VICTree: Variational Inference for Clonal Tree reconstruction

Implementation of VI method on clonal trees probabilistic model

Requirements

For reproducibility, we include the environment.yml file generated from the conda environment inside which all experiments have been run.

Run

To run the script, just execute it with python3

python ./src/main.py --input input_data.h5ad --output out_path -n-nodes 10 --n-iter 100

Options

Arguments such as input and VI parameters can be set through command line interface. Run the main script with the -h flag to view all accepted arguments with their description.

Synthetic data

To generate synthetic data, run the simul.py script with arguments passed from CLI (as for main.py, check the help page of the script for accepted arguments).