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5 months ago

Semi-Supervised Classification with Graph Convolutional Networks

Thomas N. Kipf; Max Welling

Semi-Supervised Classification with Graph Convolutional Networks

Abstract

We present a scalable approach for semi-supervised learning on graph-structured data that is based on an efficient variant of convolutional neural networks which operate directly on graphs. We motivate the choice of our convolutional architecture via a localized first-order approximation of spectral graph convolutions. Our model scales linearly in the number of graph edges and learns hidden layer representations that encode both local graph structure and features of nodes. In a number of experiments on citation networks and on a knowledge graph dataset we demonstrate that our approach outperforms related methods by a significant margin.

Code Repositories

kiharalab/gnn_pocket
pytorch
Mentioned in GitHub
udlf/wsef
pytorch
Mentioned in GitHub
lipingcoding/pygcn
pytorch
Mentioned in GitHub
mahsa91/RA-GCN
pytorch
Mentioned in GitHub
deepchem/moleculenet
pytorch
Mentioned in GitHub
yangjun1994/CAGCN
Mentioned in GitHub
tk-rusch/graphcon
pytorch
Mentioned in GitHub
alexOarga/haiku-geometric
jax
Mentioned in GitHub
fanzhenliu/dagad
pytorch
Mentioned in GitHub
tkipf/gcn
tf
Mentioned in GitHub
emartinezs44/SparkGCN
Mentioned in GitHub
KimMeen/GCN
pytorch
Mentioned in GitHub
thanhtrunghuynh93/pygcn
pytorch
Mentioned in GitHub
clin366/pygcn
pytorch
Mentioned in GitHub
tkipf/pygcn
Official
pytorch
Mentioned in GitHub
negarhdr/PGCN
pytorch
Mentioned in GitHub
jiangboahu/glcn-tf
tf
Mentioned in GitHub
bcsrn/gcn
pytorch
Mentioned in GitHub
HoganZhang/pygcn_python3
pytorch
Mentioned in GitHub
yCobanoglu/infinite-width-gnns
jax
Mentioned in GitHub
basiralab/reproduciblefedgnn
pytorch
Mentioned in GitHub
mahendrathapa/graph-convolution-network
pytorch
Mentioned in GitHub
LouisDumont/GCN---re-implementation
pytorch
Mentioned in GitHub
darnbi/pygcn
pytorch
Mentioned in GitHub
1075225782/GCN
pytorch
Mentioned in GitHub
hazdzz/GCN
pytorch
Mentioned in GitHub
zhiqiang00/Hon-GCN
pytorch
Mentioned in GitHub
meliketoy/graph-cnn.pytorch
pytorch
Mentioned in GitHub
basiralab/RG-Select
pytorch
Mentioned in GitHub
ajbisberg/gcn
tf
Mentioned in GitHub
cybermonic/cage-4-submission
pytorch
Mentioned in GitHub
tkipf/keras-gcn
tf
Mentioned in GitHub
mahsa91/GKD
pytorch
Mentioned in GitHub
nieci2024/pyglcn
pytorch
Mentioned in GitHub
nnaakkaaii/g2-MLP
pytorch
Mentioned in GitHub
ykrmm/sota_gnn
pytorch
Mentioned in GitHub
IllinoisGraphBenchmark/IGB-Datasets
pytorch
Mentioned in GitHub
selmiss/gp-tlstgcn
pytorch
Mentioned in GitHub

