Genetic programming for anticancer therapeutic response prediction using the NCI-60 dataset

Statistical methods, and in particular machine learning, have been increasingly used in the drug development workflow. Among the existing machine learning methods, we have been specifically concerned with genetic programming. We present a genetic programming-based framework for predicting anticancer therapeutic response. We use the NCI-60 microarray dataset and we look for a relationship between gene expressions and responses to oncology drugs Fluorouracil, Fludarabine, Floxuridine and Cytarabine. We aim at identifying, from genomic measurements of biopsies, the likelihood to develop drug resistance. Experimental results, and their comparison with the ones obtained by Linear Regression and Least Square Regression, hint that genetic programming is a promising technique for this kind of application. Moreover, genetic programming output may potentially highlight some relations between genes which could support the identification of biological meaningful pathways. The structures that appear more frequently in the ‘best’ solutions found by genetic programming are presented.