On the data imbalance problem in SVM-based subcellular localization

Pao Yue-kong Library Electronic Theses Database

On the data imbalance problem in SVM-based subcellular localization

 

Author: Tang, Jing
Title: On the data imbalance problem in SVM-based subcellular localization
Degree: M.Sc.
Year: 2011
Subject: Support vector machines
Bioinformatics
Machine learning
Hong Kong Polytechnic University -- Dissertations
Department: Dept. of Electronic and Information Engineering
Pages: 37 leaves : col. ill. ; 30 cm.
InnoPac Record: http://library.polyu.edu.hk/record=b2446838
URI: http://theses.lib.polyu.edu.hk/handle/200/6140
Abstract: Several computational methods have been proposed for protein subcellular localization. SVMs perform well when classes are equally represented, but are limited in their performance on highly imbalanced datasets. Here we propose two novel methods to overcome this data-imbalance problem. The proposed methods use over-sampling techniques to create new minority-class patterns to rebalance the datasets. Pairwise alignment is used to align query sequences with training sequences and obtain score vectors with dimensionality equal to the number of training sequences. Experimental results on two subcellular localization datasets show that the proposed over-sampling methods are able to improve the total accuracy. We believe that the proposed methods will not only be applicable to subcellular localization, but also to other machine learning applications.

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