Benchmarks

BenchmarkMethodologyMetrics
graph-classification-on-ddGCN
Accuracy: 78.151±3.465
graph-classification-on-enzymesGCN
Accuracy: 73.466±4.372
graph-classification-on-imdb-bGCN
Accuracy: 79.500±3.109
graph-classification-on-nci1GCN
Accuracy: 84.185±0.644
graph-classification-on-nci109GCN
Accuracy: 83.140±1.248
graph-classification-on-proteinsGCN
Accuracy: 75.536±1.622
graph-property-prediction-on-ogbg-code2GCN
Ext. data: No
Number of params: 11033210
Test F1 score: 0.1507 ± 0.0018
Validation F1 score: 0.1399 ± 0.0017
graph-property-prediction-on-ogbg-code2GCN+virtual node
Ext. data: No
Number of params: 12484310
Test F1 score: 0.1595 ± 0.0018
Validation F1 score: 0.1461 ± 0.0013
graph-property-prediction-on-ogbg-molhivGCN (in Julia)
Ext. data: No
Number of params: 527701
Test ROC-AUC: 0.7549 ± 0.0163
Validation ROC-AUC: 0.8042 ± 0.0107
graph-property-prediction-on-ogbg-molhivGCN+virtual node
Ext. data: No
Number of params: 1978801
Test ROC-AUC: 0.7599 ± 0.0119
Validation ROC-AUC: 0.8384 ± 0.0091
graph-property-prediction-on-ogbg-molhivGCN
Ext. data: No
Number of params: 527701
Test ROC-AUC: 0.7606 ± 0.0097
Validation ROC-AUC: 0.8204 ± 0.0141
graph-property-prediction-on-ogbg-molpcbaGCN
Ext. data: No
Number of params: 565928
Test AP: 0.2020 ± 0.0024
Validation AP: 0.2059 ± 0.0033
graph-property-prediction-on-ogbg-molpcbaGCN+virtual node
Ext. data: No
Number of params: 2017028
Test AP: 0.2424 ± 0.0034
Validation AP: 0.2495 ± 0.0042
graph-property-prediction-on-ogbg-ppaGCN
Ext. data: No
Number of params: 479437
Test Accuracy: 0.6839 ± 0.0084
Validation Accuracy: 0.6497 ± 0.0034
graph-property-prediction-on-ogbg-ppaGCN+virtual node
Ext. data: No
Number of params: 1930537
Test Accuracy: 0.6857 ± 0.0061
Validation Accuracy: 0.6511 ± 0.0048
graph-regression-on-esr2GCN
R2: 0.642±0.000
RMSE: 0.528±0.642
graph-regression-on-f2GCN
R2: 0.878±0.000
RMSE: 0.355±0.878
graph-regression-on-kitGCN
R2: 0.814±0.000
RMSE: 0.469±0.814
graph-regression-on-lipophilicityGCN
R2: 0.800±0.008
RMSE: 0.565±0.011
graph-regression-on-parp1GCN
R2: 0.912±0.000
RMSE: 0.372±0.912
graph-regression-on-pcqm4mv2-lscGCN
Test MAE: 0.1398
Validation MAE: 0.1379
graph-regression-on-pgrGCN
R2: 0.658±0.000
RMSE: 0.565±0.658
graph-regression-on-zinc-fullGCN
Test MAE: 0.152±0.023
heterogeneous-node-classification-on-acmGCN
Macro-F1: 92.17
Micro-F1: 92.12
heterogeneous-node-classification-on-dblp-2GCN
Macro-F1: 90.84
Micro-F1: 91.47
heterogeneous-node-classification-on-freebaseGCN
Macro-F1: 27.84
Micro-F1: 60.23
heterogeneous-node-classification-on-imdbGCN
Macro-F1: 57.88
Micro-F1: 64.82
link-property-prediction-on-ogbl-citation2Full-batch GCN
Ext. data: No
Number of params: 296449
Test MRR: 0.8474 ± 0.0021
Validation MRR: 0.8479 ± 0.0023
link-property-prediction-on-ogbl-collabGCN (val as input)
Ext. data: No
Number of params: 296449
Test Hits@50: 0.4714 ± 0.0145
Validation Hits@50: 0.5263 ± 0.0115
link-property-prediction-on-ogbl-collabGCN
Ext. data: No
