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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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Ten quick tips for deep learning in biology

arXiv

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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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Development and evaluation of a hospital-wide healthcare-associated surgical site infection detection algorithm

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Journal of Microbiology, Immunology and Infection 2015年第2期48卷 S43-S43页

作者： Yi-Ju Tseng Bo-Chiang Huang Hui-Chi Lin Ming-Yuan Chen Rung-Ji Shang Wang-Huei Sheng Yee-Chun Chen Feipei Lai Shan-Chwen Chang Children's Hospital Informatics Program Boston Children's Hospital Boston MA USA Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan Center for Infection Control National Taiwan University Hospital (NTUH) Taiwan Information Systems Office NTUH Taipei Taiwan Department of Internal Medicine NTUH and College of Medicine Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan Department of Computer Science and Information Engineering National Taiwan University Taiwan

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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 "Automated parameter selection for accelerated MRI reconstruction via low-rank modeling of local k-space neighborhoods" [Z Med. Phys. 33 (2023) 203-219]

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Zeitschrift fur medizinische Physik 2024年第1期35卷 119-119页

作者： Efe Ilicak Emine Ulku Saritas Tolga Çukur Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Mannheim Germany National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara Turkey. Electronic address: efe.ilicak@medma.uni-heidelberg.de. National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara Turkey Department of Electrical and Electronics Engineering Bilkent University Ankara Turkey Neuroscience Program Bilkent University Ankara Turkey.

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QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

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Current Protocols in Bioinformatics 2020年第1期70卷 e100页

作者： Estaki, Mehrbod Jiang, Lingjing Bokulich, Nicholas A. McDonald, Daniel González, Antonio Kosciolek, Tomasz Martino, Cameron Zhu, Qiyun Birmingham, Amanda Vázquez-Baeza, Yoshiki Dillon, Matthew R. Bolyen, Evan Caporaso, J. Gregory Knight, Rob Department of Pediatrics University of California San Diego La Jolla CA United States Division of Biostatistics University of California San Diego La Jolla CA United States Center for Applied Microbiome Science Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ United States Department of Biological Sciences Northern Arizona University Flagstaff AZ United States Małopolska Centre of Biotechnology Jagiellonian University Kraków Poland Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA United States Center for Microbiome Innovation University of California San Diego La Jolla CA United States Center for Computational Biology and Bioinformatics University of California San Diego La Jolla CA United States Jacobs School of Engineering University of California San Diego La Jolla CA United States Department of Computer Science and Engineering University of California San Diego La Jolla CA United States Department of Bioengineering University of California San Diego La Jolla CA United States

QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses—e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://***. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://***. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data. Support Protocol: Further microbiome analyses. © 2020 The Authors.

关键词： bioinformatics metagenomics microbiome QIIME 2 Qiita

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Molybdenum Disulfide: Scalable Fabrication of Molybdenum Disulfide Nanostructures and their Assembly (Adv. Mater. 43/2020)

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Advanced Materials 2020年第43期32卷

作者： Yun Huang Kang Yu Huaizhi Li Kai Xu Zexi Liang Debora Walker Paulo Ferreira Peer Fischer Donglei (Emma) Fan Materials Science and Engineering Program Texas Materials Institute The University of Texas at Austin Austin TX 78712 USA The Department of Advanced Electron Microscopy Imaging and Spectroscopy International Iberian Nanotechnology Laboratory Braga 4715‐330 Portugal Electrical and Computer Engineering University of Illinois at Urbana‐Champaign Urbana IL 61801 USA School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA Mechanical Engineering Department and IDMEC Instituto Superior Técnico University of Lisbon Av. Rovisco Pais Lisboa 1049‐001 Portugal Max‐Planck‐Institute for Intelligent Systems Heisenbergstr. 3 Stuttgart 70569 Germany Institute of Physical Chemistry University of Stuttgart Pfaffenwaldring 55 Stuttgart 70569 Germany Walker Department of Mechanical Engineering The University of Texas at Austin Austin TX 78712 USA

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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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PERFORMANCE OF A PRIORITIZED ON-BOARD BASEBAND SWITCH FOR A MULTISERVICE MULTIBEAM SATELLITE

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INTERNATIONAL JOURNAL OF SATELLITE COMMUNICATIONS 1994年第3期12卷 283-297页

