GraphEmbedding

This version is for the WSDM 2019 paper.

Datasets

Get the datasets from https://drive.google.com/drive/folders/1lY3pqpnUAK0H9Tgjyh7tlMVYy0gYPthC?usp=sharing and extract under data/:

• AIDS80nef
• AIDS700nef
• linux
• IMDBMulti

Get the pickle files (/save) from https://drive.google.com/drive/folders/1Eusvi4_iOKM0AsO1LhxQFkY62kDEtuMq?usp=sharing

Get the result files (/result) https://drive.google.com/drive/folders/1UXEGozaThjjuC-hnt4C7jn06L6I2Ra1v?usp=sharing

Dependencies

Install the following the tools and packages:

• python3: Assume python3 by default (use pip3 to install packages).
• numpy
• pandas
• scipy
• scikit-learn
• tensorflow (1.8.0 recommended)
• networkx==1.10 (NOT 2.1)
• beautifulsoup4
• lxml
• matplotlib
• seaborn
• colour
• pytz
• pygraphviz. The following is an example set of installation commands (tested on Ubuntu 16.04)

  sudo apt-get install graphviz libgraphviz-dev pkg-config
  pip3 install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"
  

• Graph Edit Distance (GED):
  • graph-matching-toolkit
    • cd src && git clone https://github.com/yunshengb/graph-matching-toolkit.git
    • Follow the instructions on https://github.com/yunshengb/graph-matching-toolkit to compile
  • java

Tips for PyCharm Users

• If you see red lines under import, mark src and model/Siamese as Source Root, so that PyCharm can find those files.
• Mark src/Siamese/logs and src/Siamese/exp as Excluded, so that PyCharm won't spend time inspecting those logs.

Run

The idea of creating config.py is to avoid typing in command line arguments. Instead, we can modify a few parameters in config.py and let the file handle the setting of the rest parameters via a bunch of if else statements. Then we can simply run python main.py without the following --xxxs.