This repository contains Python and Julia codes for implementing the root cause discovery methods in paper "Root cause discovery via permutations and Cholesky decomposition". We use the proposed root cause discovery method to discover the disease-causing gene of rare disease patients affected by a monogenic disorder.

We used python 3.12.5 for running the python code. You need to have the following python packages installed:

• numpy
• scipy
• random
• sklearn
• warnings
• joblib
• lingam
• tqdm

After these packages are installed, you can load the root cause discovery python codes located in python/funcs.

To use our Julia package, download Julia. Within Julia, install the package via

using Pkg
Pkg.add(PackageSpec(url="https://github.com/biona001/RootCauseDiscovery.git", subdir="julia"))

We used this package for our real data analysis due to Julia's computational efficiency.

• Python users: See python/Example.ipynb for 2 simulated examples.
• Julia users: See julia/notebook/example.ipynb for a simulated example and a real-data example.