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installation.md

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GNN Installation

To install GNN, simply clone this repository: git clone https://github.com/IBPA/GNN.git

Installing Dependencies

To run GNN successfully, ensure following dependencies are installed.

  • GUROBI: GNN uses GUROBI to solve linear programming problem during training. Download and install version 6.5 or higher following GUROBI installation instructions. You may obtain a free academic license if qualified.
  • Torch: GNN is based on th artificial neural network framework provided by Torch which uses lua language. Follow the Torch installation instructions (CPU only). We consider moving to python based frameworks such as pytorch in future.
  • Lua packages: Several lua packages are needed, hence:
    • luarocks install csv
    • luarocks install cephes
    • torch-autograd:
      • git clone https://github.com/ameenetemady/torch-autograd
      • cd torch-autograd
      • luarocks make autograd-scm-1.rockspec
    • gurobi-torch:
      • git clone https://github.com/bamos/gurobi.torch
      • cd gurobi.torch
      • luarocks make gurobi-scm-1.rockspec
  • Python3: We use python for various scripts including data processing and competing ANN methods. Install python version 3.4 or higher from here. The following python modules are needed, which you may intall using pip3:
    • pip3 install pandas
    • pip3 install numpy
    • pip3 install keras
    • pip3 install tensorflow
    • pip3 install toposort
  • R: We use R (version 3.4 or higher) for running GENIE3 and visualization of results. Follow instructions here to install R if don't already have it. To install necessary R packages run the following using R:
    • install.packages(c("ggplot2","stringr", "dplyr", "tidyverse", "reshape2", "BiocManager", "argparse"))
    • BiocManager::install("GENIE3")