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All Journal International Journal of Electrical and Computer Engineering IAES International Journal of Artificial Intelligence (IJ-AI) Jurnal Teknologi Dan Industri Pangan Jurnal Pustakawan Indonesia ComEngApp : Computer Engineering and Applications Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences TELKOMNIKA (Telecommunication Computing Electronics and Control) Jurnal Ilmu Komputer dan Agri-Informatika Jurnal Ilmiah Kursor Biogenesis: Jurnal Ilmiah Biologi Jurnal Teknologi Informasi dan Ilmu Komputer Journal of ICT Research and Applications International Journal of Advances in Intelligent Informatics Indonesian Journal of Biotechnology Seminar Nasional Informatika (SEMNASIF) Sosio Konsepsia Khazanah Informatika: Jurnal Ilmu Komputer dan Informatika Jurnal Teknologi dan Sistem Komputer INTENSIF: Jurnal Ilmiah Penelitian dan Penerapan Teknologi Sistem Informasi Jurnal Penelitian Pendidikan IPA (JPPIPA) Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control ILKOM Jurnal Ilmiah Jurnal Nasional Pendidikan Teknik Informatika (JANAPATI) Komputasi: Jurnal Ilmiah Ilmu Komputer dan Matematika Jurnal Jamu Indonesia Journal of Electronics, Electromedical Engineering, and Medical Informatics VISI PUSTAKA: Buletin Jaringan Informasi Antar Perpustakaan JURNAL Al-AZHAR INDONESIA SERI SAINS DAN TEKNOLOGI Indonesian Journal of Electrical Engineering and Computer Science Nusantara Science and Technology Proceedings Bioinformatics and Biomedical Research Journal Jurnal Pustakawan Indonesia Jurnal Nasional Teknik Elektro dan Teknologi Informasi J-Icon : Jurnal Komputer dan Informatika Indonesian Journal of Jamu
Wisnu Ananta Kusuma
Department Of Computer Science, Faculty Of Mathematics And Natural Sciences, IPB University, Jl Meranti Kampus IPB Dramaga, Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Law, Crime, Criminology & Criminal Justice Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Physics Public Health Social Sciences Other

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Journal : TELKOMNIKA (Telecommunication Computing Electronics and Control)

 1 
Hadoop Performance Analysis on Raspberry Pi for DNA Sequence Alignment Jaya Sena Turana; Heru Sukoco; Wisnu Ananta Kusuma
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 3: September 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i3.1886

Abstract

The rapid development of electronic data has brought two major challenges, namely, how to store big data and how to process it. Two main problems in processing big data are the high cost and the computational power. Hadoop, one of the open source frameworks for processing big data, uses distributed computational model designed to be able to run on commodity hardware. The aim of this research is to analyze Hadoop cluster on Raspberry Pi as a commodity hardware for DNA sequence alignment. Six B Model Raspberry Pi and a Biodoop library were used in this research for DNA sequence alignment. The length of the DNA used in this research is between 5,639 bp and 13,271 bp. The results showed that the Hadoop cluster was running on the Raspberry Pi with average usage of processor 73.08%, 334.69 MB of memory and 19.89 minutes of job time completion. The distribution of Hadoop data file blocks was found to reduce processor usage as much as 24.14% and memory usage as much as 8.49%. However this increased job processing time as much as 31.53%.
Twitter’s Sentiment Analysis on Gsm Services using Multinomial Naïve Bayes Aisah Rini Susanti; Taufik Djatna; Wisnu Ananta Kusuma
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 15, No 3: September 2017
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v15i3.4284

Abstract

Telecommunication users are rapidly growing each year. As people keep demanding a better service level of Short Message Service (SMS), telephone or data use, service providers compete to attract their customer, while customer feedbacks in some platforms, for example Twitter, are their souce of information. Multinomial Naïve Bayes Tree, adapted from the method of Multinomial Naïve Bayes and Decision Tree, is one technique in data mining used to classify the raw data or feedback from customers.Multinomial Naïve Bayes method used specifically addressing frequency in the text of the sentence or document. Documents used in this study are comments of Twitter users on the GSM telecommunications provider in Indonesia.This research employed Multinomial Naïve Bayes Tree classification technique to categorize customers sentiment opinion towards telecommunication providers in Indonesia. Sentiment analysis only included the class of positive, negative and neutral. This research generated a Decision Tree roots in the feature "aktif" in which the probability of the feature "aktif" was from positive class in Multinomial Naive Bayes method. The evaluation showed that the highest accuracy of classification using Multinomial Naïve Bayes Tree (MNBTree) method was 16.26% using 145 features. Moreover, the Multinomial Naïve Bayes (MNB) yielded the highest accuracy of 73,15% by using all dataset of 1665 features. The expected benefits in this research are that the Indonesian telecommunications provider can evaluate the performance and services to reach customer satisfaction of various needs.
Cluster Analysis for SME Risk Analysis Documents Based on Pillar K-Means Irfan Wahyudin; Taufik Djatna; Wisnu Ananta Kusuma
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 2: June 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i2.2385

