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A Design of Polygenic Risk Model with Deep Learning for Colorectal Cancer in Multiethnic Indonesians

Procedia computer science 2021年 179卷 632-639页

作者： Steven Amadeus Tjeng Wawan Cenggoro Arif Budiarto Bens Pardamean Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480

Recently, health management is emerging and attract attention to how to provide better prognostication and health management systems. The challenges in the prognostication are how to develop a model that can self-learn the prognostication features and how to get a high accuracy prediction. Prognostication in health disease involves SNPs which is a genetic marker. In this paper, we propose a polygenic risk model using deep learning: Transformer with self-attention mechanism and DeepLIFT. The use of these deep learning model allows us to predict the risk of colorectal cancer and see the correlation between SNPs.

关键词： Prognostication Polygenic Risk Model Transformer Model DeepLIFT Colorectal Cancer

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Deep Learning as a Vector Embedding Model for Customer Churn

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Procedia computer science 2021年 179卷 624-631页

作者： Tjeng Wawan Cenggoro Raditya Ayu Wirastari Edy Rudianto Mochamad Ilham Mohadi Dinne Ratj Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

To face the tight competition in the telecommunication industry, it is important to minimize the rate of customers stopping their service subscription, which is known as customer churn. For that goal, an explainable predictive customer churn model is an essential tool to be owned by a telecommunication provider. In this paper, we developed the explainable model by utilizing the concept of vector embedding in Deep Learning. We show that the model can reveal churning customers that can potentially be converted back to use the previous telecommunication service. The generated vectors are also highly discriminative between the churning and loyal customers, which enable the developed models to be highly predictive for determining whether a customer would cease his/her service subscription or not. The best model in our experiment achieved a predictive performance of 81.16%, measured by the F1 Score. Further analysis on the clusters similarity and t-SNE plot also confirmed that the generated vectors are discriminative for churn prediction.

关键词： customer churn customer behavior deep learning vector embedding representation learning

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A Bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Rudi Nirwantono Khoirunnisa Assidqi Alam Ahmad Hidayat Joko Pebrianto Trinugroho Bens Pardamean Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Food Biotechnology Research Center Bina Nusantara University Jakarta Indonesia Mathematics Departement School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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Contribution of Virtual Reality Technology to Increase Student Interest in Vocational High Schools

Contribution of Virtual Reality Technology to Increase Stude...

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2021 International Seminar on Intelligent Technology and Its Application, ISITIA 2021

作者： Maulana, Fairuz Iqbal Pangestu, Gusti Sano, Albert Verasius Dian Purnomo, Agung Rahmadika, Sandi Widartha, Vandha Pradwiyasma Bina Nusantara University School of Computer Science Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Business School Undergraduate Program Entrepreneurship Department Jakarta11480 Indonesia Graduate School Pknu Pukyong National University Interdisciplinary Program of Information Security Busan Korea Republic of Telkom University Information System of Industrial Engineering Faculty Bandung Indonesia

ISBN: (纸本)9781665428477

This research investigates the feasibility of school-based learning using Virtual Reality technology in Electric Power Generation learning during the COVID-19 pandemic. This research employs a qualitative approach. Vocational High School Nurul Jadid Paiton Probolinggo is the site of this study. Data was gathered through observation, literature review, and interviews. In the Electrical Engineering section, interviews were conducted with a teaching instructor. Triangulation was used to investigate the data's authenticity, in addition to further interviews with the curriculum staff and instructors at the school. The teacher's assessment of learning media using Virtual Reality application technology shows valid criteria with an average value of 3.6. In comparison, after using the Virtual Reality application learning media, the assessment of students obtained an average value of 3.77 compared to conventional assessments with an interval of 2.71. The use of Virtual Reality technology has proven that it can help and facilitate student learning. The use of technologies of Virtual Reality as a means of learning in classrooms will also be an alternate option for virtual laboratories during the COVID-19 pandemic. © 2021 IEEE.

关键词： Virtual reality

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IoT for Water Quality Categorization

IoT for Water Quality Categorization

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Hermantoro Sastrohartono Andreas Wahyu Krisdiarto Arief Ika Uktoro Reza Rahutomo Teddy Suparyanto Bens Pardamean Agricultural Engineering Department Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia

In agricultural water research, the adoption of Internet of Things (IoT) technology has emerged as a pivotal approach for large-scale data collection. Water availability in the context of water quality is very important, both for domestic and industrial purposes. For domestic purposes, drinking water and bathing water are separated. Meanwhile, for the palm oil industry, boiler filler is differentiated from additional process water (dilution water). Water quality parameters can be assessed from turbidity and Total Dissolve Solid (TDS). Measurements using measuring instruments separately and repeatedly require significant energy, time, and costs. This research was conducted with the primary objective of presenting a novel method for categorizing water quality with the approach of IoT sensor technology. The research methodology entailed the utilization of an integrated IoT water sensors system in conjunction with manual water categorization. The methods consist of (1) system design, (2) design and installation of sensor and IoT-based microcontrollers, and (3) accuracy and precision testing compared with laboratory measurements. The precision of the integrated IoT water sensors was assessed through a dedicated sensor precision test, resulting in an accuracy rate of 94.4% for the turbidity sensor and 97.5% for the TDS sensor. Notably, this approach successfully discriminated drinking water with valid categorization, while other water types, including groundwater, water with tea, and water with coffee, yielded null categorization results.

