CDSML

Classification of Drug Sensitivity using Machine Learning applies a manifold learning method on the discretized sensitive/resistant lables and can efficiently predict the sensitive or resistant cell line-drug pairs.

Fatemeh Ahmadi Moughari, Changiz Eslahchi; CDSML: Classification of Drug Sensitivity using Machine Learning

This repository contains the implementated codes of CDSML, off-the-shelf machine learning methods used in the paper, tuning the hyper-parametrs, and depicting the figures of paper. It also contains the preprocessed data and computed similarity matrices for cell lines and drugs in all dataset and tissue specific conditions.

A giude to run CDSML

Please make sure to have the following libraries installed.

Required libraries

Python 3.6 and upper:

• Numpy
• sklearn
• Argparse
• random
• copy
• math
• sys

Input parameters

To execute the codes, the user must provide three input files

• label_dirc: the directory to a file which contains the binary sensitivity matrix (Number of rows = number of cell lines and number of columns = number of drugs)
• simC_dirc: the directory to a file that is a square matrix containing the similarity of cell lines
• simD_dirc: the directory to a file that is a square matrix containing the similarity of drugs.
• dim: the dimension of latent space
• miu: the regularization coefficient for latent matrices
• lambda: the coefficient that controls the similarity conservation while manifold learning
• CV: the number of folds in cross validation
• repetition: the number of repeting the cross validation

The binary sensitivity matrix for GDSC is presented in Data/Features/GDSC_R_sensitive.csv. Moreover, the required similarity files are provided in Data/Similarities both for all dataset and for tissue specific conditions. There are several types of cell line similarity based on Expression, Mutation, and CNV. The recommended values for hyper-parametrs are dim=0.7, miu=2.7, lambda=4, CV=5, repetition=30.

Command

The following command is a sample of executing ADRML

python CDSML.py label_dirc=../Data/Features/B_Sensitivity.csv  simC_dirc=../Data/SC_GeneExpression.csv simD_dric=../Data/SD_Chemical.csv dim=0.7 miu=2.7 lambda=4 CV=5 repetition=30

Contact

Please do not hesitate to contact us at ([email protected]) or ([email protected]) if there is any question.