edge2evc

The open source code for our paper "edge2vec: Learning Node Representation Using Edge Semantics".

Installation

Install in development mode with::

$ git clone https://github.com/RoyZhengGao/edge2vec.git
$ cd edge2vec
$ pip install -e .

Usage

Dataset

The dataset we offer for test is data/data.csv. The data contains four columns, which refer to Source ID, Target ID, Edge Type, Edge ID. And columns are separated by space ' '.

For unweighted graph, please see unweighted_graph.txt. The four columns are Source ID, Target ID, Edge Type, Edge ID. And columns are separated by space ' '. For weighted graph, please see weighted_graph.txt. The five columns are Source ID, Target ID, Edge Type, Edge Weight, Edge ID. And columns are separated by space ' '.

Run the code

There are two steps for running the code. First, to calculate transition matrix in heterogeneous networks, run edge2vec-transition from the shell:

$ edge2vec-transition \
    --input data/data.csv \
    --output data/matrix.txt \
    --type_size 3 \
    --em_iteration 5 \
    --walk-length 3

The output is matrix.txt, which stores the edge transition matrix. Second, run edge2vec to the node embeddings via biased random walk. To use it from the shell:

$ edge2vec \
    --input data/data.csv \
    --matrix data/matrix.txt \
    --output data/vector.txt \
    --dimensions 128 \
    --walk-length 3 \
    --p 1 \
    --q 1

The output is the node embedding file vector.txt.

Data repository for medical dataset in the link: http://ella.ils.indiana.edu/~gao27/data_repo/edge2vec%20vector.zip or https://figshare.com/articles/edge2vec_vector_zip/8097539 (It is a re-computed version so the evaluation output may be a little bit different with the paper reported results.)

Citations

if you use the code, please cite:

• Gao, Zheng, Gang Fu, Chunping Ouyang, Satoshi Tsutsui, Xiaozhong Liu, and Ying Ding. "edge2vec: Learning Node Representation Using Edge Semantics." arXiv preprint arXiv:1809.02269 (2018).

License

The code is released under BSD 3-Clause License.

Contributor

• Zheng Gao - gao27@indiana.edu