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Application of XGBoost algorithm in classification of 28 types of cancer based on ctDNA mutations

AIP Conference Proceedings 2024年第1期2970卷

作者： Favorisen R. Lumbanraja Rachelia Dita Anggraini Yohana Tri Utami Rosma Hasibuan Computer Science Study Program Faculty of Mathematics and Natural Sciences University of Lampung Jl. Prof. Dr. Sumantri Brojonegoro No. 1 Bandar Lampung 35145 Indonesia Department of Agrotechnology Faculty of Agriculture University of Lampung Jl. Prof. Dr. Sumantri Brojonegoro No. 1 Bandar Lampung 35145 Indonesia

Circulating Tumor DNA (ctDNA) in blood samples of cancer patients contains components for the diagnosis of cancer. These components when combined with bioinformatics using machine learning algorithms can facilitate the classification of cancer. Extreme gradient boosting (XGBoost) is an ensemble learning method that works by combining basic models to produce an optimal predictive model. This study aims to determine the results of the XGBoost algorithm classification using somatic mutations and copy number changes that occur in ctDNA. This study performs a classification using XGBoost with two types of cross-validation, 10-fold and holdout cross-validation, using data from Soh et al., 2017 [1]. For holdout cross-validation, training and testing data will be divided into 60:40, 70:30, 75:25, 80:20, and 90:10. Each classification experiment conducted in this study was tested using two types of data, namely data with overall features and data with the top 900 features as a result of feature selection. The highest accuracy result was obtained by XGBoost holdout cross-validation 90:10 using 900 features with an accuracy value of 89.91%, while the lowest accuracy value was obtained by XGBoost 10-fold cross-validation 900 features, which was 70.01%. The accuracy value tends to be higher in the 900-feature experiment compared to the overall feature. The holdout cross-validation experiment gets a better accuracy value than the 10-fold cross-validation experiment. For holdout cross-validation, the greater the percentage of training data, the higher the accuracy obtained.

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*** - A plug-and-play solution for online systems medicine and network-based drug repurposing

arXiv

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arXiv 2023年

作者： Maier, Andreas Hartung, Michael Abovsky, Mark Adamowicz, Klaudia Bader, Gary D. Baier, Sylvie Blumenthal, David B. Chen, Jing Elkjaer, Maria L. Garcia-Hernandez, Carlos Helmy, Mohamed Hoffmann, Markus Jurisica, Igor Kotlyar, Max Lazareva, Olga Levi, Hagai List, Markus Lobentanzer, Sebastian Loscalzo, Joseph Malod-Dognin, Noel Manz, Quirin Matschinske, Julian Mee, Miles Oubounyt, Mhaned Pico, Alexander R. Pillich, Rudolf T. Poschenrieder, Julian M. Pratt, Dexter Pržulj, Nataša Sadegh, Sepideh Saez-Rodriguez, Julio Sarkar, Suryadipto Shaked, Gideon Shamir, Ron Trummer, Nico Turhan, Ugur Wang, Ruisheng Zolotareva, Olga Baumbach, Jan Institute for Computational Systems Biology University of Hamburg Hamburg Germany Division of Orthopaedic Surgery Schroeder Arthritis Institute Data Science Discovery Centre Osteoarthritis Research Program Krembil Research Institute UHN Toronto Canada Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network 60 Leonard Avenue 5KD-407 TorontoONM5T 0S8 Canada Department of Molecular Genetics University of Toronto TorontoON Canada The Donnelly Centre University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada Princess Margaret Cancer Centre University Health Network TorontoON Canada The Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital TorontoON Canada TUM School of Life Sciences Technical University of Munich Munich Germany Erlangen91052 Germany Department of Medicine University of California San Diego 9500 Gilman Drive La Jolla CA92093 United States Department of Neurology Odense University Hospital Odense Denmark Institute of Clinical Research University of Southern Denmark Odense Denmark Institute of Molecular Medicine University of Southern Denmark Odense Denmark Barcelona08034 Spain Institute for Advanced Study Lichtenbergstrasse 2a GarchingD-85748 Germany Technical University of Munich Germany National Institute of Diabetes Digestive and Kidney Diseases BethesdaMD20892 United States Departments of Medical Biophysics and Computer Science University of Toronto Toronto Canada Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia Heidelberg69120 Germany Heidelberg Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg69117 Germany Blavatnik School of Computer Science Tel-Aviv University Tel-Aviv Israel Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany Department of Medicine Bri

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce ***, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, *** turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, *** has been successfully integrated with 21 computational systems medicine tools. Available at https://***, *** has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research. © 2023, CC BY.

