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
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 158 | GraphSAGE | 0.9040
±0.0780 | |
| 183 | GAT | 0.9010
±0.0580 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: The Expressive Power of Graph Neural Networks: A Survey (2023) |
| 217 | ChebNet | 0.8970
±0.0641 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) |
| 333 | A-NLSF | 0.8794
±0.0090 | This paper |
| 403 | MLP | 0.8660
±0.0495 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) |
| 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 |
| # | Model | Accuracy ↑ | 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 | 0.6850
±0.0524 best reported | best at pub: GNNBenchmark (JMLR 2023) |
| 26 | GraphSAGE | 0.6817
±0.0545 | |
| 32 | GIN | 0.6767
±0.0583 best reported | best at pub: GNNBenchmark (JMLR 2023) |
| 36 | GCN | 0.6650
±0.0691 best reported | best at pub: Hierarchical Graph Capsule Network (AAAI 2020) |
| 41 | NLSF | 0.6594
±0.0160 | This paper |
| 59 | ChebNet | 0.6380
±0.0792 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) |
| 65 | S^2GNN | 0.6326
±0.0280 | This paper |
| 109 | OAP+GIN | 0.5840
±0.0160 | This paper |
| 124 | MLP | 0.5583
±0.0352 best reported | best at pub: GNNBenchmark (JMLR 2023) |
| 148 | FA+GIN | 0.5264
±0.0220 | This paper |
OGB
| # | Model | ROC-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 | 0.8090
±0.0160 best reported | best at pub: Deep Prompt Tuning for Graph Transformers (2023) |
| 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 | 0.7780
±0.0182 best reported | best at pub: GRPE: Relative Positional Encoding for Graph Transformer (2022) Difference within reported uncertainty; not counted as underperformance. |
| 160 | GraphSAGE | 0.7690
±0.0136 | |
| 184 | GCN | 0.7630
±0.0030 best reported | best at pub: Motif-based Graph Representation Learning with Application to Chemical Molecules (2022) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | AP ↑ | 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 | 0.2902
±0.0017 best reported | best at pub: GRPE: Relative Positional Encoding for Graph Transformer (2022) |
| 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 | 0.2690
±0.0020 best reported | |
| 57 | GatedGCN | 0.2670
±0.0020 | prev best: Deep Prompt Tuning for Graph Transformers (2023) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | 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 | 0.7037
±0.0107 | Improvement within reported uncertainty; not highlighted. |
| 38 | GCN | 0.6857
±0.0061 | Improvement within reported uncertainty; not highlighted. |
Other Graph Benchmarks
| # | Model | F1 ↑ | 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 |
