Deep Learning Predicts Tuberculosis Drug Resistance Status from Whole-Genome Sequencing Data.

This repository contains code to recreate the results from Chen et. al:

Chen, M.L., Doddi, A., Royer, J., Freschi, L., Schito, M., Ezewudo, M., Kohane, I.S., Beam, A. and Farhat, M., 2018. Deep Learning Predicts Tuberculosis Drug Resistance Status from Whole-Genome Sequencing Data. bioRxiv, p.275628.

Dependencies

• Keras version >= 2.0
• Tensorflow version >= 1.7
• sklearn
• numpy
• pandas

To run the code, clone this repository and add the folder to your python path.

• evaluation.py will recreate the cross-validation results
• validation.py will produce the results on the validation data