Abstract

In Small Medium Enterprise’s (SME) financing risk analysis, the implementation of qualitative model by giving opinion regarding business risk is to overcome the subjectivity in quantitative model. However, there is another problem that the decision makers have difficulity to quantify the risk’s weight that delivered through those opinions. Thus, we focused on three objectives to overcome the problems that oftenly occur in qualitative model implementation. First, we modelled risk clusters using K-Means clustering, optimized by Pillar Algorithm to get the optimum number of clusters. Secondly, we performed risk measurement by calculating term-importance scores using TF-IDF combined with term-sentiment scores based on SentiWordNet 3.0 for Bahasa Indonesia. Eventually, we summarized the result by correlating the featured terms in each cluster with the 5Cs Credit Criteria. The result shows that the model is effective to group and measure the level of the risk and can be used as a basis for the decision makers in approving the loan proposal. 
Improving DNA Barcode-based Fish Identification System on Imbalanced Data using SMOTE Wisnu Ananta Kusuma; Nurdevi Noviana; Lailan Sahrina Hasibuan; Mala Nurilmala
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 15, No 3: September 2017
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v15i3.5011

Abstract

Problem in imbalanced data is very common in classification or identification. The problem is raised when the number of instances of one class far exceeds the other. In the previous research, our DNA barcode-based Identification System of Tuna and Mackerel was developed in imbalanced dataset. The number of samples of Tuna and Mackerel were much more than those of other fish samples. Therefore, the accuracy of the classification model was probably still in bias. This research aimed at employing Synthetic Minority Oversampling Technique (SMOTE) to yield balanced dataset. We used k-mers frequencies from DNA barcode sequences as features and Support Vector Machine (SVM) as classification method. In this research we used trinucleotide (3-mers) and tetranucleotide (4-mers). The training dataset was taken from Barcode of Life Database (BOLD). For evaluating the model, we compared the accuracy of model using SMOTE and without SMOTE in order to classify DNA barcode sequences which is taken from Department of Aquatic Product Technology, Bogor Agricultural University. The results showed that the accuracy of the model in the species level using SMOTE was 7% and 13% higher than those of non-SMOTE for trinucleotide (3-mers) and tetranucleotide (4-mers), respectively. It is expected that the use of SMOTE, as one of data balancing technique, could increase the accuracy of DNA barcode based fish classification system, particularly in the species level which is difficult to be identified.
Comparison of Data Partitioning Schema of Parallel Pairwise Alignment on Shared Memory System Auriza Rahmad Akbar; Heru Sukoco; Wisnu Ananta Kusuma
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 13, No 2: June 2015
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v13i2.1415

Abstract

The pairwise alignment (PA) algorithm is widely used in bioinformatics to analyze biological sequence. With the advance of sequencer technology, a massive amount of DNA fragments are sequenced much quicker and cheaper. The alignment algorithm needs to be parallelized to be able to align them in a shorter time. Many previous researches have parallelize PA algorithm using various data partitioning schema, but it is unclear which one is the best. The data partitioning schema is important for parallel PA performance, because this algorithm use dynamic programming technique that needs intense inter-thread communication. In this paper, we compared four partitioning schemas to find the best performing one on shared memory system. Those schemas are: blocked columnwise, rowwise, antidiagonal, and blocked columnwise with manual scheduling and loop unrolling. The last schema gave the best performance of 89% efficiency on 4 threads. This result provided fine-grain parallelism that can be used further to develop parallel multiple sequence alignment (MSA).
Algorithm for Predicting Compound Protein Interaction Using Tanimoto Similarity and Klekota-roth Fingerprint Isnan Mulia; Wisnu Ananta Kusuma; Farit Mochamad Afendi
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 16, No 4: August 2018
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v16i4.5916

Abstract

This research aimed to develop a method for predicting interaction between chemical compounds contained in herbs and proteins related to particular disease. The algorithm of this method is based on binary local models algorithm, with protein similarity section is omitted. Klekota-Roth fingerprint is used for the compound's representation. In the development process of the method, three similarity functions are compared: Tanimoto, Cosine, and Dice. Youden’s index is used to evaluate optimum threshold value. The result showed that Tanimoto similarity function yielded higher similarity values and higher AUC value than those of the other two functions. Moreover, the optimum threshold value obtained is 0.65. Therefore, Tanimoto similarity function and threshold value 0.65 are selected to be used on the prediction method. The average evaluation accuracy of the developed algorithm is only about 50%. The low accuracy value is allegedly caused by the only use of compound similarity on the prediction method, without including the protein similarity.
Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer Kana Saputra S; Wisnu Ananta Kusuma; Agus Buono
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 2: June 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i2.2395