关键词： Data visualization

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Nonreciprocal transport in a bilayer of MnBi2Te4 and Pt

arXiv

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arXiv 2022年

作者： Ye, Chen Xie, Xiangnan Lv, Wenxing Huang, Ke Yang, Allen Jian Jiang, Sicong Liu, Xue Zhu, Dapeng Qiu, Xuepeng Tong, Mingyu Zhou, Tong Hsu, Chuang-Han Chang, Guoqing Lin, Hsin Li, Peisen Yang, Kesong Wang, Zhenyu Jiang, Tian Wang, Xiao Renshaw Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore State Key Laboratory of High Performance Computing College of Computer Science and Technology National University of Defense Technology Changsha410073 China Physics Laboratory Industrial Training Center Shenzhen Polytechnic Guangdong Shenzhen518055 China Department of NanoEngineering Program of Chemical Engineering University of California La Jolla San DiegoCA92093-0448 United States Program of Materials Science and Engineering University of California La Jolla San DiegoCA92093-0418 United States Institutes of Physical Science and Information Technology Anhui University Hefei230601 China Fert Beijing Institute MIIT Key Laboratory of Spintronics School of Integrated Circuit Science and Engineering Beihang University Beijing100191 China Beihang-Goertek Joint Microelectronics Institute Qingdao Research Institute Beihang University Qingdao266000 China Shanghai Key Laboratory of Special Artificial Microstructure Materials and Technology School of Physics Science and Engineering Tongji University Shanghai200092 China College of Advanced Interdisciplinary Studies National University of Defense Technology Changsha410073 China Insitute of Physics Academia Sinica Taipei115229 Taiwan College of Intelligence Science and Technology National University of Defense Technology Changsha410073 China National Innovation Institute of Defense Technology Academy of Military Sciences PLA China Beijing100010 China Beijing Academy of Quantum Information Sciences Beijing100084 China Beijing Institute for Advanced Study National University of Defense Technology Changsha410073 China School of Electrical and Electronic Engineering Nanyang Technological University 50 Nanyang Ave 639798 Singapore

MnBi2Te4 (MBT) is the first intrinsic magnetic topological insulator with the interaction of spin-momentum locked surface electrons and intrinsic magnetism, and it exhibits novel magnetic and topological phenomena. Recent studies suggested that the interaction of electrons and magnetism can be affected by the Mn-doped Bi2Te3 phase at the surface due to inevitable structural defects. Here we report an observation of nonreciprocal transport, i.e. current-direction-dependent resistance, in a bilayer composed of antiferromagnetic MBT and nonmagnetic Pt. The emergence of the nonreciprocal response below the Néel temperature confirms a correlation between nonreciprocity and intrinsic magnetism in the surface state of MBT. The angular dependence of the nonreciprocal transport indicates that nonreciprocal response originates from the asymmetry scattering of electrons at the surface of MBT mediated by magnon. Our work provides an insight into nonreciprocity arising from the correlation between magnetism and Dirac surface electrons in intrinsic magnetic topological insulators. © 2022, CC BY.

关键词： Magnetism

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In silico analysis of tetrahydroxycurcumin compound in tumeric (Curcuma longa) as inhibitor of SARS-CoV-2 virus replication

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AIP Conference Proceedings 2023年第1期2748卷

作者： Mohamad Amin Nanda Hilda Khikmawati Suryadi Suryadi Rifcha Fachrunnisa Ihya Fakhrurizal Amin Dina Maulina Ahya Zhilalikbar Amin Nik Ahmad Nizam Nik Malek Restu Fitriani Department of Biology Faculty of Mathematics and Natural Sciences Universitas Negeri Malang Jl. Semarang No.5 Malang 65145 Indonesia Special Education Department Faculty of Education Universitas Negeri Malang Jl. Semarang No.5 Malang 65145 Indonesia Faculty of Medicine Universitas Indonesia Jakarta Indonesia Biology Education Study Program Faculty of Teacher Training and Education Universitas Lampung Lampung Indonesia Department of Biosciences Faculty of Science Universiti Teknologi Malaysia Johor Malaysia Study Program of Informatics Engineering Faculty of Computer Sciencies Universitas Brawijaya Malang Indonesia Biotechnology Program Faculty of Mathematics and Natural Sciences Universitas Negeri Malang Jl. Semarang No.5 Malang 65145 Indonesia

