Adaptive thresholding for multi-label SVM classification with application to protein subcellular localization prediction

Shibiao Wan, Man Wai Mak, Sun-Yuan Kung

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Scopus citations

Abstract

Multi-label classification has received increasing attention in computational proteomics, especially in protein subcellular localization. Many existing multi-label protein predictors suffer from over-prediction because they use a fixed decision threshold to determine the number of labels to which a query protein should be assigned. To address this problem, this paper proposes an adaptive thresholding scheme for multi-label support vector machine (SVM) classifiers. Specifically, each one-vs-rest SVM has an adaptive threshold that is a fraction of the maximum score of the one-vs-rest SVMs in the classifier. Therefore, the number of class labels of the query protein depends on the confidence of the SVMs in the classification. This scheme is integrated into our recently proposed subcellular localization predictor that uses the frequency of occurrences of gene-ontology terms as feature vectors and one-vs-rest SVMs as classifiers. Experimental results on two recent datasets suggest that the scheme can effectively avoid both over-prediction and under-prediction, resulting in performance significantly better than other gene-ontology based subcellular localization predictors.

Original languageEnglish (US)
Title of host publication2013 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2013 - Proceedings
Pages3547-3551
Number of pages5
DOIs
StatePublished - Oct 18 2013
Event2013 38th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2013 - Vancouver, BC, Canada
Duration: May 26 2013May 31 2013

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
ISSN (Print)1520-6149

Other

Other2013 38th IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2013
CountryCanada
CityVancouver, BC
Period5/26/135/31/13

All Science Journal Classification (ASJC) codes

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

Keywords

  • Adaptive thresholding
  • Gene Ontology
  • Multi-label SVM
  • Multi-label classification
  • Protein subcellular localization

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