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Azhari Azhari
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Journal : JUITA : Jurnal Informatika

 1 
The Empirical Comparison of Machine Learning Algorithm for the Class Imbalanced Problem in Conformational Epitope Prediction Binti Solihah; Azhari Azhari; Aina Musdholifah
JUITA : Jurnal Informatika JUITA Vol. 9 No. 1, May 2021
Publisher : Department of Informatics Engineering, Universitas Muhammadiyah Purwokerto

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (972.975 KB) | DOI: 10.30595/juita.v9i1.9969

Abstract

A conformational epitope is a part of a protein-based vaccine. It is challenging to identify using an experiment. A computational model is developed to support identification. However, the imbalance class is one of the constraints to achieving optimal performance on the conformational epitope B cell prediction. In this paper, we compare several conformational epitope B cell prediction models from non-ensemble and ensemble approaches. A sampling method from Random undersampling, SMOTE, and cluster-based undersampling is combined with a decision tree or SVM to build a non-ensemble model. A random forest model and several variants of the bagging method is used to construct the ensemble model. A 10-fold cross-validation method is used to validate the model.  The experiment results show that the combination of the cluster-based under-sampling and decision tree outperformed the other sampling method when combined with the non-ensemble and the ensemble method. This study provides a baseline to improve existing models for dealing with the class imbalance in the conformational epitope prediction.
Co-Authors Abdul Rahman Adzanmi Urka Aga Satria Nurrachman Agusti Restu Ahmad Nayan Aina Musdholifah Alex Kurniawandy ansar mulkin Anshori Anshori Arie Putra Arif Setiawan Azhari Azhari Barnes Ar Binti Solihah Darmawan Darmawan Darmawi Darmawi Deassy Siska Destiarini Destiarini Edi Kamal Eko Rahman Wisuda Eko Subiyantoro Elisa Nur Emy Rahmawati Erina Erina Esther Oktavia Fadhlil Ulum A. Rahman Faiza Yuniati Fakhrurrazi Fakhrurrazi Fazzan Fazzan Firmansyah Firmansyah Hairudinor Hairudinor Heni Pujiastuti Imam Syaifudin Imawan Sugiharto Ira Zulfa Ismail Suardi Wekke Ismar Agustin Jalaluddin Jalaluddin Jamal Fakhri Jarnawi Jarnawi Juli Andria Karlina Ibrahim Khairil Khairil Khairul Aswadi Lusi Epsilawati M Daud AK Mahdi Abrar Masda Admi Masrullita Masrullita Mirnawati limbong lebok Monica Rafihasnah Muhammad Hambal Muhammad Idham Muliyadi Muliyadi Novi Sylvia Novita Novita NURLIANA NURLIANA Nursim Nursim Poppy Mayang Sari Qazwini Bin Athaillah Rastina Rastina Retantyo Wardoyo Rika Maya Sari Riski Ayu Maulida Rita Anugerah Roslina Roslina RR. Ella Evrita Hestiandari Safarudin Safarudin Sandy Pamadya Sarifah, Norlaila Sherly Ramadhani Siswadi Siswadi Siti Rani Ayuti Somakim, Somakim Sri Hartati Suci M.Hum SH Hartati T Armansyah TR Teuku Reza Ferasyi Tongku Nizwan Siregar Ummu Balqis Wahyu Ramadhani Watimena Wildan Wildan Yulis Manizal Yuvita Fitriana Zamhir Basem Zulbahridar Zulbahridar