Graph convolutional kernel networks

Updates Nov.2022: We have supported Pytorch Geometric datasets now! If you want to reproduce results in our paper, please use the icml 2022 branch.

The repository implements Graph Convolutional Kernel Networks (GCKNs) described in the following paper

Dexiong Chen, Laurent Jacob, Julien Mairal. Convolutional Kernel Networks for Graph-Structured Data. In ICML, 2020.

Citation

Please use the following bibtex to cite our work:

@inproceedings{chen2020convolutional,
  title={Convolutional kernel networks for graph-structured data},
  author={Chen, Dexiong and Jacob, Laurent and Mairal, Julien},
  booktitle={International Conference on Machine Learning},
  year={2020},
}

Installation

We strongly recommend users to use miniconda to install the following packages (link to pytorch)

python>=3.6
numpy
scikit-learn
pytorch=1.9.0
pyg=2.0.2
pandas
networkx
Cython

(OPTIONAL) To perform model visualization, you also need to install the following packages

matplotlib

Finally run make.

Examples of how to use GCKN

First run the following to make Python recognize gckn

source s

A simple example of using GCKN on PyG datasets

Below you can find a quick-start example on the MUTAG dataset provided by PyG, more details can be found in ./experiments/gckn_unsup.py.

click to see the example code:

from torch_geometric import datasets
from gckn.data import GraphLoader, convert_dataset
from gckn.models import GCKNetFeature

# Load the dataset from PyG
dset = datasets.TUDataset('./datasets/TUDataset', 'MUTAG')
graphloader = GraphLoader(path_size=3, batch_size=32, dataset='MUTAG')

# Convert PyG dataset to GCKN dataset and create data_loader
converted_dset = convert_dataset(dset)
data_loader = graphloader.transform(converted_dset)
input_size = data_loader.input_size

# Build an unsupervised GCKN model
model = GCKNetFeature(
    input_size,
    hidden_size=32, # hidden dimensions
    path_size=3, # path length used in GCKN
    kernel_args_list=0.6, # sigma in the Gaussian kernel
    pooling='sum', # pooling method for aggregating path features
    global_pooling='sum', # global pooling method for aggregating node features
    aggregation=True # use features aggregated by path size from 0 to k
)

model.unsup_train(data_loader, n_sampling_paths=300000)

Training unsupervised models

First go to the ./experiments folder.

• GCKN-path

  To train a one-layer (GCKN-path) model, run

  python gckn_unsup.py --dataset MUTAG --path-size 3 --sigma 1.5 --hidden-size 32  --aggregation

  Running python gckn_unsup.py --help for more information about options.

• GCKN-subtree

  To train a two-layer (GCKN-subtree) model, run

  python gckn_unsup.py --dataset MUTAG --path-size 3 1 --sigma 1.5 1.5 --hidden-size 32 32 --aggregation

• GCKN with more layers

  You can train a deeper GCKN model by listing the values of parameters (path size, hidden size, sigma) at each layer. You can also use pooling operators like mean or max rather than the default sum pooling. For example

  python gckn_unsup.py --dataset MUTAG --path-size 3 3 3 3 1 --sigma 1.5 1.5 1.5 1.5 1.5 --hidden-size 32 32 32 32 32 --aggregation --pooling mean --global-pooling max

Training supervised models

The options for training supervised models are the same as unsupervised models with some additional parameters such as number of epochs epochs, initial learning rate lr and regularization parameter weight-decay. For instance, to train a GCKN-subtree model, run

python gckn_sup.py --dataset MUTAG --path-size 3 1 --sigma 1.5 1.5 --hidden-size 32 32 --aggregation --weight-decay 1e-04