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Exploration of dark chemical genomics space via portal learning: Applied to targeting the undruggable genome and COVID-19 anti-infective polypharmacology

arXiv

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arXiv 2021年

作者： Cai, Tian Xie, Li Chen, Muge Liu, Yang He, Di Zhang, Shuo Mura, Cameron Bourne, Philip E. Xie, Lei Ph.D. Program in Computer Science The Graduate Center The City University of New York New York10016 United States Department of Computer Science Hunter College The City University of New York New York10065 United States Master Program in Computer Science Courant Institute of Mathematical Sciences New York University United States School of Data Science Department of Biomedical Engineering University of Virginia VA22903 United States Helen and Robert Appel Alzheimer’s Disease Research Institute Feil Family Brain & Mind Research Institute Weill Cornell Medicine Cornell University New York10021 United States

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones—a common dilemma in scientific inquiry. We have developed a new deep learning framework, called Portal Learning, to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology’s sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) problem in statistical machine learning. Here, we have implemented Portal Learning to predict chemical-protein interactions on a genome-wide scale. Systematic studies demonstrate that Portal Learning can effectively assign ligands to unexplored gene families (unknown functions), versus existing state-of-the-art methods, thereby allowing us to target previously "undruggable" proteins and design novel polypharmacological agents for disrupting interactions between SARS-CoV-2 and human proteins. Portal Learning is general-purpose and can be further applied to other areas of scientific *** Codes 68T07 © 2021, CC BY.

关键词： Genes

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Detection of Vehicle Position and Speed using Camera Calibration and Image Projection Methods

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Procedia computer science 2019年 157卷 255-265页

作者： Alexander A S Gunawan Deasy Aprilia Tanjung Fergyanto E. Gunawan Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480

Traffic congestion is the main problem faced by big cities, such as Jakarta. One approach to reduce congestion levels is to improve traffic management that regulates and controls the number of vehicles. To evaluate the impact of traffic management before direct implementation on the highway, traffic modeling can be carried out. Parameters in modeling traffic must be determined from a calibration process where the vehicle is accurately measured for its position and speed. This study aims to propose an efficient calibration procedure with accurate results, based on recorded vehicle movement in perspective view. First, the road image is projected using the Direct Linear Transformation (DLT) method, then the vehicle position is detected using the Background Subtraction and tracked using Mixture of Gaussian (MoG) to determine the vehicle speed. Finally, we develop a prototype of Automated Traffic Flow Monitoring based on Python programming. In the experiment results, the accuracy of vehicle position detection is evaluated based on the Euclidean distance. The average difference between the results of position detection with ground-truth is 12.07 pixels with a camera angle 40 °. The percentage of speed measurement accuracy using the DLT projection method is 96.14%.

关键词： Music recommender system Convolutional recurrent neural network Similarity distance

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Analysis of Acoustic Features in Gender Identification Model for English and Bahasa Indonesia Telephone Speeches

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Procedia computer science 2019年 157卷 199-204页

作者： Muhamad Fitra Kacamarga Tjeng Wawan Cenggoro Arif Budiarto Reza Rahutomo Bens Pardamean Eureka.ai 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

One of the most interesting topics in auditory problem is determining gender of the speaker. In recent years, machine learning has gained significant attentions as a way to build a classifier from labeled data which also can be implemented to build a gender classifier. In this study we develop gender classifier using two different datasets with different languages, English and Bahasa Indonesia. Each data from both datasets is represented by 20 acoustic features. Multi Layer Perceptron (MLP) is used to build the classification model using all these features and trained only on English dataset. This model is evaluated in both dataset to get the performance matrices consist of accuracy, AUROC, precision and recall. Ultimately, using this model we also identify and compare important features from both dataset to see the different characteristics of English and Bahasa Indonesia speeches.

关键词： Gender Identification Acoustic Feature Speech Recognition

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Defying the certification diploma forgery with blockchain platform: A proposed model 12

Defying the certification diploma forgery with blockchain pl...

