Papers › Principal Neighbourhood Aggregation for Graph Nets

Principal Neighbourhood Aggregation for Graph Nets

12 Apr 2020NeurIPS 2020 12arXiv:2004.05718archive 2025-07-28

Gabriele Corso, Luca Cavalleri, Dominique Beaini, Pietro Liò, Petar Veličković

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.

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lukecavabarrett/pna officialmentioned in papermentioned on GitHubpytorch report
asarigun/GraphMixerNetworks mentioned on GitHubpytorch report
changminwu/expandergnn mentioned on GitHubpytorch report
cvignac/SMP mentioned on GitHubpytorch report
dmlc/dgl mentioned on GitHubpytorch report
rusty1s/pytorch_geometric mentioned on GitHubpytorchMIT report
Saro00/DGN pytorch report

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ExpanderScatterLinear changminwu/expandergnn/layers/pna_layer.py community (archive-listed) ran no licence file found · pointer only · 528a64a346d98ccd · report
Linear cvignac/SMP/models/smp_layers.py community (archive-listed) ran · metamorphic tier: invariant MIT (permissive) · e511d58ec99ede06 · report
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Tasks

Graph ClassificationGraph RegressionMolecular Property PredictionNode Classification

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Graph Classification CIFAR10 100k PNA Accuracy (%) 70.47 #12 of 20 Archive leaderboard report
Graph Classification D&D PNA Accuracy 78.992±4.407 #19 of 53 Archive leaderboard report
Graph Classification ENZYMES PNA Accuracy 73.021±2.512 #9 of 54 Archive leaderboard report
Graph Classification IMDb-B PNA Accuracy 78.000±3.808 #13 of 51 Archive leaderboard report
Graph Classification NCI1 PNA Accuracy 84.964±1.391 #16 of 69 Archive leaderboard report
Graph Classification NCI109 PNA Accuracy 83.382±1.045 #12 of 38 Archive leaderboard report
Graph Classification PROTEINS PNA Accuracy 77.679±3.281 #29 of 103 Archive leaderboard report
Graph Property Prediction ogbg-molhiv PNA Ext. data No #25 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv PNA Number of params 326081 #25 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv PNA Test ROC-AUC 0.7905 ± 0.0132 #25 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv PNA Validation ROC-AUC 0.8519 ± 0.0099 #25 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molpcba PNA Ext. data No #24 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba PNA Number of params 6550839 #24 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba PNA Test AP 0.2838 ± 0.0035 #24 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba PNA Validation AP 0.2926 ± 0.0026 #24 of 36 Archive leaderboard report
Graph Regression ESR2 PNA R2 0.696±0.000 #2 of 9 Archive leaderboard report
Graph Regression ESR2 PNA RMSE 0.486±0.696 #2 of 9 Archive leaderboard report
Graph Regression F2 PNA R2 0.891±0.000 #2 of 9 Archive leaderboard report
Graph Regression F2 PNA RMSE 0.336±0.891 #2 of 9 Archive leaderboard report
Graph Regression KIT PNA R2 0.843±0.000 #1 of 9 Archive leaderboard report
Graph Regression KIT PNA RMSE 0.430±0.843 #1 of 9 Archive leaderboard report
Graph Regression Lipophilicity PNA R2 0.830±0.007 #1 of 23 Archive leaderboard report
Graph Regression Lipophilicity PNA RMSE 0.520±0.011 #1 of 23 Archive leaderboard report
Graph Regression PARP1 PNA R2 0.924±0.000 #2 of 9 Archive leaderboard report
Graph Regression PARP1 PNA RMSE 0.346±0.924 #2 of 9 Archive leaderboard report
Graph Regression PGR PNA R2 0.717±0.000 #2 of 9 Archive leaderboard report
Graph Regression PGR PNA RMSE 0.514±0.717 #2 of 9 Archive leaderboard report
Graph Regression ZINC PNA MAE 0.142 #22 of 27 Archive leaderboard report
Graph Regression ZINC-full PNA Test MAE 0.057±0.007 #14 of 19 Archive leaderboard report
Molecular Property Prediction ESOL PNA R2 0.942±0.006 #2 of 20 Archive leaderboard report
Molecular Property Prediction ESOL PNA RMSE 0.493±0.026 #2 of 20 Archive leaderboard report
Molecular Property Prediction FreeSolv PNA R2 0.951±0.009 #7 of 22 Archive leaderboard report
Molecular Property Prediction FreeSolv PNA RMSE 0.870±0.081 #7 of 22 Archive leaderboard report
Node Classification PATTERN 100k PNA Accuracy (%) 86.567 #4 of 9 Archive leaderboard report

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

Methods

Introduced by this paper: PNA

PNA

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