Scaling up drug combination surface prediction

Abstract

Drug combinations are required to treat advanced cancers and other complex diseases. Compared to monotherapy, combination treatments can enhance efficacy and reduce toxicity by lowering the doses of single drugs - and there especially synergistic combinations are of interest. Since drug combination screening experiments are costly and time consuming, reliable machine learning models are needed for prioritizing potential combinations for further studies. Most of the current machine learning models are based on scalar-valued approaches, which predict individual response values or synergy scores for drug combinations. We take a functional output prediction approach, in which full, continuous dose-response combination surfaces are predicted for each drug combination on the cell lines. We investigate the predictive power of the recently proposed comboKR method, which is based on a powerful input-output kernel regression technique and functional modelling of the response surface. In this work, we develop a scaled-up formulation of the comboKR, that also implements improved modeling choices: 1) we incorporate new modeling choices for the output drug combination response surfaces to the comboKR framework, and 2) propose a projected gradient descent method to solve the challenging pre-image problem that traditionally is solved with simple candidate set approaches. We provide thorough experimental analysis of comboKR 2.0 with three real-word datasets within various challenging experimental settings, including cases where drugs or cell lines have not been encountered in the training data. Our comparison with synergy score prediction methods further highlights the relevance of dose-response prediction approaches, instead of relying on simple scoring methods.