Abstract
Machine learning methods trained on cancer cell line panels are intensively studied for the prediction of optimal anti-cancer therapies. While classification approaches distinguish effective from ineffective drugs, regression approaches aim to quantify the degree of drug effectiveness. However, the high specificity of most anti-cancer drugs induces a skewed distribution of drug response values in favor of the more drug-resistant cell lines, negatively affecting the classification performance (class imbalance) and regression performance (regression imbalance) for the sensitive cell lines. Here, we present a novel approach called SimultAneoUs Regression and classificatiON Random Forests (SAURON-RF) based on the idea of performing a joint regression and classification analysis. We demonstrate that SAURON-RF improves the classification and regression performance for the sensitive cell lines at the expense of a moderate loss for the resistant ones. Furthermore, our results show that simultaneous classification and regression can be superior to regression or classification alone.
