Papers › How Powerful are Graph Neural Networks?

How Powerful are Graph Neural Networks?

1 Oct 2018ICLR 2019 5arXiv:1810.00826archive 2025-07-28

Keyulu Xu, Weihua Hu, Jure Leskovec, Stefanie Jegelka

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.

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

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GraphCNN weihua916/powerful-gnns/models/graphcnn.py official repository ran · metamorphic tier: deterministic MIT (permissive) · 201255c60d21f681 · report
MLP weihua916/powerful-gnns/models/graphcnn.py official repository ran · metamorphic tier: deterministic MIT (permissive) · 315335a707b61ec4 · report
Discriminator egyptdj/graph-neural-mapping/models/graphcnn.py community (archive-listed) ran · metamorphic tier: invariant fingerprinted GPL-3.0 (copyleft) · pointer only · 6e6181d4f831ff7a · report
GIN_InfoMaxReg egyptdj/graph-neural-mapping/models/graphcnn.py community (archive-listed) unverified GPL-3.0 (copyleft) · pointer only · 7a017149093e4cd2 · report
GinMultiGraph PurdueMINDS/RelationalPooling/GIN/GIN_model.py community (archive-listed) unverified no licence file found · pointer only · c36f76cf05961797 · report
GinParent PurdueMINDS/RelationalPooling/GIN/GIN_model.py community (archive-listed) unverified no licence file found · pointer only · c29df0a91a98fef7 · report
MLP PurdueMINDS/RelationalPooling/GIN/GIN_model.py community (archive-listed) unverified no licence file found · pointer only · a514a7e4552016d2 · report
calculate_prec_at_k gospodima/extended-simgnn/src/utils.py community (archive-listed) unverified MIT (permissive) · c3ce89e1da779042 · report
calculate_ranking_correlation gospodima/extended-simgnn/src/utils.py community (archive-listed) unverified MIT (permissive) · 1697183cb2ca07d3 · report
denormalize_sim_score gospodima/extended-simgnn/src/utils.py community (archive-listed) unverified MIT (permissive) · 47f530d7cd2a3985 · report

Tasks

General ClassificationGraph ClassificationGraph RegressionGraph Representation LearningMolecular Property PredictionNode ClassificationRepresentation Learning

