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4 months ago

How Powerful are Graph Neural Networks?

Keyulu Xu; Weihua Hu; Jure Leskovec; Stefanie Jegelka

How Powerful are Graph Neural Networks?

Abstract

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

Code Repositories

PurdueMINDS/RelationalPooling
pytorch
Mentioned in GitHub
weihua916/powerful-gnns
Official
pytorch
Mentioned in GitHub
igorsterner/commute-opt-gnn
pytorch
Mentioned in GitHub
zhliping/Deep-Learning
pytorch
Mentioned in GitHub
gmum/umwpl2021
Mentioned in GitHub
guillaumejaume/tuto-dl-on-graphs
pytorch
Mentioned in GitHub
gospodima/extended-simgnn
pytorch
Mentioned in GitHub
willy-b/tiny-GIN-for-ogbg-molhiv
pytorch
Mentioned in GitHub
mfmceneaney/Lambda-GNNs
pytorch
Mentioned in GitHub
k4my4r/ECG-Classification
pytorch
Mentioned in GitHub
yuwvandy/g2gnn
pytorch
Mentioned in GitHub
egyptdj/graph-neural-mapping
pytorch
Mentioned in GitHub
karolismart/dropgnn
pytorch
Mentioned in GitHub

Benchmarks

BenchmarkMethodologyMetrics
graph-classification-on-bp-fmri-97GIN
Accuracy: 45.4%
F1: 42.3%
graph-classification-on-cifar10-100kGIN
Accuracy (%): 53.28
graph-classification-on-collabGIN-0
Accuracy: 80.2%
graph-classification-on-cox2GIN-0
Accuracy(10-fold): 81.13
graph-classification-on-ddGIN
Accuracy: 77.311±2.223
graph-classification-on-enzymesGIN
Accuracy: 68.303±4.170
graph-classification-on-hiv-dti-77GIN
Accuracy: 55.1%
F1: 53.6%
graph-classification-on-hiv-fmri-77GIN
Accuracy: 52.5%
F1: 35.6%
graph-classification-on-imdb-bGIN-0
Accuracy: 75.1%
graph-classification-on-imdb-bGIN
Accuracy: 81.250±3.775
graph-classification-on-imdb-mGIN-0
Accuracy: 52.3%
graph-classification-on-mutagGIN-0
Accuracy: 89.4%
graph-classification-on-nci1GIN
Accuracy: 84.818±0.936
graph-classification-on-nci1GIN-0
Accuracy: 82.7%
graph-classification-on-nci109GIN
Accuracy: 84.155±0.812
graph-classification-on-peptides-funcGIN
AP: 0.6043±0.0216
graph-classification-on-proteinsGIN
Accuracy: 75.536±1.851
graph-classification-on-proteinsGIN-0
Accuracy: 76,2%
graph-classification-on-ptcGIN-0
Accuracy: 64.40%
graph-classification-on-re-m5kGIN-0
Accuracy: 57.5%
graph-classification-on-reddit-bGIN-0
Accuracy: 92.4
graph-property-prediction-on-ogbg-code2GIN+virtual node
Ext. data: No
Number of params: 13841815
Test F1 score: 0.1581 ± 0.0026
Validation F1 score: 0.1439 ± 0.0020
graph-property-prediction-on-ogbg-code2GIN
Ext. data: No
Number of params: 12390715
Test F1 score: 0.1495 ± 0.0023
Validation F1 score: 0.1376 ± 0.0016
graph-property-prediction-on-ogbg-molhivGIN+virtual node
Ext. data: No
Number of params: 3336306
Test ROC-AUC: 0.7707 ± 0.0149
Validation ROC-AUC: 0.8479 ± 0.0068
graph-property-prediction-on-ogbg-molhivGIN
Ext. data: No
Number of params: 1885206
Test ROC-AUC: 0.7558 ± 0.0140
Validation ROC-AUC: 0.8232 ± 0.0090
graph-property-prediction-on-ogbg-molpcbaGIN+virtual node
Ext. data: No
Number of params: 3374533
Test AP: 0.2703 ± 0.0023
Validation AP: 0.2798 ± 0.0025
graph-property-prediction-on-ogbg-molpcbaGIN
Ext. data: No
Number of params: 1923433
Test AP: 0.2266 ± 0.0028
Validation AP: 0.2305 ± 0.0027
graph-property-prediction-on-ogbg-ppaGIN+virtual node
Ext. data: No
Number of params: 3288042
Test Accuracy: 0.7037 ± 0.0107
Validation Accuracy: 0.6678 ± 0.0105
graph-property-prediction-on-ogbg-ppaGIN
Ext. data: No
Number of params: 1836942
Test Accuracy: 0.6892 ± 0.0100
Validation Accuracy: 0.6562 ± 0.0107
graph-regression-on-esr2GIN
R2: 0.668±0.000
RMSE: 0.509±0.668
graph-regression-on-f2GIN
R2: 0.887±0.000
RMSE: 0.342±0.887
graph-regression-on-kitGIN
R2: 0.833±0.000
RMSE: 0.444±0.833
graph-regression-on-lipophilicityGIN
R2: 0.819±0.007
RMSE: 0.537±0.010
graph-regression-on-parp1GIN
R2: 0.922±0.000
RMSE: 0.349±0.922
graph-regression-on-pcqm4mv2-lscGIN
Test MAE: 0.1218
Validation MAE: 0.1195
graph-regression-on-pgrGIN
R2: 0.696±0.000
RMSE: 0.532±0.696
graph-regression-on-zinc-500kGIN
MAE: 0.526
graph-regression-on-zinc-fullGIN
Test MAE: 0.068±0.004
molecular-property-prediction-on-esolGIN
R2: 0.938±0.011
RMSE: 0.509±0.044
molecular-property-prediction-on-freesolvGIN
R2: 0.964±0.008
RMSE: 0.744±0.083
node-classification-on-pattern-100kGIN
Accuracy (%): 85.590

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How Powerful are Graph Neural Networks? | Papers | HyperAI