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12th International Conference on ICT, Society and Human Beings, ICT 2019, 5th International Conference on Connected Smart Cities, CSC 2019 and the 16th International Conference on Web Based Communities and Social Media, WBC 2019

作者： Meyliana Chandra, Yakob Utama Cassandra, Cadelina Surjandy Eka Widjaja, Henry Antonius Fernando, Erick Prabowo, Harjanto Joseph, Charles Information Systems Department School of Information Systems Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Bloocys Foundation Pte. Ltd 079903 Singapore

ISBN: (纸本)9789898533906

In the University setting, part of management recorded all education transaction since the students register until they graduate. In this point, the transaction raises several new and crucial challenges. At a closer look, the concerns appeared due to no data integration, verification, and validation from parties both inside or outside of the university. In this respect, the data is not centralized or integrated. As this backdrop, this causes repeated data confirmation, and no one can authenticate the data validity when distributed to other parties. In this point of entry, the diploma certification forgery has become one of the significant issues in education in Indonesia. As a framework that enables the data integration, Blockchain contains verified data on every single of a transaction, so the data is trustworthy. With this in mind, this paper aims to discuss the best blockchain model for the university level. This study is qualitative-based research. As a result, McRhys model is introduced as a potential and implementable blockchain model in university in Indonesia. © 2019 IADIS Press. All rights reserved.

关键词： Blockchain

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DNAku Consumers Profile: One of The First Direct to Customer Genetics Testing in Indonesia

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IOP Conference Series: Earth and Environmental science 2021年第1期794卷

作者： Deby Erina Parung Kians Azizatikarna Dian Amirulloh Erlin Listiyaningsih Bharuno Mahesworo Arif Budiarto Simon Bens Pardamean Genetics Indonesia Jakarta Indonesia 12940 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

DNAku test is one of the first direct to customer genetics testing in Indonesia. DNAku test came with a different approach as it gave their customer reports of their genetic predisposition to corresponding traits. Four months after launch, we create consumer report of this genetics testing based on DNAku questionnaire results. We applied three statistical methods, including descriptive statistics, multivariate normality test, and t-test to the demographic data of the DNAku customers. The result shows population clusters which may represent population groups that are interested in genetics testing. The questionnaire also has questions about the customer's lifestyle. The results of these questions were processed to find the lifestyle of DNAku customers.

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Design Project Management System Based on SOA Approach

Design Project Management System Based on SOA Approach

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International Conference on Computation in science and Engineering, ICCSE 2017

作者： Girsang, Abba Suganda Jafar, Fahmi Fajar, Ahmad Nurul Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia Information System Computer Science Department BINUS Graduate Program-Master of Information Systems Management Bina Nusantara University Jakarta11480 Indonesia

Application architecture and information technology systems in the company should be able to support the company's policy that leads to their alignment with the business objectives. The alignment of the implementation of information technology systems to the needs and goals of the organization will be able to be answered by taking into account the integration in the development, so that the gap of these two things can be minimized. As a company engaged in IT consulting, project management system is one form of application systems that support core business objective of the company: to produce high-quality software. Nevertheless, the project management system should be able to work together with other supporting information systems, so that the flow of information within the company can run effectively. To achieve these objectives, required the analysis and design of an integrated system, which can be achieved through a service-oriented architecture based system. which includes the stages of requirements and analysis, design and development, and the last is the IT operations. The final result expected is the design of the service-oriented architecture based project management system which built through top-down approach that focuses on improving the effectiveness of business process. © Published under licence by IOP Publishing Ltd.

关键词： Service oriented architecture (SOA)

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Snake and digital ladder applications involving the behavior of children applying the health protocols

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Journal of Physics: Conference Series 2021年第1期1869卷

作者： H D Ariessanti F L Gaol S H Supangkat B Ranti Computer Science Department BINUS Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department Esa Unggul University Jakarta Indonesia 11510 Computer Science Department Indonesia University Jakarta Indonesia 16424

This study defines the problem of how understanding health protocols during a pandemic is correctly conveyed according to age levels. This problem for the Government to implement gamification by modifying game media through snake and ladder game that can socialize health protocols for pre-school. Measuring the acceptance of a snake and ladder game media can be considered as a learning medium from the Government which will refer to four components (game content, ease of play, appearance, and active player involvement). The purpose of this study was to modify online-based games as a learning media and to measure children's active interaction with parents in practicing health protocols during game play. This study will use a quantitative approach with data techniques through playing together experiments and filling in online research questionnaires from 115 samples as participants (7 Kindergartens). The results show that the snake and ladder digital game can have a significant effect on changes behavior in implementing health protocols. This research can provide a contribution that can be used as a reference for the Government to design a strategy for socialization through gamification.

