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arXiv 2020年

作者： Lei, Chon Lok Ghosh, Sanmitra Whittaker, Dominic G. Aboelkassem, Yasser Beattie, Kylie A. Cantwell, Chris D. Delhaas, Tammo Houston, Charles Novaes, Gustavo Montes Panfilov, Alexander V. Pathmanathan, Pras Riabiz, Marina Weber dos Santos, Rodrigo Worden, Keith Mirams, Gary R. Wilkinson, Richard D. Computational Biology & Health Informatics Dept. of Computer Science University of Oxford United Kingdom MRC Biostatistics Unit University of Cambridge United Kingdom Centre for Mathematical Medicine & Biology School of Mathematical Sciences University of Nottingham United Kingdom Department of Bioengineering University of California San Diego United States Systems Modeling and Translational Biology GlaxoSmithKline R&D Stevenage United Kingdom ElectroCardioMaths Programme Centre for Cardiac Engineering Imperial College London United Kingdom CARIM School for Cardiovascular Diseases Maastricht University Netherlands Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil Department of Physics and Astronomy Ghent University Belgium Laboratory of Computational Biology and Medicine Ural Federal University Ekaterinburg Russia U.S. Food and Drug Administration Center for Devices and Radiological Health Office of Science and Engineering Laboratories United States Department of Biomedical Engineering King’s College London Alan Turing Institute United Kingdom Dynamics Research Group Department of Mechanical Engineering University of Sheffield United Kingdom School of Mathematics and Statistics University of Sheffield United Kingdom

Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterise uncertainty in model inputs and how that propagates through to outputs or predictions. In this perspective piece we draw attention to an important and under-addressed source of uncertainty in our predictions — that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes (GPs) and autoregressive-moving-average (ARMA) models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. Copyright © 2020, The Authors. All rights reserved.

关键词： Uncertainty analysis

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Application of the conditional gradient method to a network resource allocation problem with several classes of users

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Journal of Physics: Conference Series 2019年第3期1158卷

作者： I V Konnov A Yu Kashuba Department of System Analysis and Information Technologies Kazan Federal University Kazan 420008 Russia Scientific Research Laboratory 'Computational Technologies and Computer Modeling' Institute of Computational Mathematics and Information Technologies Kazan Federal University Kazan 420008 Russia

We consider a general problem of optimal allocation of a limited resource in a telecommunication network. The users are divided into several different groups (or classes), which correspond to different levels of service. The network manager has to satisfy users requirements and maximize the network profit, which gives a convex optimization problem with balance and capacity constraints. We suggest to solve this problem with a two-level iterative method where the conditional gradient method is used at its upper level. Then we can solve the lower level problem with simple decomposition algorithms. The computational experiments show rather satisfactory convergence of the suggested method.

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OPTIMAL EXPERIMENTAL DESIGN FOR CONSTRAINED INVERSE PROBLEMS

arXiv

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arXiv 2017年

作者： Ruthotto, Lars Chung, Julianne Chung, Matthias Department of Mathematics and Computer Science Emory University AtlantaGA United States Department of Mathematics Computational Modeling and Data Analytics Division Academy of Integrated Science Virginia Tech BlacksburgVA United States

In this paper, we address the challenging problem of optimal experimental design (OED) of constrained inverse problems. We consider two OED formulations that allow to reduce the experimental costs by minimizing the number of measurements. The first formulation assumes a fine discretization of the design parameter space and uses sparsity promoting regularization to obtain an efficient design. The second formulation parameterizes the design and seeks optimal placement for these measurements by solving a small-dimensional optimization problem. We consider both problems in a Bayes risk as well as an empirical Bayes risk minimization framework. For the unconstrained inverse state problem, we exploit the closed form solution for the inner problem to efficiently compute derivatives for the outer OED problem. The empirical formulation does not require an explicit solution of the inverse problem and therefore allows to integrate constraints efficiently. A key contribution is an efficient optimization method for solving the resulting, typically high-dimensional, bilevel optimization problem using derivative-based methods. To overcome the lack of non-differentiability in active set methods for inequality constraints problems, we use a relaxed interior point method. To address the growing computational complexity of empirical Bayes OED, we parallelize the computation over the training models. Numerical examples and illustrations from tomographic reconstruction, for various data sets and under different constraints, demonstrate the impact of constraints on the optimal design and highlight the importance of OED for constrained problems.62K05, 65F22, 80M50 Copyright © 2017, The Authors. All rights reserved.

