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Multilabel Learning via Random Label Selection for Protein Subcellular Multilocations Prediction
March-April 2013 (vol. 10 no. 2)
pp. 436-446
Xiao Wang, Dept. of Control Sci. & Eng., Tongji Univ., Shanghai, China
Guo-Zheng Li, Dept. of Control Sci. & Eng., Tongji Univ., Shanghai, China
Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multilocation proteins to multiple proteins with single location, which does not take correlations among different subcellular locations into account. In this paper, a novel method named random label selection (RALS) (multilabel learning via RALS), which extends the simple binary relevance (BR) method, is proposed to learn from multilocation proteins in an effective and efficient way. RALS does not explicitly find the correlations among labels, but rather implicitly attempts to learn the label correlations from data by augmenting original feature space with randomly selected labels as its additional input features. Through the fivefold cross-validation test on a benchmark data set, we demonstrate our proposed method with consideration of label correlations obviously outperforms the baseline BR method without consideration of label correlations, indicating correlations among different subcellular locations really exist and contribute to improvement of prediction performance. Experimental results on two benchmark data sets also show that our proposed methods achieve significantly higher performance than some other state-of-the-art methods in predicting subcellular multilocations of proteins. The prediction web server is available at http://levis.tongji.edu.cn:8080/bioinfo/MLPred-Euk/ for the public usage.
Index Terms:
proteomics,biology computing,cellular biophysics,learning (artificial intelligence),molecular biophysics,proteins,multilocation proteins,multilabel learning,random label selection,protein subcellular multilocations prediction,RALS,binary relevance,Multilabel learning,Proteins,Random label selection,Benchmark testing,multilabel learning,random label selection,Protein subcellular localization,multilocation proteins
Citation:
Xiao Wang, Guo-Zheng Li, "Multilabel Learning via Random Label Selection for Protein Subcellular Multilocations Prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, pp. 436-446, March-April 2013, doi:10.1109/TCBB.2013.21
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