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Intelligent E-commerce for Special Needs 7

Intelligent E-commerce for Special Needs

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7th International Conference on Cyber and IT Service Management, CITSM 2019

作者： Warnars, Diana Teresia Spits Putra, Leonardo Primadala Logiansa Warnars, Harco Leslie Hendric Spits Utomo, Wiranto Herry School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia BINUS Graduate Program Doctor of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Department of Magister Science of Information Technology Faculty of Computing President University Bekasi17550 Indonesia

ISBN: (纸本)9781728129099

Special need is a person who need assistance for their disabilities which include medical, physical, mental or psychological such as person with autism, down syndrome, dyslexia, Attention Deficit Hyperactivity Disorder (ADHD), multiple sclerosis, schizophrenia, cystic fibrosis, cerebral palsy, muscular dystrophy, blindness, deafness, epilepsy, chronic asthma and so on. In this proposed research idea about intelligent E-commerce for special needs, we limited to four types of difficulties such as hearing difficulty, vision difficulty, language difficulty, and learning difficulty. In this paper, we interest in those special needs persons who can use e-commerce and how to model a system that can help them to joy and easy to join with e-commerce. For some, this intelligent e-commerce is not only for shopping only but will become part of their healing for special needs in order to engage with daily human activities and increase their daily confidence in life. This paper also a preliminary investigation that can be used for Ph.D. or Doctoral research degree who is interested in building e-commerce framework for people with a special need or disability. © 2019 IEEE.

关键词： Electronic commerce

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An integrated system of mobile application and IoT solution for pond monitoring

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IOP Conference Series: Earth and Environmental science 2021年第1期794卷

作者： Ferdinan Darmalim Alam Ahmad Hidayat Tjeng Wawan Cenggoro Kartika Purwandari Sutristo Darmalim Bens Pardamean NusaNet Jakarta Indonesia 12710 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The current progress of information and communication technology has been critical to the development of the Internet of Things (IoT) in a aquaculture system. IoT solution in this system utilizes interconnectivity between devices to obtain fish pond monitoring data from sensing devices and then transmit the data to a remote server to be analyzed for decision-making in pond management. In this paper, we propose a smart pond IoT solution that provides a continuous and real-time pond monitoring. The system principally embeds five sensors that measure critical environmental parameters to determine water quality: temperature, pH, dissolved oxygen (DO), total dissolved solids (TDS), and salinity. The IoT solution also integrates the development of a mobile application on the android platform that allows remote monitoring capabilities for users to maintain efficient pond management. The application is designed with a friendly-user interface that helps the farmer to monitor sensor measurements, manage fish production cycle, record fish feeding schedule, and also monitor the health status of fish from multiple ponds.

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Comparing the Accuracy of Multiple Commercial Wearable Devices: A Method

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Procedia computer science 2019年 157卷 567-572页

作者： Bens Pardamean Haryono Soeparno Bharuno Mahesworo Arif Budiarto James Baurley Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 BioRealm LLC USA

To maintain a good fitness level, performing a minimum daily physical activity is important. Many people think that they have already met the suggested guidelines. However, most of them were wrong when they quantify their activity level using a personal activity tracker device. This problem indicates the need for personal physical activity tracker or wearable device to maintain the fitness level. However, as wide-range wearable devices available today, it is difficult to find the most suitable one regarding the price and quality. This paper proposes a study to explore the association between the quality and the price of the devices. The quality is evaluated by comparing the accuracy of the heart rate sensor and step counter of several wearable devices with the ground truth measurements. The test result is then analyzed using a series of statistical methods including, a paired t-test, Pearson’s correlation test, and Bland-Altman plot. Both t-test and correlation coefficient is used to plot the association between quality and price.

关键词： Wearable Device Fitness Tracker Correlation Heart Rate Step Counting Bland-Altman

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