Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction

Machine learning techniques have been widely applied to solve the problem of predicting protein secondary structure from the amino acid sequence. They have gained substantial success in this research area. Many methods have been used including k-Nearest Neighbors (k-NNs), Hidden Markov Models (HMMs)...

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Bibliographic Details
Published in:Evolutionary Bioinformatics 2011-01, Vol.2011 (2011), p.171-189
Main Authors: Bouziane, Hafida, Messabih, Belhadri, Chouarfia, Abdallah
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Bioinformatics
Chemical properties
Classifiers
Evolutionary
Gain
Machine learning
Markov processes
Mathematical models
Methods
Neural networks
Original Research
Proteins
Scoring
Voting
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Summary:Machine learning techniques have been widely applied to solve the problem of predicting protein secondary structure from the amino acid sequence. They have gained substantial success in this research area. Many methods have been used including k-Nearest Neighbors (k-NNs), Hidden Markov Models (HMMs), Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs), which have attracted attention recently. Today, the main goal remains to improve the prediction quality of the secondary structure elements. The prediction accuracy has been continuously improved over the years, especially by using hybrid or ensemble methods and incorporating evolutionary information in the form of profiles extracted from alignments of multiple homologous sequences. In this paper, we investigate how best to combine k-NNs, ANNs and Multi-class SVMs (M-SVMs) to improve secondary structure prediction of globular proteins. An ensemble method which combines the outputs of two feed-forward ANNs, k-NN and three M-SVM classifiers has been applied. Ensemble members are combined using two variants of majority voting rule. An heuristic based filter has also been applied to refine the prediction. To investigate how much improvement the general ensemble method can give rather than the individual classifiers that make up the ensemble, we have experimented with the proposed system on the two widely used benchmark datasets RS 126 and CB513 using cross-validation tests by including PSI-BLAST position-specific scoring matrix (PSSM) profiles as inputs. The experimental results reveal that the proposed system yields significant performance gains when compared with the best individual classifier.
ISSN:1176-9343
1176-9343
DOI:10.4137/EBO.S7931