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Nur Choiriyati
Department of Computer Science, IPB University
Computer Science & IT Electrical & Electronics Engineering

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Model deep learning untuk klasifikasi fragmen metagenom dengan spaced k-mers sebagai ekstraksi fitur Nur Choiriyati; Yandra Arkeman; Wisnu Ananta Kusuma
Jurnal Teknologi dan Sistem Komputer Volume 8, Issue 3, Year 2020 (July 2020)
Publisher : Department of Computer Engineering, Engineering Faculty, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jtsiskom.2020.13407

Abstract

An open challenge in bioinformatics is the analysis of the sequenced metagenomes from the various environments. Several studies demonstrated bacteria classification at the genus level using k-mers as feature extraction where the highest value of k gives better accuracy but it is costly in terms of computational resources and computational time. Spaced k-mers method was used to extract the feature of the sequence using 111 1111 10001 where 1 was a match and 0 was the condition that could be a match or did not match. Currently, deep learning provides the best solutions to many problems in image recognition, speech recognition, and natural language processing. In this research, two different deep learning architectures, namely Deep Neural Network (DNN) and Convolutional Neural Network (CNN), trained to approach the taxonomic classification of metagenome data and spaced k-mers method for feature extraction. The result showed the DNN classifier reached 90.89 % and the CNN classifier reached 88.89 % accuracy at the genus level taxonomy.
Co-Authors Wisnu Ananta Kusuma Yandra Arkeman