Abstract

Next generation sequencing technology is able to generate short read in large numbers and in a relatively short in single running programs. Graph based DNA sequence assembly used to handle these big data in assembly step. The graph based DNA sequence assembly is very sensitive to DNA sequencing error. This problem could be solved by performing an error correction step before the assembly process. This research proposed fuzzy inference system (FIS) model based spectral alignment method which can detect and correct DNA sequencing error. The spectral alignment technique was implemented as a pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. The number of nodes yielded by the Velvet assembler become a measure of the success of error correction. The results shows that FIS model based spectral alignment created small number of nodes and therefore it successfully corrected the DNA reads.
Identification of Tuna and Mackerel based on DNA Barcodes using Support Vector Machine Mulyati Mulyati; Wisnu Ananta Kusuma; Mala Nurilmala
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 2: June 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i2.2469

Abstract

Tuna and mackerel are important fish in Indonesia that have great demand in the community and contain good nutrients for health. Many of the processed products have been faked including processed fish, by replacing the content of products that have high sales value to other lower price one. For ensuring food safety, fraudulent should be prevented by identifying the content of refined product. In this research, we implemented support vector machine (SVM), one of the popular methods in machine learning, to yield a model for identifying the content of refined product based on DNA barcode sequences. The feature extraction of DNA barcode Sequences was conducted by calculating k-mers frequency of each sequences. In this study, we used trinucleotide (3-mers) and tetranucleotide (4-mers). These features were inputted to SVM to classify and identify whether the DNA barcode sequences belong to the class of tuna, mackerel, or other fish. The evaluation results showed model SVM was able to perform identification with the accuracy 88%.
Co-Authors Abdul Aziz Abdul Rahman Saleh Agus Buono Ahmad, Tarmizi Aini Fazriani Aisah Rini Susanti Alami, Tegar Albert Adrianus Ali Djamhuri Annisa Annisa Annisa , Annisa Annisa Annisa Annisa Annisa Annisa Annisa Annisa Annisa Anton Suryatama Arini Aha Pekuwali Arini Pekuwali Arwan Subakti Ary Prabowo Auliatifani, Reza Auliya Ilmiawati Auriza Rahmad Akbar Badollahi Mustafa Badrut Tamam Bahrul Ulum Budi Tjahjono BUDI TJAHJONO Dahrul Syah Diah Handayani Dian Indah Savitri Dian Kartika Utami Essy Harnelly Fadli , Aulia Fahrury Romdendine, Muhammad Farhan Ramadhani , Hilmi Farit Mochamad Afendi Farohaji Kurniawan Fatriani, Rizka Fazriani, Aini Firman Ardiansyah Halida Ernita Handayani, Vitri Aprilla Hanifah Nuryani Lioe Hardi, Wishnu Hasibuan, Lailan Sahrina Hendra Rahmawan Hendra Rahmawan Hera Dwi Novita Heru Sukoco Imas Sukaesih Sitanggang Indra Astuti Ira Maryati Irfan Wahyudin Irma Herawati Suparto Irman Hermadi Irmanida Batubara Irvan Lewenusa ISKANDAR ZULKARNAEN SIREGAR Isnan Mulia Janti G. Sudjana Jaya Sena Turana Joni Prasetyo Kana Saputra S Kangko, Danang Dwijo Karlisa Priandana Khaydanur Khaydanur Khaydanur, Khaydanur Laela Wulansari Larasati Larasati Lina Herlina Tresnawati Listina Setyarini Lusi Agus Setiani Maggy T. Suhartono Mala Nurilmala Medria Kusuma Dewi Hardhienata Mohamad Rafi Mohamad Rafi Mohamad Rafi Mohammad Romano Diansyah Mohammad Romano Diansyah Muchlishah Rosyadah Muh Fadhil Al-Haaq Ginoga Muhammad Asyhar Agmalaro Muhammad Subianto Mulyati Mulyati Mushthofa Mushthofa Mushthofa Muttaqin, Muhammad Rafi Nabila Sekar Ramadhanti Nasution, Tegar Alami Nengsih, Nunuk Kurniati Norma Nur Azizah Nunuk Kurniati Nengsih Nur Choiriyati Nurdevi Noviana Ovi Sofia Pramita Andarwati Prihasuti Harsani Priyo Raharjo Pudji Muljono Purnajaya, Akhmad Rezki Purnomo, Tsania Firqin Ramdan Satra Ratu Mutiara Siregar Refianto Damai Darmawan Refianto Damai Darmawan Resnawati Reza Auliatifani Rif’ati, Lutfah Rizky Maulidya Afifa Ronald Marseno Rosy Aldina Rudi Heryanto SATRIYAS ILYAS Septaningsih, Dewi Anggraini Siti Syahidatul Helma Sony Hartono Wijaya Sri Nurdiati Sulistyo Basuki Sulistyo Basuki Supriyanto, Arif Syahid Abdullah Syarifah Aini Syarifah Fathimah Azzahra Syukriyansyah Taufik Djatna Toni Afandi Tsania Firqin Purnomo Usman, Muhammad Syafiuddin Wa Ode Rahma Agus Udaya Manarfa Wahjuni, Sri Widya Sari Wijaya, Eko Praja Hamid Wina Yulianti Wishnu Hardi Wulansari, Laela Yandra Arkeman Yessy Yanitasari Yudhi Trisna Atmajaya Yulianah Yulianah Yunita Fauzia Achmad Zulkarnaen, Silvia Alviani