There are many uses of natural ingredients to find out their potential in overcoming Coronavirus Disease 2019. One of the plants that is often used to treat various diseases, including SARS-Cov2 infection is turmeric. Turmeric contains Tetrahydroxycurcumin compounds. The aim of this research was to study the potential of Tetrahydroxycurcumin in preventing infection with the SARS-CoV-2 virus. The results showed that Tetrahydroxicurcumin has the potential to inhibit Tyrosine protein kinase ABL1, which is a protein that plays a role in the preparation of the cytoskeleton during viral infection. The binding affinity of Tetrahydroxycurcumin for this protein is -8.4 kcal/mol.

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Retraction: Sylabus and Matrials Design for Vocational Student and Its Dissemination Using Website (J. Phys.: Conf. Ser. 1114 012023)

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Journal of Physics: Conference Series 2018年第1期1114卷

作者： Astro Julida Harahap Ongko, Erianto Manurung, Hotler Kurnia, Dian Hartono, H Dahlan Abdullah Cut Ita Erliana Saddhono, Kundharu Rianita, Dian Setiawan, Muhammad Ikhsan Yuliyanto, Budi Setiawan Manurung, Rosida Tiurma Sriadhi, S Sinurat, Mangasi Siregar, Aisyah Rapat Piter Soni Hutauruk Sibarani, Nico Benjamain 1 Department of Informatics Akademi Teknologi Industri Immanuel Medan Indonesia Department of Computer Systems Universitas Pancabudi Medan Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Graduate Program Universitas Sebelas Maret Surakarta Indonesia Department of Administration University of Lancang Kuning Pekanbaru Indonesia Department of Law Universitas Tompotika Luwuk Banggai Indonesia Study Program of Communication Studies Universitas Semarang Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia STIE Bina Karya Tebing Tinggi Indonesia

This paper was retracted by IOP Publishing on 12 December 2018. This paper was published due to a technical error and was not intended to be included in this journal.Retraction published: 8 February 2019

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Application of Message Security Application Using Vigenere Cipher Algorithm Utilizing One Time Pad (OTP) Algorithm as a Key Generator

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Journal of Physics: Conference Series 2019年第1期1363卷 012080-012080页

作者： Pardede, A M H Lorena Perbina Br Sitepu Zarlis, Muhammad Tulus Iskandar, Akbar Sriadhi, S Manurung, Rosida Tiurma Nurintan Asyiah Siregar Sari, Ayu Esteka Yunawati, Sri Mursyidah, M Mursalin, M Kurniasih, Nuning Kurniawan, Citra Winarno, Edy STMIK Kaputama Binjai Sumatera Utara Indonesia Department of Computer Science Universitas Sumatera Utara Medan Indonesia Department of Mathematics Universitas Sumatera Utara Medan Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Management STIE Labuhanbatu Sumatera Utara Indonesia Department of Management STIE Sakti Alam Kerinci Jambi Indonesia Program Study of Accounting Pasir Pengaraian University Riau Indonesia Departement of Information Technology and Computer Politeknik Negeri Lhokseumawe Aceh Indonesia Department of Mathematics Education Universitas Malikussaleh Aceh Indonesia Faculty of Communication Sciences Library and Information Science Program Universitas Padjadjaran Bandung Indonesia Department of Electrical Engineering Sekolah Tinggi Teknik Malang Indonesia Faculty of Information Technology Universitas Stikubank Semarang Indonesia

Cryptography is the science and art of maintaining the security of messages when messages are sent from one place to another. One of the ways securing the form of text message information is by the encryption process using the Vigenere Cipher algorithm and utilizing the One Time Pad (OTP) algorithm as a key generator, where the message will be random when it is opened. The message encryption process used the vigenere cipher algorithm while OTP is used to secure the key with the same formula. After this research has been done, an application was designed to secure text messages by converting the text message into a random message so that the message was unreadable due to a secret message that could not be known by others. The results achieved can secure an encrypted message that cannot be reopened and if those messages were reopened, they must be decrypted.

