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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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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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SHIPBOARD DAMAGED STABILITY ASSESSMENT - THE FLOODING CASUALTY CONTROL SOFTWARE

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NAVAL ENGINEERS JOURNAL 1993年第3期105卷 152-166页

作者： ZAHN, PB ROSBOROUGH, J CARLSTROM, R Peter B. Zahn:is a section chief in the Naval Architecture Department at Advanced Marine Enterprises. He is responsible for software development and special trials support. He has led the Flooding Casualty Control Software (FCCS) development effort since joining AME in 1989. He is also responsible for the material handling strikedown and stowage (MHS&S) software development program as well as special trials support for the ACVLAP and T-AGOS 19 programs. Prior to joining AME Mr. Zahn spent nine years with various companies of the ARCTEC Group. His experience includes field trials in venues from the Caribbean to the Bering Sea as well as model tests and engineering design and development efforts. Mr. Zahn received his B.S. in naval architecture and marine engineering from Webb Institute in 1980 and has published various papers on pollution prevention offshore systems and icebreaker design and performance. He is a member of ASNE and SNAME. John Rosborough:has been a naval architect for the Naval Sea Systems Command (NavSea) for the past 15 years. He is currently assigned to the Hydrodynamics Division with responsibility for aircraft carrier stability evaluations and as a task leader for computer-aided ship design development. In the Stability Division he was previously responsible for stability analyses on various amphibious ships SWATHs and foreign ships. He manages the upgrade and augmentation of SHCP at NavSea and is the Navy's technical point of contact for evaluating shipboard stability software and transitioning technology to the fleet. Mr. Rosborough received his B.S. in naval architecture and marine engineering from the University of Michigan in 1977. He is a member of USNI and the Association of Scientists and Engineers at NavSea. Richard Carlstrom:is a naval architect with Advanced Marine Enterprises. He has been responsible for software development in support of a variety of major programs including FCCS and SHCP and is a specialist in stability evaluations for complex ships such as CVs CVNs

The Flooding Casualty Control Software (FCCS) was developed under the auspices of the Naval Sea systems Command (NavSea) and is currently being deployed on a variety of ships in the neets of both the U.S. Navy and the U.S. Coast Guard. The primary objective of FCCS is to enable damage control personnel to identify critical stability conditions, especially when related to the loss of reserve buoyancy due to battle damage and the destabilizing effects of large quantities of firefighting water, in a timely manner. FCCS was initially deploved in 1990. It utilizes the standard algorithms of the Ship Hull Characteristics program (SHCP). The user interface was designed to allow quick familiarity for shipboard users, primarily the damage control assistant (DCA) and his staff. Intact stability evaluations include the effects of topside icing, high winds, personnel crowding, heavy lifts over the side, high speed turns, and towing. FCCS also supports ballasting analysis for amphibious ships as well as providing bottom reaction and beached stability data for grounding incidents. Bv providing a tool for the ''fuel king'' and DCA to generate the required daily updates on the current ship load and liquids status, FCCS is assured of an accurate baseline in the event of damage. The design allows the evaluation of the ultimate ship stability status for a damage event using simple compartmentation and flooding status inputs. Evaluation of the adequacy of resulting stabilitv, as well as identification of such critical stability parameters as off center loading, margin line immersion, and negative GM, are accomplished by the program. Guidance is provided for the user to initiate appropriate flooding related damage control activities. Initially fitted on USS Oliver Hazard Perry Class frigates, FCCS databases have been for the USCG Hamilton class high endurance cutters, USS Arleigh Burke class Aegis destroyers, and a variety of other U.S. Navy and U.S. Coast Guard ship classes. The progra

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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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MODELING AND CONTROL OF ELEVATORS BY STATECHARTS

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Asian Journal of Control 2008年第2期6卷

