This repository stores the code used in the following preprint: https://www.biorxiv.org/content/10.1101/558403v1 (accepted in AIAI 2019).
We cannot share the original data used in the paper so we provide example files in example_data/
folder so the code in this repository can be executed.
Dependencies to execute the code are listed in environment_paper.yml. One can easily install all the dependencias by using an Anaconda environment, and running the following commands:
# Creating the environment with the file we provided
$ conda env create --force --file environment_paper.yml
# Activating the environment
$ conda activate env-paper
The main packages and respective versions that were used in this work (and defined in environment_paper.yml
) are:
- jupyterlab 0.35.4
- matplotlib 3.0.2
- numpy 1.15.4
- pandas 0.24.1
- python 3.6.8
- scikit-learn 0.20.2
- scipy 1.2.0
- shap 0.27.0
- xgboost 0.81
All the descriptions are in the folder notebooks/
, which you can see by executing, for example, Jupyter Lab:
(env-paper) $ jupyter lab
If you have any questions please just open an issue.