R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics

Abstract

The increasing availability of complex data in biology and medicine has promoted the use of machine learning in classification tasks to address important problems in translational and fundamental science. Two important obstacles, however, may limit the unraveling of the full potential of machine learning in these fields: the lack of generalization of the resulting models and the limited number of labeled data sets in some applications. To address these important problems, we developed an unsupervised ensemble algorithm called strategy for unsupervised multiple method aggregation (SUMMA). By virtue of being an ensemble method, SUMMA is more robust to generalization than the predictions it combines. By virtue of being unsupervised, SUMMA does not require labeled data. SUMMA receives as input predictions from a diversity of models and estimates their classification performance even when labeled data are unavailable. It then uses these performance estimates to combine these different predictions into an ensemble model. SUMMA can be applied to a variety of binary classification problems in bioinformatics including but not limited to gene network inference, cancer diagnostics, drug response prediction, somatic mutation, and differential expression calling. In this application note, we introduce the R/PY-SUMMA packages, available in R or Python, that implement the SUMMA algorithm.

Keywords: aggregation of predictions; ensemble learning; machine learning; unsupervised methods; wisdom of crowds.