Subcellular localization of Gram-negative bacterial proteins using sparse learning.
One of the main challenges faced by biological applications is to predict protein subcellular localization in an automatic fashion accurately. To achieve this in these applications, a wide variety of machine learning methods have been proposed in recent years. Most of them focus on finding the optimal classification scheme and less of them take the simplifying the complexity of biological system into account. Traditionally such bio-data are analyzed by first performing a feature selection before classification. Motivated by CS (Compressive Sensing), we propose a method which performs locality preserving projection with a sparseness criterion such that the feature selection and dimension reduction are merged into one analysis. The proposed sparse method decreases the complexity of biological system, while increases protein subcellular localization accuracy. Experimental results are quite encouraging, indicating that the aforementioned sparse method is quite promising in dealing with complicated biological problems, such as predicting the subcellular localization of Gram-negative bacterial proteins.
Zheng
Zhonglong
Z
Department of Computer Science, Zhejiang Normal University, Zhejiang, China. zhonglong@zjnu.cn
Yang
Jie
J
D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D006090:Gram-Negative Bacteria / Q000737:chemistry / Q000166:cytology / Q000378:metabolism*; D008954:Models, Biological; D016571:Neural Networks, Computer; D013223:Statistics as Topic; D013347:Subcellular Fractions / Q000737:chemistry / Q000378:metabolism*
D001426:Bacterial Proteins