Number of params: 296449
Test Hits@50: 0.4475 ± 0.0107
Validation Hits@50: 0.5263 ± 0.0115
link-property-prediction-on-ogbl-ddiGCN+JKNet
Ext. data: No
Number of params: 1421571
Test Hits@20: 0.6056 ± 0.0869
Validation Hits@20: 0.6776 ± 0.0095
link-property-prediction-on-ogbl-ddiGCN
Ext. data: No
Number of params: 1289985
Test Hits@20: 0.3707 ± 0.0507
Validation Hits@20: 0.5550 ± 0.0208
link-property-prediction-on-ogbl-ppaGCN
Ext. data: No
Number of params: 278529
Test Hits@100: 0.1867 ± 0.0132
Validation Hits@100: 0.1845 ± 0.0140
molecular-property-prediction-on-esolGCN
R2: 0.936±0.006
RMSE: 0.520±0.024
molecular-property-prediction-on-freesolvGCN
R2: 0.957±0.009
RMSE: 0.815±0.086
node-classification-on-brazil-air-trafficGCN_cheby (Kipf and Welling, 2017)
Accuracy: 0.516
node-classification-on-chameleon-60-20-20GCN
1:1 Accuracy: 64.18 ± 2.62
node-classification-on-citeseerGCN
Accuracy: 70.3
node-classification-on-citeseer-60-20-20GCN
1:1 Accuracy: 81.39 ± 1.23
node-classification-on-coraGCN
Accuracy: 81.5%
node-classification-on-cora-60-20-20-randomGCN
1:1 Accuracy: 87.78 ± 0.96
node-classification-on-cornell-60-20-20GCN
1:1 Accuracy: 82.46 ± 3.11
node-classification-on-europe-air-trafficGCN_cheby (Kipf and Welling, 2017)
Accuracy: 46.0
node-classification-on-europe-air-trafficGCN (Kipf and Welling, 2017)
Accuracy: 37.1
node-classification-on-facebookGCN_cheby (Kipf and Welling, 2017)
Accuracy: 64.6
node-classification-on-facebookGCN (Kipf and Welling, 2017)
Accuracy: 57.5
node-classification-on-film-60-20-20-randomGCN
1:1 Accuracy: 35.51 ± 0.99
node-classification-on-flickrGCN_cheby (Kipf and Welling, 2017)
Accuracy: 0.479
node-classification-on-flickrGCN (Kipf and Welling, 2017)
Accuracy: 0.546
node-classification-on-geniusGCN
Accuracy: 87.42 ± 0.37
node-classification-on-nellGCN
Accuracy: 66.0
node-classification-on-non-homophilicGCN
1:1 Accuracy: 82.46 ± 3.11
node-classification-on-non-homophilic-1GCN
1:1 Accuracy: 75.5 ± 2.92
node-classification-on-non-homophilic-13GCN
1:1 Accuracy: 82.47 ± 0.27
node-classification-on-non-homophilic-14GCN
1:1 Accuracy: 87.42 ± 0.37
node-classification-on-non-homophilic-15GCN
1:1 Accuracy: 62.18 ± 0.26
node-classification-on-non-homophilic-2GCN
1:1 Accuracy: 83.11 ± 3.2
node-classification-on-non-homophilic-4GCN
1:1 Accuracy: 64.18 ± 2.62
node-classification-on-non-homophilic-6GCN
1:1 Accuracy: 62.23±0.53
node-classification-on-penn94GCN
Accuracy: 82.47 ± 0.27
node-classification-on-pubmedGCN
Accuracy: 79.0
node-classification-on-pubmed-60-20-20-randomGCN
1:1 Accuracy: 88.9 ± 0.32
node-classification-on-squirrel-60-20-20GCN
1:1 Accuracy: 44.76 ± 1.39
node-classification-on-texas-60-20-20-randomGCN
1:1 Accuracy: 83.11 ± 3.2
node-classification-on-wiki-voteGCN_cheby (Kipf and Welling, 2017)
Accuracy: 49.5
node-classification-on-wiki-voteGCN (Kipf and Welling, 2017)
Accuracy: 32.9
node-classification-on-wisconsin-60-20-20GCN
1:1 Accuracy: 75.5 ± 2.92

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