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Code-Mixed Sentiment Analysis Using Machine Learning Approach – A Systematic Literature Review

Code-Mixed Sentiment Analysis Using Machine Learning Approac...

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International Conference on Informatics and Computational sciences (ICICoS)

作者： Cuk Tho Harco Leslie Hendric Spits Warnars Benfano Soewito Ford Lumban Gaol BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia 11480

ISBN: (数字)9781728195261

ISBN: (纸本)9781728195278

Code-mixed language is ubiquitous. Having been commonly practiced among bilingual communities, code-mixed language has emerged as a common language among social media users. Despite its popularity, the analysis of a code-mixed text is challenging as the text does not typically comply with the monolingual grammar. Therefore, the popularity of social media in the past ten years has raised wide attention to develop methods for analyzing code-mixed text such as extracting popularity sentiment from the text. Machine learning-based classifier such as Support Vector Machine, Naïve Bayes, Decision Tree, Logistic Regression have been widely used to analyze the sentiment. This paper intends to further explore machine learning classifiers, their performances, variables, and most common classifiers for the code-mixed sentiment analysis. Prisma Methodology was used in this paper, extracting 12 from 230 papers that met predefined required criteria, including publication year within the last 5 years. Our findings suggested that the most common classifiers found in the papers were Support Vector Machine, Naïve Bayes, and Logistic Regression. By using the accuracy and F1 as the performance measures, the Support Vector Machine exhibited a better performance compared to Naïve Bayes and Logistic Regression. Thus, this study supported the use of Support Vector Machine, Naïve Bayes and Logistic Regression as the main classifiers for the code-mixed sentiment analysis.

关键词： Support vector machines Sentiment analysis Systematics Social networking (online) Machine learning Regression tree analysis Logistics

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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Alam Ahmad Hidayat Rudi Nirwantono Mahmud Isnan Joko Pebrianto Trinugroho Bens Pardamean Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department Bioinformatics and Data Science Research Center BINUS Graduate Program Jakarta Indonesia

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features.

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Database management system design for COVID-19 symptom analysis 6

Database management system design for COVID-19 symptom analy...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Rahutomo, Reza Darmalim, Ferdinan Cen, Andrew Brilianto, Jayaku Pardamean, Bens School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia PT. Mega Medica Pharmaceuticals IT Department Jakarta Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Faculty of Technology and Design Bunda Mulia University Jakarta Indonesia BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

Applying a digital strategy is proven to be one way to reduce the infection rate of COVID-19. As a fundamental part of it, database is capable to create a data repository to predict uncertain impacts of the pandemic. The research proposed a database design for project C-Beta that emphasized on creating an ideal system to record and monitor the daily health condition of people with COVID-19. Mainly, the research adopted Connolly and Begg principles of Database Software Development Life Cycle. As a result, the database design activities produced blueprints in the forms of data dictionary, ERD, and user views. The database design delivered in the research included with several features namely user verification, restricted research membership, and flexibility in survey creation. Based on analysis and design phase, C-Beta provides a method to collect data for COVID-19 clinical study. Researchers who utilize C-Beta is able to manage multiple surveys and extract all collected records at the same time. © 2021 IEEE.

关键词： COVID-19

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Development of Key Performance Indicators in e-Learning Implementation in Higher Education Institutions

Development of Key Performance Indicators in e-Learning Impl...

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International Conference on Information Management and Technology (ICIMTech)

作者： Wahyu Sardjono Desi Maya Kristin Gustian Rama Putra Information Systems Management Department BINUS Graduate Program - Master of Information Systems Management Bina Nusantara University Jakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Computer Science Study Program Faculty of Mathematics & Natural Sciences Pakuan University Bogor Indonesia

Companies or organizations usually use key performance indicators (KPI) as indicators to determine their performance. The company's performance achievements are reflected in the set indicators that will describe the overall performance, as well as higher education institutions can also set key performance indicators, to see their performance achievements. The use of e-learning as a tool to support teaching and learning processes to be more effective and efficient is an example of which performance needs to be measured. This article discusses how the process of developing key performance indicators is carried out through the stages of designing questionnaires and distributing questionnaires to students, data is processed using the method of factor analysis to obtain the main indicators determining performance and the method of regression analysis is also used to build performance models. obtain KPI determinants, and then develop KPI models. The results show that there are indicators of sharing knowledge, managing knowledge, understanding knowledge, and utilization knowledge as performance measurement indicators.

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Improvement of Jakarta's air quality during large scale social restriction 2

Improvement of Jakarta's air quality during large scale soci...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Rahutomo, R. Purwandari, K. Sigalingging, J.W.C. Pardamean, B. Information System Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Database Center Division of BMKG Meteorological Climatological and Geophysical Agency Jakarta10720 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

After Large-Scale Social Restriction (PSBB) established in Jakarta, a change of air quality was indicated by the citizens. Representatives of Indonesia's Agency for Meteorology, Climatology, and Geophysics (BMKG) supported as the fact that mobility of Jakarta's citizen and commuters were reduced. With utilizing Weather Data Acquisition System managed by BMKG, this research compared fluctuations of Jakarta's air quality during two periods of time: Pre-PSBB and During-PSBB. This study proved that Jakarta's air quality has positively improved compared to the previous year, although in the lower range of unhealthy level. © Published under licence by IOP Publishing Ltd.

关键词： Air quality

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