A drug recommendation system based on response prediction: Integrating gene expression and K-mer fragmentation of drug SMILES using LightGBM

Abstract

Medical experts and physicians examine the gene expression abnormality in glioblastoma (GBM) cancer patients to identify the drug response. The main objective of this research is to build a machine learning (ML) based model for improve the outcome of cancer medication to save the time and effort of medical practitioners. Developing a drug response recommendation system is our goal that uses the gene expression data of cancer cell lines to predict the response of anticancer drugs in terms of half-maximal inhibitory concentration (IC50). Genetic data from a GBM cancer patient is used as input into a system to predict and recommend the response of multiple anticancer drugs in a particular cancer sample. In this research, we used K-mer molecular fragmentation to process drug SMILES in a novel way, which enabled us to build a competent model that provides drug response. We used the Light Gradient Boosting Machine (LightGBM) regression algorithm and Genomics of Drug Sensitivity of Cancer (GDSC) data for this proposed recommendation system. The results showed that all predicted IC50 values are fall within the range of the real values when examining GBM data. Two drugs, temozolomide and carmustine, were predicted with a Mean Squared Error (MSE) of 0.10 and 0.11 respectively, and 0.41 in unseen test samples. These recommended responses were then verified by expert doctors, who confirmed that the responses to these drugs were very close to the actual response. These recommendation are also effective in slowing the growth of these tumors and improving patients quality of life by monitoring medication effects.