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Sylabus and Matrials Design for Vocational Student and Its Dissemination Using Website

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Journal of Physics: Conference Series 2018年第1期1114卷

作者： Astro Julida Harahap Erianto Ongko Hotler Manurung Dian Kurnia H Hartono Dahlan Abdullah Cut Ita Erliana Hardianto Djanggih Kundharu Saddhono Dian Rianita Muhammad Ikhsan Setiawan Yuliyanto Budi Setiawan Rosida Tiurma Manurung S Sriadhi Mangasi Sinurat Aisyah Siregar Rapat Piter Soni Hutauruk Nico Benjamain Sibarani Department of Informatics Akademi Teknologi Industri Immanuel Medan Indonesia Department of Computer Systems Universitas Pancabudi Medan Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Law Universitas Tompotika Luwuk Banggai Indonesia Graduate Program Universitas Sebelas Maret Surakarta Indonesia Department of Administration University of Lancang Kuning Pekanbaru Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia Study Program of Communication Studies Universitas Semarang Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia STIE Bina Karya Tebing Tinggi Indonesia

The learners' needs are an important factor in designing syllabus and materials design, this research deals with the syllabus and material design based on the professional's needs. It is expected that the syllabus and materials designes are communicatively applicable to the professional academy. Descriptive method is applied in this research. The sample of this research is 30 students of ATII Immanuel Academy Medan. They were selected by random sampling to get the data, the questioners were administered to students. the questioners consisted of 54 items and the semi structured interview consisted of 5 questions, the finding indicated that learners' needs were focused on reading and speaking skills. With reference appropriately and proportionally derived for students of the Professional Academy. Further on the basis of the syllabus, materials are designed in which the skills of using language become a priority. The results of this research will be disseminated using the website

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Identification of types of tree damage based on forest health monitoring (FHM) in the management of TAHURA WAR utilization blocks

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AIP Conference Proceedings 2024年第1期2970卷

作者： Rahmat Safe’i Rico Andrian Tri Maryono Sepia Tapasya Tri Rizky Putra Master of Forestry Study Program Forestry Department Faculty of Agriculture University of Lampung Jl. Prof. Dr. Ir. Soemantri Brodjonegoro No. 1 Bandar Lampung Lampung 35145 Indonesia Dept. Computer Science Faculty of Mathematics and Natural Science University of Lampung Jl. Prof. Dr. Ir. Soemantri Brodjonegoro No. 1 Bandar Lampung Lampung 35145 Indonesia Plant Protection Study Program Faculty of Agriculture University of Lampung Jl. Prof. Dr. Ir. Soemantri Brodjonegoro No. 1 Bandar Lampung Lampung 35145 Indonesia Departement of Forestry Faculty of Agriculture University of Lampung Jl. Prof. Dr. Ir. Soemantri Brodjonegoro No. 1 Bandar Lampung Lampung 35145 Indonesia

Regarding management, TAHURA WAR is divided into blocks, one of which is the utilization block. In this block, the community can carry out utilization and use of forest areas. One of the causes of forest use by the community in this block is damage to trees due to high human activities or other concomitant causes. This study aimed to identify the damage to trees based on FHM in the TAHURA WAR utilization block. This research was conducted on five FHM cluster plots of utilization blocks that have been built. Identification is made by measuring and analyzing trees’ location, type, and severity based on the FHM method. The results showed 14 varieties of tree damage from 345 trees. The most common types of damage found were open wounds (code 03) with 162 trees and cancer (code 01) with 78 trees with an average severity of 20-29%. The two types of tree damage were often found at the location of the lower bole (code 3) and lower and upper bole (code 4), with the status of the level of tree damage in the moderate category (6.7 – 9.9). Thus, in the TAHURA WAR utilization block, two dominant types of tree damage were identified. This condition resulted in a considerable decrease in the quantity and quality of wood in the TAHURA WAR utilization block.

