Protein subcellular localization based on deep image features and criterion learning strategy

摘要

The spatial distribution of proteome at subcellular levels provides clues for protein functions, thus is important to human biology and disease. Imaging-based methods are one of the most important approaches for predicting protein subcellular location. Although deep neural networks (DNNs) have shown impressive performance in a number of imaging tasks, its application to protein subcellular localisation has not been sufficiently explored. In this study, we developed a deep imaging-based approach to localise the proteins at subcellular levels. Based on deep image features extracted from convolutional neural networks (CNNs), both single-label and multi-label locations can be accurately predicted. Particularly, the multi-label prediction is quite a challenging task. Here we developed a criterion learning strategy to exploit the labelattribute relevancy and label-label relevancy. A criterion which was used to determine the final label-set was automatically obtained during the learning procedure.We concluded an optimal CNN architecture that could give the best results. Besides, experiments show that compared with the hand-crafted features, the deep features present more accurate prediction with less features. The implementation for the proposed method is available at https://github.com/RanSuLab/ProteinSubcellularLocation.

出版物
In Briefings in Bioinformatics