Graph Generative Model for Benchmarking Graph Neural Networks

We propose a novel, modern graph generation problem to enable generating privacy-controlled, synthetic substitutes of large-scale real-world graphs that can be effectively used to evaluate GNN models. Our proposed graph generative model, Computation Graph Transformer (CGT) 1) operates on minibatches rather than the whole graph, avoiding scalability issues, and 2) reduces the task of learning graph distributions to learning feature vector sequence distributions, which we approach with a novel Transformer architecture.

You can see our ICML 2023 paper for more details.

Setup

Create a new conda environment, install PyTorch and the remaining requirements:

conda create python==3.7 -n cgt
conda activate cgt
pip install -r requirement.txt
pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117

The code is implemented on PyTorch DataParallel.

Dataset

You can download public graph datasets in the npz format from GNN-Benchmark. Place the dataset in data/ directory. For your convenience, cora.npz and citeseer.npz are already saved in data\. We also support ogbn-arxiv and ogbn-products dataset from OGBN benchmark.

Usage

In run.sh, you write down a list of graph datasets that you want to learn distributions into DATASETS. First, we add different sizes of noisy neighbors to augment the original graphs using NOISES. By executing run.sh, we learn three different distributions with different noise sizes NOISES=(0 2 4) for each dataset. For each dataset, we train three different GCN models (GCN, GIN, SGC) on a pair of original and synthetic graphs, and then compare their performance. The details of other hyperparameters can be found in args.py.

Differential Privacy module

As described in the main paper, DP-SGD on transformer performs badly. Thus we provide only DP-k-means module in this repository. To run DP-k-means, you need to download an open-source library from: https://github.com/google/differential-privacy/tree/main/learning/clustering Then you can uncomment line 11-12 in generator/cluster.py and set dp_feature in args.py to True.

File description

We provide brief descriptions for each file as follows:

Directory/File	description
run.sh	script to run experiments
args.py	set hyperparameters
test.py	main file: prepare models, read datasets, graph generation, GNN evaluation
data/	download datasets
generator/	codes related to graph transformer
generator/cluster.py	k-means or DP k-means clustering
generator/gpt	CGT main directory
generator/gpt/gpt.py	prepare models, prepare datasets, train/generation loops
generator/gpt/dataset.py	dataset for flatten computation graphs
generator/gpt/model.py	XLNet model
generator/gpt/trainer.py	training loop
generator/gpt/utils.py	generation loop
task/	GNN models
task/aggregation	GNN models with different aggregation strategies (GCN, GAT, SGN, GIN)
task/utils/dataset.py	Computation Graph Dataset for PyTorch DataParallel
task/utils/utils.py	ogbn/npz format datasets loading, utility functions

Citation

Please consider citing the following paper when using our code for your application.

@article{yoon2022scalable,
  title={Scalable Privacy-enhanced Benchmark Graph Generative Model for Graph Convolutional Networks},
  author={Yoon, Minji and Wu, Yue and Palowitch, John and Perozzi, Bryan and Salakhutdinov, Ruslan},
  journal={arXiv preprint arXiv:2207.04396},
  year={2022}
}