gdewael / COS-engineering

Code supporting machine learning for engineering of COS production in E. coli

COS-engineering

Code supporting machine learning for engineering of COS production in E. coli.

Contents

• data.csv contains all supporting data, including OD $_{600}$, growth rate $\mu$ and to which split each sample belongs (either test or val0, val1, val2, val3 for either of the cross-validation folds)
• utils.py supporting python helper functions to load in data and train models
• example_script_PLS.py, example_scripts_PLS_B.py and example_script_PLS.py example script of usage to reproduce our results.
• PLS_res.txt, PLS_B_res.txt & XGB_res.txt full list of feature importances.

Dependencies

The following code was tested on Python version 3.10 with:

pandas==1.4.3
numpy==1.21.5
xgboost==1.5.0
matplotlib
seaborn==0.11.2
scikit-learn==1.1.1
shap==0.39.0