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Perception analysis of the Indonesian society on twitter social media on the increase in BPJS kesehatan contribution in the Covid 19 pandemic era

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Journal of Physics: Conference Series 2021年第1期1722卷

作者： F C Permana Z M Wicaksono C Kurniawan A S Abdullah B N Ruchjana Study Program of Multimedia Education Universitas Pendidikan Indonesia Jl. Dr. Setiabudi No.229 Bandung 40154 Indonesia. Student of Master of Management Program Universitas Padjadjaran Jl. Raya Bandung Sumedang km 21 Jatinangor Sumedang 45363 Indonesia. Department of Computer Science Universitas Padjadjaran Jl. Raya Bandung Sumedang km 21 Jatinangor Sumedang 45363 Indonesia. Department of Mathematics Universitas Padjadjaran Jl. Raya Bandung Sumedang km 21 Jatinangor Sumedang 45363 Indonesia.

In the conditions of the Covid-19 Pandemic, the president of Indonesia, Ir Joko Widodo, on May 13, 2020, announced an increase in BPJS Kesehatan contribution. This announcement made everyone in the community boisterous, including Indonesians on social media twitter. Currently, Indonesia is ranked fifth in the world using social media twitter, so data mining on Twitter is a good opportunity to see the public's response to a developing issue. This paper will discuss perceptions analysis of the Indonesian people on social media regarding the issue of increasing the contribution of BPJS Kesehatan. The issue of increasing the contribution of BPJS Kesehatan has been a topic of conversation on Twitter for a long time. After 30 days of data crawling, 145,359 tweets were obtained. This amount of data proves that the Indonesian people are very active in issuing opinions regarding the issue of increasing contribution BPJS Kesehatan. Various kinds of differences of opinion in each conversation are classified into three types of opinion using the Naive Bayes method. The three types of opinions are classified into positive opinions, negative opinions, and neutral opinions. The opinion classification results obtained were 73% containing negative opinions, 18% positive opinions, and 9% neutral opinions. This can serve as an early warning for the government to see the public's response in every policy taken. So that each policy can be evaluated for the better.

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ARCTIC TRAFFICABILITY program - A REVIEW

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NAVAL ENGINEERS JOURNAL 1984年第3期96卷 169-175页

作者： VOELKER, R GLEN, IF SEIBOLD, F BAYLY, I Richard Voelker:is Vice President of ARCTEC Incorporated a firm specializing in cold regions technology. He has been responsible for the management of thePolarClass Traffic-ability Program since its inception and annually participates in the field data collection in the Arctic. His prior experience includes positions with the U.S. Coast Guard in the icebreaker design project the Military Sealift Command and at Newport News Shipbuilding. He is a graduate of N. Y.S. Maritime College and has a MS degree from the University of Michigan. I.F. Glen:received his professional degrees in naval architecture from the Royal Naval Engineering College Manadon Plymouth and RN College Greenwich London entering the Royal Corps of Naval Constructors in 1967. After serving as a Constructor Lieutenant in the Royal Navy's Far East Fleet for a short period he joined the Polaris submarine project team in Bath England in 1968. In 1971 he was seconded to the Canadian Department of National Defense in Ottawa as a Constructor Lieutenant Commander under NATO exchange arrangements where he had responsibilities initially for conventional submarines and latterly for computer aided conceptual design. He ventured to Bath England in 1974 and joined Forward Design Group. In 1975 he took a position as a civilian engineer in the Canadian Defense Department and was Head of Hull Systems Engineering from 1977 to 1979. He joined ARCTEC CANADA LIMITED in 1980 and in addition to managing ice model testing projects and full scale trials has specialized in structural response of ships to ice impact. He headed ARCTEC's Kanata Laboratory from 1981 to 1983 when he was promoted to president. Frederick Seibold:is a research program manager with the Maritime Administration's Office of Advanced Ship Development and Technology. He is responsible for the marine science program which includes research in the areas of ship powering structures and propeller performance and Arctic technology. Mr. Seibold has been employed by Mar Ad since 1961 having hel

This paper describes a multiyear program to make an operational assessment on the feasibility of a year-round Arctic marine transportation system to serve Alaska. Specifically, the three objectives were to: collect meteorological and ice data along potential marine routes; instrument the hull and propulsion machinery to improve design critera for ice-worthy ships; and demonstrate that ships can operate in midwinter Alaskan Arctic ice conditions. The U.S. Coast Guard's Polar class icebreakers were used to make the operational assessment by annually extending the route northward and by operating throughout the winter season. This paper reviews some of the operational and technical achievements to date, as well as plans for future Arctic deployments.

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