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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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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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The role of input imaging combination and ADC threshold on segmentation of acute ischemic stroke lesion using U-Net

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European Radiology 2023年第9期33卷 6157-6167页

作者： Li, Ya-Hui Lin, Shao-Chieh Chung, Hsiao-Wen Chang, Chia-Ching Peng, Hsu-Hsia Huang, Teng-Yi Shen, Wu-Chung Tsai, Chon-Haw Lo, Yu-Chien Lee, Tung-Yang Juan, Cheng-Hsuan Juan, Cheng-En Chang, Hing-Chiu Liu, Yi-Jui Juan, Chun-Jung Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Department of Medical Imaging China Medical University Hsinchu Hospital No. 199 Sec. 1 Xinglong Rd. Zhubei City Hsinchu County 302 Hsinchu Taiwan Ph.D. Program in Electrical and Communication Engineering Feng Chia University Taichung Taiwan Department of Electrical Engineering National Taiwan University Taipei Taiwan Department of Management Science National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biomedical Engineering and Environmental Sciences National Tsing Hua University Hsinchu Taiwan Department of Electrical Engineering National Taiwan University of Science and Technology Taipei Taiwan Department of Radiology School of Medicine College of Medicine China Medical University Taichung Taiwan Department of Medical Imaging Medical University Hospital Taichung Taiwan Department of Neurology China Medical University Hospital Taichung Taiwan Cheng Ching Hospital Taichung Taiwan Master’s Program of Biomedical Informatics and Biomedical Engineering Feng Chia University Taichung Taiwan Department of Automatic Control Engineering Feng Chia University No. 100 Wenhwa Rd. Seatwen Taichung 40724 Taiwan Department of Biomedical Engineering The Chinese University of Hong Kong ERB1112 11/F William M.W. Mong Engineering Building N.T Shatin Hong Kong Multi-Scale Medical Robotics Center The Chinese University of Hong Kong N.T Shatin Hong Kong Department of Biomedical Engineering National Defense Medical Center Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan

Background: To evaluate the effect of the weighting of input imaging combo and ADC threshold on the performance of the U-Net and to find an optimized input imaging combo and ADC threshold in segmenting acute ischemic stroke (AIS) lesion. Methods: This study retrospectively enrolled a total of 212 patients having AIS. Four combos, including ADC-ADC-ADC (AAA), DWI-ADC-ADC (DAA), DWI-DWI-ADC (DDA), and DWI-DWI-DWI (DDD), were used as input images, respectively. Three ADC thresholds including 0.6, 0.8 and 1.8 × 10^–3 mm²/s were applied. Dice similarity coefficient (DSC) was used to evaluate the segmentation performance of U-Nets. Nonparametric Kruskal–Wallis test with Tukey–Kramer post-hoc tests were used for comparison. A p <.05 was considered statistically significant. Results: The DSC significantly varied among different combos of images and different ADC thresholds. Hybrid U-Nets outperformed uniform U-Nets at ADC thresholds of 0.6 × 10^–3 mm²/s and 0.8 × 10^–3 mm²/s (p <.001). The U-Net with imaging combo of DDD had segmentation performance similar to hybrid U-Nets at an ADC threshold of 1.8 × 10^–3 mm²/s (p =.062 to 1). The U-Net using the imaging combo of DAA at the ADC threshold of 0.6 × 10^–3 mm²/s achieved the highest DSC in the segmentation of AIS lesion. Conclusions: The segmentation performance of U-Net for AIS varies among the input imaging combos and ADC thresholds. The U-Net is optimized by choosing the imaging combo of DAA at an ADC threshold of 0.6 × 10^–3 mm²/s in segmentating AIS lesion with highest DSC. Key Points: • Segmentation performance of U-Net for AIS differs among input imaging combos. • Segmentation performance of U-Net for AIS differs among ADC thresholds. • U-Net is optimized using DAA with ADC = 0.6 × 10^–3mm²/s. © 2023, The Author(s), under exclusive licence to European Society of Radiology.

关键词： Deep Learning Diffusion Magnetic Resonance Imaging Ischemic Stroke Neural Networks, computer Retrospective Study

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Decision Support Model for Supplier Selection Using Fuzzy Logic Concept 3

Decision Support Model for Supplier Selection Using Fuzzy Lo...

