DOI: https://doi.org/10.14710/jtsiskom.2020.13407

Model deep learning untuk klasifikasi fragmen metagenom dengan spaced k-mers sebagai ekstraksi fitur

Deep learning model for metagenome fragment classification using spaced k-mers feature extraction

Nur Choiriyati  -  Department of Computer Science, IPB University, Indonesia
Yandra Arkeman  -  Department of Agro-Industrial Engineering, IPB University, Indonesia
*Wisnu Ananta Kusuma  -  Department of Computer Science, IPB University, Indonesia
Received: 3 Jul 2019; Revised: 5 May 2020; Accepted: 25 May 2020; Published: 31 Jul 2020; Available online: 3 Jul 2020.
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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.
Keywords: classification; deep learning; metagenomes; spaced k-mers
Funding: Institut Pertanian Bogor

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