Multi label learning for prediction of human protein subcellular localizations

Predicting protein subcellular locations has attracted much attention in the past decade. However, one of the most challenging problems is that many proteins were found simultaneously existing in, or moving between, two or more different cell components in a eukaryotic cell. Seldom previous predictors were able to deal with such multiplex proteins although they have extremely important implications in future drug discovery in terms of their specific subcellular targeting. Approximately 20% of the human proteome consists of such multiplex proteins with multiple sample labels. In order to efficiently handle such multiplex human proteins, we have developed a novel multi-label (ML) learning and prediction framework called ML-PLoc, which decomposes the multi-label prediction problem into multiple independent binary classification problems. ML-PLoc is constructed based on support vector machine (SVM) and sequential evolution information. Experimental results show that ML-PLoc can achieve an overall accuracy 64.6% and recall ratio 67.2% on a benchmark dataset consisting of 14 human subcellular locations, and is very powerful for dealing with multiplex proteins. The current approach represents a new strategy to deal with the multi-label biological problems. ML-PLoc software is freely available for academic use at: http://www.csbio.sjtu.edu.cn/bioinf/ML-PLoc .