Load bio and chem dataset to GL2vec

I used GL2vec model to get the embedding of biology and chemistry data.

The model is from the following paper:

Chen, Hong, and Hisashi Koga. "Gl2vec: Graph embedding enriched by line graphs with edge features." International Conference on Neural Information Processing. Springer, Cham, 2019.

Installation

I used the following Python packages for core development. I tested on Python 3.6.

pytorch                   1.8.1
torch-geometric           1.0.3
torch-scatter             2.6.0 
torch-sparse              0.6.9
rdkit                     2019.03.1.0
typing-extension          3.7.4.3
numpy                     1.18.1
networkx                  2.5.1
karateclub                1.0.24
gensim                    3.8.3
tqdm                      4.60.0

Dataset download

All the necessary data files can be downloaded from the following links.

For the chemistry dataset, download from chem data (2.5GB), unzip it, and put it under chem/. For the biology dataset, download from bio data (2GB), unzip it, and put it under bio/.

Dataset from the following paper:

Weihua Hu*, Bowen Liu*, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, Jure Leskovec. Strategies for Pre-training Graph Neural Networks. ICLR 2020.

Print embedding

If you want to print the biology(chemistry) embedding , you should first go to the bio/( chem/).

For biology embedding.

python GL2vec.py --dataset unsupervised

For chemistry embedding.

python GL2vec.py