作者： BOHM, S ELHAKEEM, AK HACHICHA, M Department of Electrical and Computer Engineering Concordia University 1455 De Maisonneuve Blvd. West Montreal H3A 1M8 Canada Was born in Montreal Canada on 14 September 1966. He received the B. Eng. degree in electrical engineering from Concordia University Montreal Canada in 1989. He is at present completing the M.A.Sc. degree in electrical engineering at Concordia University. (S'75–S'79–M'79–SM'86) received the Ph.D. degree from Southern Methodist University Dallas TX in 1979. He spent the next two years working as a Visiting Professor in Egypt after which he moved to Ottawa Canada in 1982. He assumed teaching and research positions in Carleton and Manitoba Univerities and later moved to Concordia University Montreal Canada in 1983 where he is now a Professor in the Electrical and Computer Engineering Department. He has published numerous papers in IEEE and international journals in the areas of spread spectrum and networking. He is a well-known expert in these areas and serves as a consultant to many companies. His current research interests include wide-band metropolitan networks switching architectures and performance of on-board multibeam satellites acquisitionless CDMA networks code distribution and orthogonalization of CDMA signals responsive congestion control for ATM-based networks ARQ techniques and investigation of the novel SUGAR CDMA systems in fading channels. Dr. Elhakeem is a Senior Member of the Canadian Electrical Engineering Society and Armed Forces Association. He has chaired numerous technical sessions in IEEE Conferences was the Technical Program Chairman for IEEE Montech 1986 Montreal Canada. Dr. Elhakeem is the key guest editor of theIEEE Journal of Selected Areas in Communicationsfor the May June issues 1993 covering CDMA networks. Advanced Technology & Networks VISTAR Telecommunications Inc. Ottawa Ontario K1G 3J4 Canada An Associate Director of Advanced Technology & Networks Group VISTAR Telecommunications Inc. Ottawa Canada. He is also an Adjunct Pr

In this paper, we study the performance of a prioritized on-board baseband switch in conjunction with a multibeam satellite handling integrated services. The services considered for the analysis include voice, video, file transfer and interactive data. The prioritized switch uses both input and output buffering, switch speed-up as well as a two-phase head-of-line resolution algorithm, in order to reduce the buffer loss while maintaining acceptable user delays. The minimum required buffer capacity and switch speed-up for each service in a prioritized environment are found under uniform traffic conditions. It is shown that under uniform traffic conditions, only minimal buffering and switch speed-up are needed even for the lowest priority users. The performance dependence on the switch size is also substantially reduced with head of line resolution and buffering even in a prioritized environment.

关键词： SWITCH ON-BOARD BASEBAND MULTIBEAM PRIORITIZED HEAD-OF-LINE UNIFORM LOAD SPEED-UP

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Time-Varying ℓ₀ Optimization for Spike Inference from Multi-Trial Calcium Recordings

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Data Science in Science 2024年第1期3卷

作者： Shen, Tong Du, Mingyu Johnston, Kevin Grieco, Steven F. Crary, Rachel Guzowski, John F. Lur, Gyorgy Xu, Xiangmin Ombao, Hernando Guindani, Michele Yu, Zhaoxia Department of Statistics University of California Irvine 92697 CA United States Center for Complex Biological Systems University of California Irvine 92697 CA United States Department of Mathematics and The NSF-Simons Center for Multiscale Cell Fate Research University of California Irvine 92697 CA United States Department of Anatomy and Neurobiology School of Medicine University of California Irvine 92697 CA United States Department of Neurobiology and Behavior University of California Irvine 92697 CA United States The Center for the Neurobiology of Learning and Memory University of California Irvine 92697 CA United States Department of Biomedical Engineering University of California Irvine 92697 CA United States Department of Computer Science University of California Irvine 92697 CA United States The Center for Neural Circuit Mapping University of California Irvine 92697 CA United States Statistics Program KAUST Thuwal Saudi Arabia Department of Biostatistics University of California Los Angeles CA United States

Optical imaging of genetically encoded calcium indicators is a powerful tool to record the activity of a large number of neurons simultaneously over a long period of time from freely behaving animals. However, determining the exact time at which a neuron spikes and estimating the underlying firing rate from calcium fluorescence data remains challenging, especially for calcium imaging data obtained from a longitudinal study. We propose a multi-trial time-varying ℓ₀ penalized method to jointly detect spikes and estimate firing rates by robustly integrating evolving neural dynamics across trials. Our simulation study shows that the proposed method performs well in both spike detection and firing rate estimation. We demonstrate the usefulness of our method on calcium fluorescence trace data from two studies, with the first study showing differential firing rate functions between two behaviors and the second study showing evolving firing rate functions across trials due to learning. © 2024 The Author(s). Published with license by Taylor & Francis Group, LLC.

关键词： calcium imaging firing rate spike detection Time-varying penalty ℓ0 regularization

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