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arXiv 2021年

作者： Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others. © 2021, CC BY.

关键词： Learning algorithms

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Author Correction: Generation of accurate, expandable phylogenomic trees with uDance

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Nature biotechnology 2024年第5期42卷 814页

作者： Metin Balaban Yueyu Jiang Qiyun Zhu Daniel McDonald Rob Knight Siavash Mirarab Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. Biodesign Center for Fundamental and Applied Microbiomics Arizona State University Tempe AZ USA. School of Life Sciences Arizona State University Tempe AZ USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Bioengineering University of California San Diego La Jolla CA USA. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Department of Computer Science and Engineering Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. smirarab@ucsd.edu.

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RETROFITTING OF BULBOUS BOWS ON UNITED-STATES NAVY AUXILIARY AND AMPHIBIOUS WARSHIPS

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NAVAL ENGINEERS JOURNAL 1984年第6期96卷 40-51页

作者： CHUN, SK HOUGH, JJ ENGLE, AH FUNG, SC Stephen K. Chunis a graduate of the Maritime College of the State University of New York class of 1981 from which he received a B.E. degree in naval architecture and his license as a Third Assistant Engineer from the U.S. Coast Guard. Since graduation he has worked for the U.S. Navy as a naval architect with the Hull Form and Hydrodynamics Performance Division (SEA 55W3) of the Naval Sea Systems Command. Currently he is the task leader for hydrodynamic design for the DDG-51. He is also responsible for bulbous bow and appendage design for surf ace ships. Mr. Chun is a member of ASNE SNAME and ASE. Jeffrey J. Hough:is currently a naval architect with the Hull Form and Hydrodynamic Performance Division (SEA 55VV3) of the Naval Sea Systems Command (NA VSEA). In his current capacity he is a member of the Surface Ship Hydrodynamics Branch and is the divisional coordinator for computer supported design (CSD) technical director for the hull form design system (HFDS) Hull Engineering Group (SEA 55) assistant coordinator for CSD SEA 55 CSD coordinator for the DDG-51 contract design and SEA 55W3 project engineer for aircraft carrier/aviation support ship hydrodynamics. Mr. Hough received his B.S.E. degree in naval architecture and marine engineering in 1978 and his M.S.E. degree in naval architecture and marine engineering in 1979 from the University of Michigan. He began his career with the U.S. Navy in 1979 as an Engineer-in-Training in the Ship Design and Integration Directorate of NAVSEA. Prior to his current assignment Mr. Hough was the technical director responsible for the hull form and hydrodynamics energy conservation program and technical specialist for design practices for resistance and powering margins and hull form geometry. A member of ASNE since 1979 Mr. Hough is also a member of SNAME ASE and the U.S. Naval Institute. Allen H. Engleis a naval architect with the Hull Form Design and Performance Division of the Naval Sea Systems Command. He received his B.S. degree in engineering science from th

To meet energy conservation goals of the U.S. Navy, its attention has been focused on ways to reduce individual ship total resistance and powering requirements. One possible method of improving ship powering characteristics is by modifying existing individual ship hulls with the addition of bulbous bows. This paper will identify the merits of retrofitting bow bulbs on selected U.S. Navy auxiliary and amphibious warfare ships. A procedure for performing a cost-benefit analysis will be shown for candidate ship classes. An example of this technique for an amphibious warfare ship will also be provided. A brief discussion of future methods to be used for bulbous bow design such as application of systematic model test data and numerical hydrodynamic techniques will be given.

关键词： NAVAL VESSELS

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Web based testing application security system using semantic comparison method

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IOP Conference Series: Materials Science and engineering 2018年第1期420卷

作者： Akbar Iskandar Muhammad Resa Fahlepi Tuasamu Suryadi Syamsu M Mansyur Tri Listyorini Sulfikar Sallu S Supriyono Kundharu Saddhono Darmawan Napitupulu Robbi Rahim Informatics Engineering STMIK AKBA Makassar Indonesia. Graduate Program Universitas Negeri Makassar Makassar Indonesia. Informatics Engineering Universitas Maria Kudus Central Java Indonesia. Computer Information Systems Universitas Sembilan Belas November Kolaka Indonesia. Department of Geography Education Universitas Prof Dr Hazairin SH Bengkulu Indonesia. Indonesian Language Education Departement Faculty of Teacher Training and Education Universitas Sebelas Maret Surakarta Indonesia. Research Center for Quality System and Testing Technology Indonesian Institute of Sciences Indonesia. Sekolah Tinggi Ilmu Manajemen Sukma Medan Indonesia

computer and web security system is an attempt to avoid attacks from crackers because a form and method of crime on internet network can not be predicted. Therefore, we just keep trying to use various methods in securing the system that is running. It is the same in web testing that can be accessed online by people who are not responsible from along distance to change and remove the test results or even damage the web testing system. So, the purpose of this paper is to design and implement web security testing system by using semantic comparison method to avoid structured query language injection (SQLI) attack and to do security on web testing application using Message Digest 5 encryption (MD5). Research data were obtained by using direct observation and documentation and literature review. After the design and application of the system, it can be obtained that by using semantic comparison method in web testing can prevent the occurrence of SQL injection attacks and can secure account from web testing users by using MD5.

