Data Type Integration for Protein Identification using Kernel Based Classification Methods
The integrated biological data is expected to obtain a higher exactness, better performance and greater robustness compared to single dataset. In this work, we present data integration using kernel-based approach to identify protein class in yeast, ribosomal proteins and membrane proteins. By using intermediate stage of integration, we change the single data source into kernel matrix format. Kernel weighting was used in the establishment of integrated data. We propose three weighting methods approach i.e. KTA (Kernel Target Alignment), FSM (Feature Space-based kernel matrix evaluation Measure), and AI (Alignment Index). We also perform the combination of these three methods. These integrated kernels will be analyzed using Support Vector Machine (SVM). Our proposed data integration methods achieve a higher performance compared to single data source. KTA is the best kernel weighting measurement method and always obtain a better performance to recognize membrane and ribosomal proteins classes than others.
Keywords: Data Integration, Kernel Matrix, Kernel Target Alignment, Feature Space-based kernel matrix evaluation Measure, Alignment Index, Support Vector Machine
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ABOUT THE AUTHORS
Ito Wasito
Researcher/Academic Staff at Faculty of Computer Science, Universitas Indonesia. He did PhD in Computer Science at University of London. His research interests are Data Mining and Bioinformatics.
Hadaiq R Sanabila
Research Assistant at Faculty of Computer Science, University of Indonesia. He had MSc in Computer Science from University of Indonesia
Aulia N. Istiqlal
Graduate Student, Faculty of Computer Science, University of Indonesia. She had BSc in Computer Science from University of Indonesia
Ito Wasito
Researcher/Academic Staff at Faculty of Computer Science, Universitas Indonesia. He did PhD in Computer Science at University of London. His research interests are Data Mining and Bioinformatics.
Hadaiq R Sanabila
Research Assistant at Faculty of Computer Science, University of Indonesia. He had MSc in Computer Science from University of Indonesia
Aulia N. Istiqlal
Graduate Student, Faculty of Computer Science, University of Indonesia. She had BSc in Computer Science from University of Indonesia
