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Keyulu Xu; Weihua Hu; Jure Leskovec; Stefanie Jegelka

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
Benchmarks
| Benchmark | Methodology | Metrics |
|---|---|---|
| graph-classification-on-bp-fmri-97 | GIN | Accuracy: 45.4% F1: 42.3% |
| graph-classification-on-cifar10-100k | GIN | Accuracy (%): 53.28 |
| graph-classification-on-collab | GIN-0 | Accuracy: 80.2% |
| graph-classification-on-cox2 | GIN-0 | Accuracy(10-fold): 81.13 |
| graph-classification-on-dd | GIN | Accuracy: 77.311±2.223 |
| graph-classification-on-enzymes | GIN | Accuracy: 68.303±4.170 |
| graph-classification-on-hiv-dti-77 | GIN | Accuracy: 55.1% F1: 53.6% |
| graph-classification-on-hiv-fmri-77 | GIN | Accuracy: 52.5% F1: 35.6% |
| graph-classification-on-imdb-b | GIN-0 | Accuracy: 75.1% |
| graph-classification-on-imdb-b | GIN | Accuracy: 81.250±3.775 |
| graph-classification-on-imdb-m | GIN-0 | Accuracy: 52.3% |
| graph-classification-on-mutag | GIN-0 | Accuracy: 89.4% |
| graph-classification-on-nci1 | GIN | Accuracy: 84.818±0.936 |
| graph-classification-on-nci1 | GIN-0 | Accuracy: 82.7% |
| graph-classification-on-nci109 | GIN | Accuracy: 84.155±0.812 |
| graph-classification-on-peptides-func | GIN | AP: 0.6043±0.0216 |
| graph-classification-on-proteins | GIN | Accuracy: 75.536±1.851 |
| graph-classification-on-proteins | GIN-0 | Accuracy: 76,2% |
| graph-classification-on-ptc | GIN-0 | Accuracy: 64.40% |
| graph-classification-on-re-m5k | GIN-0 | Accuracy: 57.5% |
| graph-classification-on-reddit-b | GIN-0 | Accuracy: 92.4 |
| graph-property-prediction-on-ogbg-code2 | GIN+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-code2 | GIN | 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-molhiv | GIN+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-molhiv | GIN | 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-molpcba | GIN+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-molpcba | GIN | Ext. data: No Number of params: 1923433 Test AP: 0.2266 ± 0.0028 Validation AP: 0.2305 ± 0.0027 |
| graph-property-prediction-on-ogbg-ppa | GIN+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-ppa | GIN | Ext. data: No Number of params: 1836942 Test Accuracy: 0.6892 ± 0.0100 Validation Accuracy: 0.6562 ± 0.0107 |
| graph-regression-on-esr2 | GIN | R2: 0.668±0.000 RMSE: 0.509±0.668 |
| graph-regression-on-f2 | GIN | R2: 0.887±0.000 RMSE: 0.342±0.887 |
| graph-regression-on-kit | GIN | R2: 0.833±0.000 RMSE: 0.444±0.833 |
| graph-regression-on-lipophilicity | GIN | R2: 0.819±0.007 RMSE: 0.537±0.010 |
| graph-regression-on-parp1 | GIN | R2: 0.922±0.000 RMSE: 0.349±0.922 |
| graph-regression-on-pcqm4mv2-lsc | GIN | Test MAE: 0.1218 Validation MAE: 0.1195 |
| graph-regression-on-pgr | GIN | R2: 0.696±0.000 RMSE: 0.532±0.696 |
| graph-regression-on-zinc-500k | GIN | MAE: 0.526 |
| graph-regression-on-zinc-full | GIN | Test MAE: 0.068±0.004 |
| molecular-property-prediction-on-esol | GIN | R2: 0.938±0.011 RMSE: 0.509±0.044 |
| molecular-property-prediction-on-freesolv | GIN | R2: 0.964±0.008 RMSE: 0.744±0.083 |
| node-classification-on-pattern-100k | GIN | Accuracy (%): 85.590 |
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