作者： Yi-Sheng Huang Sheng-Luen Chung Mu-Der Jeng Department of Aeronautical Engineering Chung Cheng Institute of Technology National Defense University Tashi Taoyuan 335 Taiwan R.O.C. Department of Electrical Engineering National Taiwan University of Science and Technology Taipei 106 Taiwan R.O.C. Department of Electrical Engineering National Taiwan Ocean University Kellung 202 Taiwan R.O.C. MuDer Jeng received the Ph.D. degree in computer and systems engineering from Rensselaer Polytechnic Institute Troy NY in 1992. Since August 1992 Dr. Jeng has been with National Taiwan Ocean University Keelung Taiwan where he is currently a full Professor at the Department of Electrical Engineering. His current research interests include Petri nets discrete event systems computer integrated manufacturing semiconductor factory automation embedded systems. Dr. Jeng is the author/co-author of over 120 book chapters journal papers and conference papers. Dr. Jeng received the Franklin V. Taylor Outstanding Paper Award from the IEEE Systems Man and Cybernetics Society in 1993. He was granted the Research Award by the National Science Council of Taiwan annually from 1994 to 2000. He is an Associate Editor for IEEE Transactions on Systems Man and Cybernetics-Part A IEEE Transactions on Robotics and Automation IEEE Transactions on Robotics and serves on the Editorial Board of International Journal of Computer Integrated Manufacturing. He has been a Guest Editor for eight leading journals. Dr. Jeng is the Chair of the Technical Committee on Discrete Event Systems of the IEEE SMC Society and the Founding Chair of the Technical Committee on Semiconductor Factory Automation of the IEEE Robotics and Automation Society. He served as the Exhibitions Chair of 2003 IEEE International Conference on Robotics and Automation and the Special Sessions Chair of 2004 IEEE International Conference on Networking Sensing and Control. He serves as a Program Co-Chair of 2005 IEEE International Conference on Networking Sensing and Control and the Organization Commit

Statechart has been utilized as a visual formalism for the modeling of complex and interactive systems for its illuminating features on describing properties of causality, concurrency, and synchronization. This paper presents the application of satechart to the modeling, design and implementation of an elevator system, whose system behavior involves aggregating complexity of state descriptions, and imposition of underlying control policy. Based on the operational flow of an elevator, we derive the associated statechart model by looking into the inherent hierarchical structure of the elevator. The advantage of the proposed approach is the clear presentation of system behavior in terms of conditions and events that cause the transitions in system dynamics. Implementation of the controlled elevator based on the modeled statechart is also presented.

关键词： Statechart interactive systems elevator

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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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FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