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THE STRUCTURAL SYNTHESIS DESIGN program - ITS IMPACT ON THE FLEET

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NAVAL ENGINEERS JOURNAL 1983年第3期95卷 87-99页

作者： WIERNICKI, CJ GOODING, TG NAPPI, NS Mr. Christopher J. Wiernicki:graduated from Vanderbilt University in 1980 with a B.E. degree in Structural Engineering. Upon graduation he began his professional career at the David Taylor Naval Ship Research and Development Center. As a structural engineer in the Surface Ship Structures Division Mr. Wiernicki was responsible for developing improved methods and procedures for designing and evaluating structural systems for surf ace combatants. Specific projects included design for producibility development and evaluation of automated ship structural design methods and participation in the structural design of the CG 49 Cruiser and the current DDG 51 Destroyer. In 1982 Mr. Wiernicki received his M.S. degree in Ocean Engineering from George Washington University. Mr. Wiernicki is a recipient of the SNAME 1982-82 Graduate Scholarship and is currently doing post graduate work in Naval Architecture at Massachusetts Institute of Technology he is a member of ASNE SNAME ASCE and Chi Epsilon. Mr. Thomas G. Gooding:graduated in 1975 from the University of Michigan with B.S. degrees in Oceanography and Naval Architecture. After graduation he began his professional career at the Naval Ship Engineering Center (NA VSEC) as a structural engineer. From 1975 till 1978 Mr. Gooding worked in the area of ship dry docking and was the structural task leader on the complex overhaul ofUSS Long Beach (CGN-9). Mr. Gooding returned to the University of Michigan to receive a M.S. in Naval Architecture in 1979. Currently Mr. Gooding is the structural task leader on the DDGX/DDG 51 program at the Naval Sea Systems Command (NAVSEA). Mr. Gooding is a member of SNAME and the Naval Institute. Mr. Natale S. Nappi:graduated from City College of New York in 1954 with a Bachelor of Civil Engineering and received his M.S. in Civil Engineering from Polytechnic Institute of Brooklyn in 1959. He began his professional career in 1964 at the New York Naval Shipyard as a Naval Architect (Structure) performing detail structural design and fabrication s

The structural design of a ship's section is a complicated, repetitive and time consuming task. With the advent of new technology, high speed computers have enabled the ship designer to accomplish in a matter of seconds what would formerly take days to accomplish by hand. The Structural Synthesis Design program (SSDP) is a N avy developed computer-aided design tool which is used to design (or to analyze) the longitudinal scantlings for a variety of ship cross sections, consisting of any practical combinations of decks, platforms, bulkheads and materials, i.e., various steel and aluminum alloys. The final hull section design will have the lowest practical weight for the chosen geometric configuration, structural arrangements, and imposed loadings. The scantling developed by the program will satisfy all U.S. N avy ship structural design criteria. An explanation of the objective and design elements of N avy ship structures is included. The rationale behind the SSDP design philosophy is developed along with the significant program capabilities. In an attempt to highlight the influence of automated design procedures on the current naval ship design process, the effect of the SSDP on the DDG 51 destroyer structural development is addressed.

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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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Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

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Nature computational science 2023年第7期3卷 658页

作者： Gengjie Jia Yu Li Xue Zhong Kanix Wang Milton Pividori Rabab Alomairy Aniello Esposito Hatem Ltaief Chikashi Terao Masato Akiyama Koichi Matsuda David E Keyes Hae Kyung Im Takashi Gojobori Yoichiro Kamatani Michiaki Kubo Nancy J Cox James Evans Xin Gao Andrey Rzhetsky Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China. jiagengjie@***. Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong People's Republic of China. Department of Medicine and Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN US. Department of Medicine Institute of Genomics and Systems Biology Committee on Genomics Genetics and Systems Biology University of Chicago Chicago IL US. Department of Operations Business Analytics and Information Systems University of Cincinnati Cincinnati OH US. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA US. Extreme Computing Research Center Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. College of Computer Science and Engineering University of Jeddah Jeddah Saudi Arabia. HPE HPC/AI EMEA Research Laboratory Bristol UK. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Clinical Research Center Shizuoka General Hospital Shizuoka Japan. Department of Applied Genetics The School of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan. Department of Ophthalmology Graduate School of Medical Sciences Kyushu University Fukuoka Japan. Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan. Biological and Environmenta

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

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Genome biology 2016年第1期17卷 78页

作者： Paul Muir Shantao Li Shaoke Lou Daifeng Wang Daniel J Spakowicz Leonidas Salichos Jing Zhang George M Weinstock Farren Isaacs Joel Rozowsky Mark Gerstein Department of Molecular Cellular and Developmental Biology Yale University New Haven CT 06520 USA. Systems Biology Institute Yale University West Haven CT 06516 USA. Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven CT 06520 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. mark@***. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. mark@***. Department of Computer Science Yale University New Haven CT 06520 USA. mark@***.

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