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3rd International Conference on Information Management and Technology, ICIMTech 2018

作者： Gunawan, Ferdi Wang, Gunawan Utama, Ditdit Nugeraha Komsiyah, Siti Suharjito Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Information Systems Management Department Bina Nusantara University BINUS Graduate Program-Master of Information Systems Management Jakarta11480 Indonesia Computer Science Department Bina Nusantara University BINUS Graduate Program-Master of Computer Science Jakarta11480 Indonesia Mathematics Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781538658215

Improving the company's performance to compete globally, in rapid growth market economy condition, is practically required. One of the important things is right decision in issues of supplier selection. The improper supplier affects consequence negatively to the quality of company's business process. Thus, the right way to answer the issues is incredibly crucial to be proposed. This study aims to design an application to determine the sub-criteria weight with Fuzzy-AHP method, select the best supplier via Fuzzy-TOPSIS method, and calculate the allocation of quota to each supplier thru Fuzzy-MOLP method. The study was conducted on high class store by taking the object of material gymnastic product (spandex). Simulation confidently demonstrates that the Fuzzy-AHP approach is able to be operated to generate parameter Quality Product as the best sub-criteria (with value 0.221), the Fuzzy-TOPSIS technique can be used to ring out the supplier (where CV. Maju Jaya Abadi as the best supplier), and the method Fuzzy-MOLP is exploited to calculate the allocation of quota (where CV. Maju Jaya Abadi as a supplier with the highest percentage of 44.40%). © 2018 IEEE.

关键词： Fuzzy logic

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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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Information as a service on cloud computing technology: A review

Information as a service on cloud computing technology: A re...

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2018 International Seminar on Research of Information Technology and Intelligent Systems, ISRITI 2018

作者： Taryana, Ujang Fajar, Ahmad Nurul Utama, Ditdit Nugeraha Universitas Mercu Buana Jakarta Indonesia Information Systems Management Bina Nusantara University BINUS Graduate Program-Master of Information Systems Management Jakarta11480 Indonesia Computer Science Department BINUS Bina Nusantara University Graduate Program-Master of Information Systems Management Jakarta11480 Indonesia

ISBN: (纸本)9781538674222

Information as a service (IAS) allows any applications to access all types of information thru using the application interface. A service based on everything or 'anything as a service' or 'everything as a service' is a fundamental configuration of developing IAS term that has not been studied comprehensively yet before. Based on systematic review study and also immersed analysis, IAS is proposed as part of the emerging service and specified service in the cloud technology service evolution. Thus, IAS is academically possible to be attached in the cloud service model that is realized in the cloud computing technology. © 2018 IEEE.

关键词： Distributed database systems

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A Model Configuration of Social Media Text Mining for Projecting the Online-Commerce Transaction (Case: Twitter Tweets Scraping)

A Model Configuration of Social Media Text Mining for Projec...

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International Conference on Cyber and IT Service Management (CITSM)

作者： Emil Robert Kaburuan Ang Swat Lin Lindawati Surjandy Siswantini Muhammad Ryanda Putra Ditdit Nugeraha Utama BINUS Graduate Program - Master of Information Systems Management Bina Nusantara University Jakarta Indonesia Faculty of Economics and Communication Bina Nusantara University Jakarta Indonesia School of Information Systems Bina Nusantara University Jakarta Indonesia UIN Syarif Hidayatullah Jakarta Indonesia BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

Text mining is a process to extract data based on text. The source of text mining should be coming from social media users' activities; e.g. posting, fans page, group, hashtag, tweet, etc. As raw data and information, the text mining sources are able to be gold information to be operated for academic analyzing purposes. This paper proposes the Python-based model to scrape text from Twitter user's tweets and then analyze them to see the commerce and tax-income potency in purposely Indonesia. The mathematical and statistical methods are technically operated. The constructed model finally exhibited. Also, the information on sale-behavior and tax-income forecasts are able to be portrayed.

