Δ at pub 0.2198
36
GCN
actual #36 vs paper #175 139 places worse
0.6650 ±0.0691
best reported
actual #36 vs paper #175 139 places worse
paper 0.4366 ±0.0340
best at pub: Hierarchical Graph Capsule Network (AAAI 2020)
paper 0.4366 ±0.0340 Δ at pub 0.2284
41
NLSF
0.6594 ±0.0160
This paper
59
ChebNet
actual #59 vs paper #156 97 places worse
0.6380 ±0.0792
best reported
actual #59 vs paper #156 97 places worse
paper 0.5042 ±0.0140
paper 0.5042 ±0.0140 Δ at pub 0.1338
65
S^2GNN
0.6326 ±0.0280
This paper
109
OAP+GIN
0.5840 ±0.0160
This paper
124
MLP
actual #124 vs paper #182 58 places worse
0.5583 ±0.0352
best reported
actual #124 vs paper #182 58 places worse
paper 0.4217 ±0.0280
best at pub: GNNBenchmark (JMLR 2023)
paper 0.4217 ±0.0280 Δ at pub 0.1366
148
FA+GIN
0.5264 ±0.0220
This paper

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
actual #9 vs paper #161 152 places worse
0.8090 ±0.0160
best reported
actual #9 vs paper #161 152 places worse
paper 0.7687 ±0.0136
paper 0.7687 ±0.0136 Δ at pub 0.0403
23
A-NLSF
0.8019 ±0.0152
This paper
62
PNA
0.7905 ±0.0132
This paper
69
GPS
0.7880 ±0.0101
This paper
99
OAP+GatedGCN
0.7802 ±0.0128
This paper
106
SAN
0.7785 ±0.2470
This paper
109
GIN
actual #109 vs paper #150 41 places worse
0.7780 ±0.0182
best reported
actual #109 vs paper #150 41 places worse
paper 0.7707 ±0.0149

Difference within reported uncertainty; not counted as underperformance.

paper 0.7707 ±0.0149 Δ at pub 0.0073
160
GraphSAGE
0.7690 ±0.0136
184
GCN
actual #184 vs paper #203 19 places worse
0.7630 ±0.0030
best reported
actual #184 vs paper #203 19 places worse
paper 0.7599 ±0.0119

Difference within reported uncertainty; not counted as underperformance.

paper 0.7599 ±0.0119 Δ at pub 0.0031
#ModelAP ↑Paper
1
GRPE-Large
0.3150 ±0.0010
2
Graphormer
0.3140
3
Graphormer-FLAG
0.3139 ±0.0032
14
A-NLSF
0.2968 ±0.0022
This paper
30
GPS
0.2907 ±0.0028
This paper
31
GIN
actual #31 vs paper #52 21 places worse
0.2902 ±0.0017
best reported
actual #31 vs paper #52 21 places worse
paper 0.2703 ±0.0023
paper 0.2703 ±0.0023 Δ at pub 0.0199
38
PNA
0.2838 ±0.0035
This paper
44
OAP+GatedGCN
0.2783 ±0.0024
This paper
49
SAN
0.2765 ±0.0042
This paper
50
GraphTrans
0.2761 ±0.0029
This paper
56
GCN
actual #56 vs paper #80 24 places worse
0.2690 ±0.0020
best reported
actual #56 vs paper #80 24 places worse
paper 0.2424 ±0.0034
57
GatedGCN
actual #57 vs paper #57
0.2670 ±0.0020
actual #57 vs paper #57
paper 0.2670 ±0.0020

Improvement within reported uncertainty; not highlighted.

paper 0.2670 ±0.0020 Δ at pub 0.0030
#ModelAccuracy ↑Paper
1
A-NLSF
0.8149 ±0.0067
This paper
2
differential encoding
0.8096 ±0.0029
3
MPNN + VN + NoPE
0.8055 ±0.0038
5
GPS
0.8015 ±0.0033
This paper
11
OAP+GatedGCN
0.7745 ±0.0098
This paper
16
GatedGCN
0.7531 ±0.0083
This paper
17
SAT
0.7522 ±0.0056
This paper
33
GIN
actual #33 vs paper #33
0.7037 ±0.0107
actual #33 vs paper #33
paper 0.7037 ±0.0107

Improvement within reported uncertainty; not highlighted.

paper 0.7037 ±0.0107 Δ at pub 0.0145
38
GCN
actual #38 vs paper #38
0.6857 ±0.0061
actual #38 vs paper #38
paper 0.6857 ±0.0061

Improvement within reported uncertainty; not highlighted.

paper 0.6857 ±0.0061 Δ at pub 0.0018

Other Graph Benchmarks

#ModelF1 ↑Paper
1
GPS + k-MIP
0.8268 ±0.0064
2
Exphormer
0.8262 ±0.0031
3
VN-DGCNN
0.8140
This paper
4
AC-DGCNN
0.8090 ±0.0070
This paper
6
DGCNN
0.7860
This paper
7
CN-DGCNN
0.7850 ±0.0090
This paper
9
GatedGCN
0.7620 ±0.0032
10
AC-PointNet
0.7600 ±0.0060
This paper
11
CN-PointNet
0.7360 ±0.0110
This paper
12
VN-PointNet
0.7280
This paper
15
PointNet++
0.6230
This paper
16
GCN
0.6018 ±0.0004
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 today — OK at publication; today's leaderboard best is elsewhere