关键词： Constrained optimization

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CEPC Technical Design Report

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Radiation Detection Technology and Methods 2024年第1期8卷 I0003-I0016,1-1091页

作者： Waleed Abdallah Tiago Carlos Adorno de Freitas Konstantin Afanaciev Shakeel Ahmad Ijaz Ahmed Xiaocong Ai Abid Aleem Wolfgang Altmannshofer Fabio Alves Weiming An Rui An Daniele Paolo Anderle Stefan Antusch Yasuo Arai Andrej Arbuzov Abdesslam Arhrib Mustafa Ashry Sha Bai Yu Bai Yang Bai Vipul Bairathi Csaba Balazs Philip Bambade Yong Ban Tripamo Bandyopadhyay Shou-Shan Bao Desmond P.Barber Ayse Bat Varvara Batozskaya Subash Chandra Behera Alexander Belyaev Michele Bertucci Xiao-Jun Bi Yuanjie Bi Tianjian Bian Fabrizio Bianchi Thomas Biekotter Michela Biglietti Shalva Bilanishvili Deng Binglin Denis Bodrov Anton Bogomyagkov Serge Bondarenko Stewart Boogert Maarten Boonekamp Marcello Borri Angelo Bosotti Vincent Boudry Mohammed Boukidi Igor Boyko Ivanka Bozovic Giuseppe Bozzi Jean-Claude Brient Anastasiia Budzinskaya Masroor Bukhari Vladimir Bytev Giacomo Cacciapaglia Hua Cai Wenyong Cai Wujun Cai Yijian Cai Yizhou Cai Yuchen Cai Haiying Cai Huacheng Cai Lorenzo Calibbi Junsong Cang Guofu Cao Jianshe Cao Antoine Chance Xuejun Chang Yue Chang Zhe Chang Xinyuan Chang Wei Chao Auttakit Chatrabhuti Yimin Che Yuzhi Che Bin Chen Danping Chen Fuqing Chen Fusan Chen Gang Chen Guoming Chen Hua-Xing Chen Huirun Chen Jinhui Chen Ji-Yuan Chen Kai Chen Mali Chen Mingjun Chen Mingshui Chen Ning Chen Shanhong Chen Shanzhen Chen Shao-Long Chen Shaomin Chen Shiqiang Chen Tianlu Chen Wei Chen Xiang Chen Xiaoyu Chen Xin Chen Xun Chen Xurong Chen Ye Chen Ying Chen Yukai Chen Zelin Chen Zilin Chen Gang Chen Boping Chen Chunhui Chen Hok Chuen Cheng Huajie Cheng Shan Cheng Tongguang Cheng Yunlong Chi Pietro Chimenti Wen Han Chiu Guk Cho Ming-Chung Chu Xiaotong Chu Ziliang Chu Guglielmo Coloretti Andreas Crivellin Hanhua Cui Xiaohao Cui Zhaoyuan Cui Brunella D'Anzi Ling-Yun Dai Xinchen Dai Xuwen Dai Antonio De Maria Nicola De Filippis Christophe De La Taille Francesca De Mori Chiara De Sio Elisa Del Core Shuangxue Deng Wei-Tian Deng Zhi Deng Ziyan Deng Bhupal Dev Tang Dewen Biagio Di Micco Ran Ding Siqin Dingl Yadong Ding Haiyi Dong Jianin AGH University of Science and Technology Faculty of Physics and Applied Computer ScienceKrakow Anhui University HefeiAnhui Applied Physics Department Federal Urdu University of ArtsScience and TechnologyIslamabad Banaras Hindu University Institute of ScienceVaranasi Bandirma Onyedi Eylul University Bandirma Beihang University Beijing Beijing Computational Science Research Center Beijing Beijing Conveyi LTD Beijing Beijing Glass Research Institute Co. LtdBeijing Beijing Institute of Technology Beijing Beijing Normal University Beijing Brown University ProvidenceRI Budker Institute of Nuclear Physics Novosibirsk Cadi Ayyad University Laboratory of Fundamental and Applied PhysicsPolydisciplinary FacultyMarrakech Cairo University Giza Center for Theory and Computation National Tsing Hua UniversityHsinchu Central China Normal University WuhanHubei Central South University ChangshaHunan Centro de Fisica Teorica de Particulas Universidade Tecnica de LisboaLisboa Chengdu KaitengSifang Digital Radio&TV Equipment Co. LtdChengduSichuan China academy of engineering physics MianyangSichuan China building materials academy Beijing China Center of Advanced Science and Technology Beijing China Institute of Atomic Energy Beijing China Jiliang University HangzhouZhejiang China Nuclear Instrument CO. LTDBeijing China University of Geosciences Beijing China University of Geosciences WuhanHubei China University of Mining and Technology XuzhouJiangsu China West Normal University NanchongSichuan Chongqing University Department of PhysicsChongqing Chulalongkorn University Bangkok City University of Hong Kong Department of PhysicsHong Kong Cockcroft Institute Daresbury Cornell University IthacaNY CPPM(AMU/IPhU&CNRS/INP) Marseille Dalian Minzu University DalianLiaoning Dalian University of Technology Department of PhysicsDalian Deutsches Elektronen-Synchrotron DESY Hamburg Dzhelepov Laboratory of Nuclear Problems of Joint Institute for Nuclear Research(DLNP JINR) Dubna East China University Of Science And Technol