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Interface Rotation in Cu/Nb Accumulative Roll Bonded (ARB) Nanolaminates

SSRN

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SSRN 2022年

作者： Radchenko, Ihor Zhu, Wenxin Qing, Liu Navarro, Etienne Sahay, Rahul Lee, Pooi See Raghavan, Nagarajan Thomas, Olivier Budiman, Arief Suriadi Chen, Kai State Key Laboratory for Mechanical Behavior of Materials Xi’an Jiaotong University Xi’an China School of Materials Science and Engineering Nanyang Technological University Singapore639798 Singapore Nanyang Technological University Temasek Laboratories@NTU 637553 Singapore Aix Marseille Université Université de Toulon CNRS IM2NP Marseille France Xtreme Mechanics Lab 8 Somapah Road Singapore487372 Singapore Singapore487372 Singapore Department of Manufacturing and Mechanical Engineering and Technology Oregon Institute of Technology Klamath FallsOR97601 United States Industrial Engineering Department BINUS Graduate Program—Master of Industrial Engineering Bina Nusantara University Jakarta11480 Indonesia

Metal-metal nanolaminates made by accumulative roll bonding (ARB) is a developing new class of structural nanocomposites that possesses high strength, good ductility, and can also be produced in bulk. These nanolaminates exhibit strong crystallographic textures and mechanical anisotropy. Yet, their mechanical properties are often measured only along rolling direction (RD). Using in situ pillar compression, we show that in-plane shear deformation mechanism in Cu(63 nm)/Nb(63 nm) ARB nanolaminate strongly depends on the shear direction. Plastic shear along the RD abruptly changes into crystallographic rotation and later into interface shear as the shear direction deviates away from the RD. The observed shear mechanisms are driven by competition between different slip systems in Cu layers and at the interface. We expect similar deformation anisotropy to happen in other ARB nanolaminates with sharp texture and interface orientation. Comprehensive characterization of such nanolaminates may require considering more than just the usual rolling/transverse/normal direction anisotropy. © 2022, The Authors. All rights reserved.

关键词： Anisotropy

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Fuzzy Decision Support Model for Human Resources Performance Appraisal 3

Fuzzy Decision Support Model for Human Resources Performance...

引用

3rd International Conference on Information Management and Technology, ICIMTech 2018

作者： Utama, Ditdit Nugeraha Rustamaji, Eri Computer Science Department Bina Nusantara University BINUS Graduate Program-Master of Computer Science Jakarta11480 Indonesia Information System Department Syarif Hidayatullah State Islamic University Jakart Indonesia

ISBN: (纸本)9781538658215

Human resources (HRs) performance appraisal is one of several parts of HRs planning. It plays the imperative role to encourage HRs to have a good spirit and become correctly loyal to institution. The major objective of research is to propose a constructed decision support model (DSM) for appraising the HRs performance. The methods object oriented, fuzzy logic, hill climbing, and survey are benefitted to be main methods of this study which respectively are used to analyze and design the constructed model, justify and analyze data values, optimize the suggested decision, and collect data. By scientifically taking into account four selected fundamental performance parameters (i.e. education, teaching capability, research, and community service), the study was conducted;where, the measurement of performance bonus for university lecturer is chosen as a research object. Specifically for collecting data, 35 university lecturers were occupied to estimate the significance level of parameters. The lecturers are coming from two faculties of UIN Syarif Hidayatullah (Jakarta, Indonesia);i.e. faculties of science and technology and communication. At last, the model is practically going to assist the decision makers to fairly assess HRs performance;and the study showed a simulation result of assessment based on forty empirical data of university lecturer. © 2018 IEEE.

关键词： Fuzzy logic

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Static Taint Analysis Traversal with Object Oriented Component for Web File Injection Vulnerability Pattern Detection 3

Static Taint Analysis Traversal with Object Oriented Compone...

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3rd International Conference on computer science and Computational Intelligence, ICCSCI 2018

作者： Kurniawan, Aditya Abbas, Bahtiar Saleh Trisetyarso, Agung Isa, Sani Muhammad Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia Industrial Engineering Department Faculty of Engineering Bina Nusantara University Jakarta11480 Indonesia

We introduce a composition of object-oriented component PHP grammar for taint analysis. Our novel method successfully restructured the PHP parser and reduced grammar artifact objects that must be visited in a taint analysis process by up to 52% grammar variation. Taint analysis is an analysis that detects any injection vulnerability pattern in source code. The analysis identifies the information flow of untrustworthy input that affects the sensitive sink or part of the system. The static taint analysis was run on an abstract syntax tree and traversed all nodes. A static taint analysis uses a parser to traverse abstract syntax trees of the source code. A web PHP parser has 140 grammar combinations in an abstract syntax tree, which has to be traversed to recognize the tainted flow pattern. Additionally, there are many variations of syntax and coding styles for tainted flow patterns. Therefore, the amount of combinations will consume many computation resources. © 2018 The Authors. Published by Elsevier Ltd.

关键词： Syntactics

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