Drug cell line interaction prediction (1812.11178v1)

Abstract: Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to test their models and methods. Previously, most research in these areas starts from the fingerprints or features of drugs, instead of their structures. In this paper, we introduce a model for phenotypic screening, which is called twin Convolutional Neural Network for drugs in SMILES format (tCNNS). tCNNS is comprised of CNN input channels for drugs in SMILES format and cancer cell lines respectively. Our model achieves $0.84$ for the coefficient of determinant($R^2$) and $0.92$ for Pearson correlation($R_p$), which are significantly better than previous works\cite{ammad2014integrative,haider2015copula,menden2013machine}. Besides these statistical metrics, tCNNS also provides some insights into phenotypic screening.