arXiv

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arXiv 2023年

作者： Lekadir, Karim Feragen, Aasa Fofanah, Abdul Joseph Frangi, Alejandro F. Buyx, Alena Emelie, Anais Lara, Andrea Porras, Antonio R. Chan, An-Wen Navarro, Arcadi Glocker, Ben Botwe, Benard O. Khanal, Bishesh Beger, Brigit Wu, Carol C. Cintas, Celia Langlotz, Curtis P. Rueckert, Daniel Mzurikwao, Deogratias Fotiadis, Dimitrios I. Zhussupov, Doszhan Ferrante, Enzo Meijering, Erik Weicken, Eva González, Fabio A. Asselbergs, Folkert W. Prior, Fred Krestin, Gabriel P. Collins, Gary S. Tegenaw, Geletaw S. Kaissis, Georgios Misuraca, Gianluca Tsakou, Gianna Dwivedi, Girish Kondylakis, Haridimos Jayakody, Harsha Woodruf, Henry C. Mayer, Horst Joachim Aerts, Hugo JWL Walsh, Ian Chouvarda, Ioanna Buvat, Irène Tributsch, Isabell Rekik, Islem Duncan, James Kalpathy-Cramer, Jayashree Zahir, Jihad Park, Jinah Mongan, John Gichoya, Judy W. Schnabel, Julia A. Kushibar, Kaisar Riklund, Katrine Mori, Kensaku Marias, Kostas Amugongo, Lameck M. Fromont, Lauren A. Maier-Hein, Lena Alberich, Leonor Cerdá Rittner, Leticia Phiri, Lighton Marrakchi-Kacem, Linda Donoso-Bach, Lluís Martí-Bonmatí, Luis Cardoso, M. Jorge Bobowicz, Maciej Shabani, Mahsa Tsiknakis, Manolis Zuluaga, Maria A. Bielikova, Maria Fritzsche, Marie-Christine Camacho, Marina Linguraru, Marius George Wenzel, Markus De Bruijne, Marleen Tolsgaard, Martin G. Ghassemi, Marzyeh Ashrafuzzaman, Md Goisauf, Melanie Yaqub, Mohammad Abadía, Mónica Cano Mahmoud, Mukhtar M.E. Elattar, Mustafa Rieke, Nicola Papanikolaou, Nikolaos Lazrak, Noussair Díaz, Oliver Salvado, Olivier Pujol, Oriol Sall, Ousmane Guevara, Pamela Gordebeke, Peter Lambin, Philippe Brown, Pieta Abolmaesumi, Purang Dou, Qi Lu, Qinghua Osuala, Richard Nakasi, Rose Zhou, S. Kevin Napel, Sandy Colantonio, Sara Albarqouni, Shadi Joshi, Smriti Carter, Stacy Klein, Stefan Petersen, Steffen E. Aussó, Susanna Awate, Suyash Raviv, Tammy Riklin Cook, Tessa Mutsvangwa, Tinashe E.M. Rogers, Wendy A. Niessen, Wiro J. Puig-Bosch, Xènia Zeng, Yi Mohammed, Yunusa G. Aquino, Yves Saint James Salahuddin, Zohaib Starmans, Martijn P.A. Department de Matemàtiques i Informàtica Universitat de Barcelona Barcelona Spain Barcelona Spain DTU Compute Technical University of Denmark Kgs Lyngby Denmark Department of Mathematics and Computer Science Faculty of Science and Technology Milton Margai Technical University Freetown Sierra Leone Center for Computational Imaging & Simulation Technologies in Biomedicine Schools of Computing and Medicine University of Leeds Leeds United Kingdom Cardiovascular Science and Electronic Engineering Departments KU Leuven Leuven Belgium Institute of History and Ethics in Medicine Technical University of Munich Munich Germany Faculty of Engineering of Systems Informatics and Sciences of Computing Galileo University Guatemala City Guatemala Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Anschutz Medical Campus AuroraCO United States Department of Medicine Women’s College Research Institute University of Toronto Toronto Canada Universitat Pompeu Fabra BarcelonaBeta Brain Research Center Barcelona Spain Department of Computing Imperial College London London United Kingdom School of Biomedical & Allied Health Sciences University of Ghana Accra Ghana Department of Midwifery & Radiography School of Health & Psychological Sciences City University of London United Kingdom Kathmandu Nepal European Heart Network Brussels Belgium Department of Thoracic Imaging University of Texas MD Anderson Cancer Center Houston United States IBM Research Africa Nairobi Kenya Departments of Radiology Medicine and Biomedical Data Science Stanford University School of Medicine Stanford United States Institute for AI and Informatics in Medicine Klinikum rechts der Isar Technical University Munich Munich Germany Department of Computing Imperial College London London United Kingdom Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania United Republic of Ioannina Greece Almaty AI Lab Almaty Kazakhstan

Background: Despite major advances in artificial intelligence (AI) research for healthcare, the deployment and adoption of AI technologies remain limited in clinical practice. In recent years, concerns have been raised about the clinical, technical, ethical and legal risks associated with healthcare AI. To increase adoption in the real world, it is essential that AI technologies are trusted and accepted by patients, clinicians, health organisations and authorities. This paper describes the FUTURE-AI framework as the first international consensus guideline for trustworthy AI in healthcare. Methods: The FUTURE-AI consortium was founded in 2021 and now comprises 117 interdisciplinary experts from 50 countries representing all continents, including AI scientists, clinical researchers, biomedical ethicists, and social scientists. Over a two-year period, the consortium established guiding principles and best practices for trustworthy and deployable AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. Findings: The FUTURE-AI framework was established based on six guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 30 best practices were defined, addressing technical, clinical, socio-ethical and legal dimensions of trustworthy AI. The recommendations cover the entire lifecycle of healthcare AI, from design, development and validation to regulation, deployment, and monitoring. Interpretation: FUTURE-AI is a structured, risk-informed framework which provides guidance for constructing healthcare AI tools that will be trusted, deployed and adopted in real-world clinical practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of healthcare AI. Copyright © 2023, The Authors. All rights

关键词： Clinical research

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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THE NO FRAME CONCEPT - ITS IMPACT ON SHIPYARD COST

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NAVAL ENGINEERS JOURNAL 1984年第3期96卷 218-232页

