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3 months ago

Principal Neighbourhood Aggregation for Graph Nets

Gabriele Corso Luca Cavalleri Dominique Beaini Pietro Liò Petar Veličković

Principal Neighbourhood Aggregation for Graph Nets

Abstract

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

Code Repositories

dmlc/dgl
pytorch
Mentioned in GitHub
Saro00/DGN
pytorch
asarigun/GraphMixerNetworks
pytorch
Mentioned in GitHub
rusty1s/pytorch_geometric
pytorch
Mentioned in GitHub
changminwu/expandergnn
pytorch
Mentioned in GitHub
cvignac/SMP
pytorch
Mentioned in GitHub
lukecavabarrett/pna
Official
pytorch
Mentioned in GitHub

Benchmarks

BenchmarkMethodologyMetrics
graph-classification-on-cifar10-100kPNA
Accuracy (%): 70.47
graph-classification-on-ddPNA
Accuracy: 78.992±4.407
graph-classification-on-enzymesPNA
Accuracy: 73.021±2.512
graph-classification-on-imdb-bPNA
Accuracy: 78.000±3.808
graph-classification-on-nci1PNA
Accuracy: 84.964±1.391
graph-classification-on-nci109PNA
Accuracy: 83.382±1.045
graph-classification-on-proteinsPNA
Accuracy: 77.679±3.281
graph-property-prediction-on-ogbg-molhivPNA
Ext. data: No
Number of params: 326081
Test ROC-AUC: 0.7905 ± 0.0132
Validation ROC-AUC: 0.8519 ± 0.0099
graph-property-prediction-on-ogbg-molpcbaPNA
Ext. data: No
Number of params: 6550839
Test AP: 0.2838 ± 0.0035
Validation AP: 0.2926 ± 0.0026
graph-regression-on-esr2PNA
R2: 0.696±0.000
RMSE: 0.486±0.696
graph-regression-on-f2PNA
R2: 0.891±0.000
RMSE: 0.336±0.891
graph-regression-on-kitPNA
R2: 0.843±0.000
RMSE: 0.430±0.843
graph-regression-on-lipophilicityPNA
R2: 0.830±0.007
RMSE: 0.520±0.011
graph-regression-on-parp1PNA
R2: 0.924±0.000
RMSE: 0.346±0.924
graph-regression-on-pgrPNA
R2: 0.717±0.000
RMSE: 0.514±0.717
graph-regression-on-zincPNA
MAE: 0.142
graph-regression-on-zinc-fullPNA
Test MAE: 0.057±0.007
molecular-property-prediction-on-esolPNA
R2: 0.942±0.006
RMSE: 0.493±0.026
molecular-property-prediction-on-freesolvPNA
R2: 0.951±0.009
RMSE: 0.870±0.081
node-classification-on-pattern-100kPNA
Accuracy (%): 86.567

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