Mining the forest: uncovering biological mechanisms by interpreting Random Forests

Abstract

AbstractBiological datasets are large and complex. Machine learning models are therefore essential to capture relationships in the data. Unfortunately, the inferred complex models are often difficult to understand and interpretation is limited to a list of features ranked on their importance in the model.We propose a computational approach, called Foresight, that enables interpretation of the patterns uncovered by Random Forest models trained on biological datasets. Foresight exploits the correlation structure in the data to uncover relevant groups of features and the interactions between them. This facilitates interpretation of the computational model and can provide more detailed insight in the underlying biological relationships than simply ranking features. We demonstrate Foresight on both an artificial dataset and a large gene expression dataset of breast cancer patients. Using the latter dataset we show that our approach retrieves biologically relevant features and provides a rich description of the interactions and correlation structure between these features.