Running a Curated Model

For a step-by-step example of how run LGBM see: Quickstart.

1. Clone the model and set up the environment

• IMPROVE model repositories can be found here: https://github.com/JDACS4C-IMPROVE. Clone the model repo with:

git clone <model_repo>
cd <model_repo>

• Set up the environment according to the instructions. The IMPROVE library is installed with:

pip install improvelib

2. Download the benchmark data

To download Drug Response Prediction benchmark data, run the following in the directory where you would like to store the data:

wget --cut-dirs=8 -P ./ -nH -np -m https://web.cels.anl.gov/projects/IMPROVE_FTP/candle/public/improve/benchmarks/single_drug_drp/benchmark-data-pilot1/csa_data/

3. Run the model scripts

By default everything will be saved in the current working directory. This, and all other parameters can be changed by setting parameters on the command line. See IMPROVE Parameters for more information about parameters.

python <model>_preprocess_improve.py --input_dir /path/to/dir/csa_data/raw_data
python <model>_train_improve.py
python <model>_infer_improve.py