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GraphMAE: Self-Supervised Masked Graph Autoencoders in KDD'22

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GraphMAE: Self-Supervised Masked Graph Autoencoders

Implementation for KDD'22 paper: GraphMAE: Self-Supervised Masked Graph Autoencoders.

We also have a Chinese blog about GraphMAE on Zhihu (知乎), and an English Blog on Medium.

GraphMAE is a generative self-supervised graph learning method, which achieves competitive or better performance than existing contrastive methods on tasks including node classification, graph classification, and molecular property prediction.


❗ Update

[2023-04-12] GraphMAE2 is published and the code can be found here.

[2022-12-14] The PYG implementation of GraphMAE for node / graph classification is available at this branch.

Dependencies

  • Python >= 3.7
  • Pytorch >= 1.9.0
  • dgl >= 0.7.2
  • pyyaml == 5.4.1

Quick Start

For quick start, you could run the scripts:

Node classification

sh scripts/run_transductive.sh <dataset_name> <gpu_id> # for transductive node classification
# example: sh scripts/run_transductive.sh cora/citeseer/pubmed/ogbn-arxiv 0
sh scripts/run_inductive.sh <dataset_name> <gpu_id> # for inductive node classification
# example: sh scripts/run_inductive.sh reddit/ppi 0

# Or you could run the code manually:
# for transductive node classification
python main_transductive.py --dataset cora --encoder gat --decoder gat --seed 0 --device 0
# for inductive node classification
python main_inductive.py --dataset ppi --encoder gat --decoder gat --seed 0 --device 0

Supported datasets:

  • transductive node classification: cora, citeseer, pubmed, ogbn-arxiv
  • inductive node classification: ppi, reddit

Run the scripts provided or add --use_cfg in command to reproduce the reported results.

Graph classification

sh scripts/run_graph.sh <dataset_name> <gpu_id>
# example: sh scripts/run_graph.sh mutag/imdb-b/imdb-m/proteins/... 0 

# Or you could run the code manually:
python main_graph.py --dataset IMDB-BINARY --encoder gin --decoder gin --seed 0 --device 0

Supported datasets:

  • IMDB-BINARY, IMDB-MULTI, PROTEINS, MUTAG, NCI1, REDDIT-BINERY, COLLAB

Run the scripts provided or add --use_cfg in command to reproduce the reported results.

Molecular Property Prediction

Please refer to codes in ./chem for molecular property prediction.

Datasets

Datasets used in node classification and graph classification will be downloaded automatically from https://www.dgl.ai/ when running the code.

Experimental Results

Node classification (Micro-F1, %):

Cora Citeseer PubMed Ogbn-arxiv PPI Reddit
DGI 82.3±0.6 71.8±0.7 76.8±0.6 70.34±0.16 63.80±0.20 94.0±0.10
MVGRL 83.5±0.4 73.3±0.5 80.1±0.7 - - -
BGRL 82.7±0.6 71.1±0.8 79.6±0.5 71.64±0.12 73.63±0.16 94.22±0.03
CCA-SSG 84.0±0.4 73.1±0.3 81.0±0.4 71.24±0.20 73.34±0.17 95.07±0.02
GraphMAE(ours) 84.2±0.4 73.4±0.4 81.1±0.4 71.75±0.17 74.50±0.29 96.01±0.08

Graph classification (Accuracy, %)

IMDB-B IMDB-M PROTEINS COLLAB MUTAG REDDIT-B NCI1
InfoGraph 73.03±0.87 49.69±0.53 74.44±0.31 70.65±1.13 89.01±1.13 82.50±1.42 76.20±1.06
GraphCL 71.14±0.44 48.58±0.67 74.39±0.45 71.36±1.15 86.80±1.34 89.53±0.84 77.87±0.41
MVGRL 74.20±0.70 51.20±0.50 - - 89.70±1.10 84.50±0.60 -
GraphMAE(ours) 75.52±0.66 51.63±0.52 75.30±0.39 80.32±0.46 88.19±1.26 88.01±0.19 80.40±0.30

Transfer learning on molecular property prediction (ROC-AUC, %):

BBBP Tox21 ToxCast SIDER ClinTox MUV HIV BACE Avg.
AttrMasking 64.3±2.8 76.7±0.4 64.2±0.5 61.0±0.7 71.8±4.1 74.7±1.4 77.2±1.1 79.3±1.6 71.1
GraphCL 69.7±0.7 73.9±0.7 62.4±0.6 60.5±0.9 76.0±2.7 69.8±2.7 78.5±1.2 75.4±1.4 70.8
GraphLoG 72.5±0.8 75.7±0.5 63.5±0.7 61.2±1.1 76.7±3.3 76.0±1.1 77.8±0.8 83.5±1.2 73.4
GraphMAE(ours) 72.0±0.6 75.5±0.6 64.1±0.3 60.3±1.1 82.3±1.2 76.3±2.4 77.2±1.0 83.1±0.9 73.8

Citing

If you find this work is helpful to your research, please consider citing our paper:

@inproceedings{hou2022graphmae,
  title={GraphMAE: Self-Supervised Masked Graph Autoencoders},
  author={Hou, Zhenyu and Liu, Xiao and Cen, Yukuo and Dong, Yuxiao and Yang, Hongxia and Wang, Chunjie and Tang, Jie},
  booktitle={Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining},
  pages={594--604},
  year={2022}
}