Implementation of Graph Auto-Encoders in TensorFlow

Graph Auto-Encoders

This is a TensorFlow implementation of the (Variational) Graph Auto-Encoder model as described in our paper:

T. N. Kipf, M. Welling, Variational Graph Auto-Encoders, NIPS Workshop on Bayesian Deep Learning (2016)

Graph Auto-Encoders (GAEs) are end-to-end trainable neural network models for unsupervised learning, clustering and link prediction on graphs.

GAEs have successfully been used for:

• Link prediction in large-scale relational data: M. Schlichtkrull & T. N. Kipf et al., Modeling Relational Data with Graph Convolutional Networks (2017),
• Matrix completion / recommendation with side information: R. Berg et al., Graph Convolutional Matrix Completion (2017).

GAEs are based on Graph Convolutional Networks (GCNs), a recent class of models for end-to-end (semi-)supervised learning on graphs:

T. N. Kipf, M. Welling, Semi-Supervised Classification with Graph Convolutional Networks, ICLR (2017).

A high-level introduction is given in our blog post:

Thomas Kipf, Graph Convolutional Networks (2016)

Installation

python setup.py install

Requirements

• TensorFlow (1.0 or later)
• python 2.7
• networkx
• scikit-learn
• scipy

Run the demo

python train.py

Data

In order to use your own data, you have to provide

• an N by N adjacency matrix (N is the number of nodes), and
• an N by D feature matrix (D is the number of features per node) – optional

Have a look at the load_data() function in input_data.py for an example.

In this example, we load citation network data (Cora, Citeseer or Pubmed). The original datasets can be found here: http://linqs.cs.umd.edu/projects/projects/lbc/ and here (in a different format): https://github.com/kimiyoung/planetoid

You can specify a dataset as follows:

python train.py --dataset citeseer

(or by editing train.py)

Models

You can choose between the following models:

• gcn_ae: Graph Auto-Encoder (with GCN encoder)
• gcn_vae: Variational Graph Auto-Encoder (with GCN encoder)

Cite

Please cite our paper if you use this code in your own work:

@article{kipf2016variational,
  title={Variational Graph Auto-Encoders},
  author={Kipf, Thomas N and Welling, Max},
  journal={NIPS Workshop on Bayesian Deep Learning},
  year={2016}
}