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Graph Classification BP-fMRI-97 GIN Accuracy 45.4% #7 of 7 Archive leaderboard report
Graph Classification BP-fMRI-97 GIN F1 42.3% #7 of 7 Archive leaderboard report
Graph Classification CIFAR10 100k GIN Accuracy (%) 53.28 #20 of 20 Archive leaderboard report
Graph Classification COLLAB GIN-0 Accuracy 80.2% #13 of 39 Archive leaderboard report
Graph Classification COX2 GIN-0 Accuracy(10-fold) 81.13 #1 of 3 Archive leaderboard report
Graph Classification D&D GIN Accuracy 77.311±2.223 #33 of 53 Archive leaderboard report
Graph Classification ENZYMES GIN Accuracy 68.303±4.170 #16 of 54 Archive leaderboard report
Graph Classification HIV-DTI-77 GIN Accuracy 55.1% #4 of 6 Archive leaderboard report
Graph Classification HIV-DTI-77 GIN F1 53.6% #4 of 6 Archive leaderboard report
Graph Classification HIV-fMRI-77 GIN Accuracy 52.5% #5 of 7 Archive leaderboard report
Graph Classification HIV-fMRI-77 GIN F1 35.6% #5 of 7 Archive leaderboard report
Graph Classification IMDb-B GIN Accuracy 81.250±3.775 #5 of 51 Archive leaderboard report
Graph Classification IMDb-B GIN-0 Accuracy 75.1% #25 of 51 Archive leaderboard report
Graph Classification IMDb-M GIN-0 Accuracy 52.3% #11 of 36 Archive leaderboard report
Graph Classification MUTAG GIN-0 Accuracy 89.4% #28 of 74 Archive leaderboard report
Graph Classification NCI1 GIN Accuracy 84.818±0.936 #18 of 69 Archive leaderboard report
Graph Classification NCI1 GIN-0 Accuracy 82.7% #30 of 69 Archive leaderboard report
Graph Classification NCI109 GIN Accuracy 84.155±0.812 #6 of 38 Archive leaderboard report
Graph Classification PROTEINS GIN Accuracy 75.536±1.851 #65 of 103 Archive leaderboard report
Graph Classification PROTEINS GIN-0 Accuracy 76,2% #103 of 103 Archive leaderboard report
Graph Classification PTC GIN-0 Accuracy 64.40% #24 of 37 Archive leaderboard report
Graph Classification Peptides-func GIN AP 0.6043±0.0216 #39 of 44 Archive leaderboard report
Graph Classification RE-M5K GIN-0 Accuracy 57.5% #1 of 8 Archive leaderboard report
Graph Classification REDDIT-B GIN-0 Accuracy 92.4 #3 of 12 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN+virtual node Ext. data No #14 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN+virtual node Number of params 13841815 #14 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN+virtual node Test F1 score 0.1581 ± 0.0026 #14 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN+virtual node Validation F1 score 0.1439 ± 0.0020 #14 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN Ext. data No #20 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN Number of params 12390715 #20 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN Test F1 score 0.1495 ± 0.0023 #20 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 GIN Validation F1 score 0.1376 ± 0.0016 #20 of 21 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN+virtual node Ext. data No #37 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN+virtual node Number of params 3336306 #37 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN+virtual node Test ROC-AUC 0.7707 ± 0.0149 #37 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN+virtual node Validation ROC-AUC 0.8479 ± 0.0068 #37 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN Ext. data No #42 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN Number of params 1885206 #42 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN Test ROC-AUC 0.7558 ± 0.0140 #42 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molhiv GIN Validation ROC-AUC 0.8232 ± 0.0090 #42 of 43 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN+virtual node Ext. data No #28 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN+virtual node Number of params 3374533 #28 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN+virtual node Test AP 0.2703 ± 0.0023 #28 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN+virtual node Validation AP 0.2798 ± 0.0025 #28 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN Ext. data No #33 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN Number of params 1923433 #33 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN Test AP 0.2266 ± 0.0028 #33 of 36 Archive leaderboard report
Graph Property Prediction ogbg-molpcba GIN Validation AP 0.2305 ± 0.0027 #33 of 36 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN+virtual node Ext. data No #13 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN+virtual node Number of params 3288042 #13 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN+virtual node Test Accuracy 0.7037 ± 0.0107 #13 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN+virtual node Validation Accuracy 0.6678 ± 0.0105 #13 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN Ext. data No #16 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN Number of params 1836942 #16 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN Test Accuracy 0.6892 ± 0.0100 #16 of 18 Archive leaderboard report
Graph Property Prediction ogbg-ppa GIN Validation Accuracy 0.6562 ± 0.0107 #16 of 18 Archive leaderboard report
Graph Regression ESR2 GIN R2 0.668±0.000 #4 of 9 Archive leaderboard report
Graph Regression ESR2 GIN RMSE 0.509±0.668 #4 of 9 Archive leaderboard report
Graph Regression F2 GIN R2 0.887±0.000 #3 of 9 Archive leaderboard report
Graph Regression F2 GIN RMSE 0.342±0.887 #3 of 9 Archive leaderboard report
Graph Regression KIT GIN R2 0.833±0.000 #5 of 9 Archive leaderboard report
Graph Regression KIT GIN RMSE 0.444±0.833 #5 of 9 Archive leaderboard report
Graph Regression Lipophilicity GIN R2 0.819±0.007 #4 of 23 Archive leaderboard report
Graph Regression Lipophilicity GIN RMSE 0.537±0.010 #4 of 23 Archive leaderboard report
Graph Regression PARP1 GIN R2 0.922±0.000 #3 of 9 Archive leaderboard report
Graph Regression PARP1 GIN RMSE 0.349±0.922 #3 of 9 Archive leaderboard report
Graph Regression PCQM4Mv2-LSC GIN Test MAE 0.1218 #18 of 20 Archive leaderboard report
Graph Regression PCQM4Mv2-LSC GIN Validation MAE 0.1195 #18 of 20 Archive leaderboard report
Graph Regression PGR GIN R2 0.696±0.000 #4 of 9 Archive leaderboard report
Graph Regression PGR GIN RMSE 0.532±0.696 #4 of 9 Archive leaderboard report
Graph Regression ZINC-500k GIN MAE 0.526 #35 of 36 Archive leaderboard report
Graph Regression ZINC-full GIN Test MAE 0.068±0.004 #15 of 19 Archive leaderboard report
Molecular Property Prediction ESOL GIN R2 0.938±0.011 #3 of 20 Archive leaderboard report
Molecular Property Prediction ESOL GIN RMSE 0.509±0.044 #3 of 20 Archive leaderboard report
Molecular Property Prediction FreeSolv GIN R2 0.964±0.008 #4 of 22 Archive leaderboard report
Molecular Property Prediction FreeSolv GIN RMSE 0.744±0.083 #4 of 22 Archive leaderboard report
Node Classification PATTERN 100k GIN Accuracy (%) 85.590 #5 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: GIN

GINGraph Convolutional NetworksGraphSAGE

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