作者： NAPPI, NS WALZ, RW WIERNICKI, CJ Natale S. Nappi:graduated from City College of New York in 1954 with a B.S. degree in civil engineering and received his M.S. in civil engineering from the Polytechnic Institute of Brooklyn in 1959. He began his professional career in 1954 at the New York Naval Shipyard as a naval architect (structures) performing detail structural design and fabrication studies for CVAs LPDs DDs and CGs and eventually became a supervisory naval architect (structures). From 1965 to 1973 he was a member of the staff of the Computer-Aided Design Division at the David Taylor Naval Ship Research and Development Center (DTNSRDC). As such he was involved in the development of the computer structural design tool the SSDP (in association with Frank M. Lev) and automated detail design programs (CASDOS). His current position is Senior Naval Architect Consultant in the structural integrity group of the Ship Structures Division Structures Department DTNSRDC. Mr. Nappi is the author and co-author of numerous technical papers and reports covering a wide spectrum of topics such as automated structural design process design for producibility and survivability material weight and cost trade-off studies and structural weight determination for high performance ships (i.e. SES SWATH HYSWAS). He has lectured on the subjects of design for survivability and ship structures at the Naval Post Graduate School and MIT. He is a member of ASNE ASCE U.S. Naval Institute Sigma Xi and is a registered Professional Engineer in the State of New York. Mr. Nappi was a member of the NAVSEA working commitee for the computer supported design planning effort and is currently a member of the DTNSRDC ASSET Advisory Committee. Ronald W. Walz:graduated in 1974 from Pennsylvania State University with a B.S. degree in civil engineering. He began his professional career in 1974 at the David Taylor Naval Ship Research and Development Center as a structural engineer in the structural design concepts group of the Ship Structures Division Structures Department.

A proposed cost effective alternative to current U.S. Navy structurally configured hulls is presented in this paper. This proposed design for producibility concept involves the elimination of structural stanchions and transverse web frames. The potential impact of this “no frame” concept on structural design, weight and construction and material costs for naval surface frigates and destroyers is reflected in 1) reduced costs for the installation of distributive systems and 2) a reduced number and complexity of structural details providing a more reliable and less costly structure. This study was performed in three parts: 1) Determine the most feasible length between bulkheads without frames; 2) Using this length perform detail weight studies and construction and material costs analysis comparison on a 72-foot long hull module, with and without frames, for a FFG-7, and 3) Estimate the saving in man hours of labor on the installation of distributive systems and shipfitting for an FFG-7. For the feasible length studies on the “no frame” structural configuration, thirty-seven strength, weight and vertical center of gravity studies were performed on two ship classes; twenty-two on the FFG-7 class and fifteen on the DD-963 class. The detailed weight studies and construction and material cost analyses were conducted for FFG-7 “no frame” and “as built” modules. Results indicating the “no frame” concept module was 6.8% heavier and 14.8% less costly than the “as built” module. For the impact of an FFG-7 “no frame” structurally configured hull on the cost of labor required for the installation of distributive systems and for other functional work such as ship fitting, welding, and electrical, this study indicated a reduction of 169,206 labor hours per ship, representing 7.12% of the total required man hours to fabricate an FFG-7 class ship. With the employment of the “no frame” concept, certain areas of significant concern and potential risk were addressed. These include: 1) t

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Corrigendum to: Spatial Topography of Individual-Specific Cortical Networks Predicts Human Cognition, Personality and Emotion

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Cerebral cortex (New York, N.Y. : 1991) 2021年第8期31卷 3974页

作者： Ru Kong Jingwei Li Csaba Orban Mert R Sabuncu Hesheng Liu Alexander Schaefer Nanbo Sun Xi-Nian Zuo Avram J Holmes Simon B Eickhoff B T Thomas Yeo Department of Electrical and Computer Engineering ASTAR-NUS Clinical Imaging Research Centre Singapore Institute for Neurotechnology and Memory Networks Program National University of Singapore Singapore. School of Electrical and Computer Engineering Cornell University Ithaca NY USA. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. CAS Key Laboratory of Behavioral Sciences and Research Center for Lifespan Development of Brain and Mind (CLIMB) Institute of Psychology Beijing China. University of Chinese Academy of Sciences Beijing China. Department of Psychology Yale University New Haven CT USA. Institute for Systems Neuroscience Medical Faculty Heinrich-Heine University Düsseldorf Düsseldorf Germany. Institute of Neuroscience and Medicine Brain & Behaviour (INM-7) Research Center Jülich Jülich Germany. Centre for Cognitive Neuroscience DukeNUS Medical School Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore.

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