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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