The Circular Electron Positron Collider(CEPC)is a large scientific project initiated and hosted by China,fostered through extensive collaboration with international *** complex comprises four accelerators:a 30 GeV Linac,a 1.1 GeV Damping Ring,a Booster capable of achieving energies up to 180 GeV,and a Collider operating at varying energy modes(Z,W,H,and tt).The Linac and Damping Ring are situated on the surface,while the subterranean Booster and Collider are housed in a 100 km circumference underground tunnel,strategically accommodating future expansion with provisions for a potential Super Proton Proton Collider(SPPC).The CEPC primarily serves as a Higgs *** its baseline design with synchrotron radiation(SR)power of 30 MW per beam,it can achieve a luminosity of 5×10^(34)cm^(-2)s^(-1)per interaction point(IP),resulting in an integrated luminosity of 13 ab^(-1)for two IPs over a decade,producing 2.6 million Higgs *** the SR power to 50 MW per beam expands the CEPC's capability to generate 4.3 million Higgs bosons,facilitating precise measurements of Higgs coupling at sub-percent levels,exceeding the precision expected from the HL-LHC by an order of *** Technical Design Report(TDR)follows the Preliminary Conceptual Design Report(Pre-CDR,2015)and the Conceptual Design Report(CDR,2018),comprehensively detailing the machine's layout,performance metrics,physical design and analysis,technical systems design,R&D and prototyping efforts,and associated civil engineering ***,it includes a cost estimate and a preliminary construction timeline,establishing a framework for forthcoming engineering design phase and site selection *** is anticipated to begin around 2027-2028,pending government approval,with an estimated duration of 8 *** commencement of experiments and data collection could potentially be initiated in the mid-2030s.

关键词： initiated exceeding precise

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The Automatic Learning for the Rapid Classification of Events (ALeRCE) alert broker

arXiv

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arXiv 2020年

作者： Förster, Francisco Cabrera-Vives, G. Castillo-Navarrete, E. Estévez, P.A. Sánchez-Sáez, P. Arredondo, J. Bauer, F.E. Carrasco-Davis, R. Catelan, M. Elorrieta, F. Eyheramendy, S. Huijse, P. Pignata, G. Reyes, E. Reyes, I. Rodríguez-Mancini, D. Ruz-Mieres, D. Valenzuela, C. Álvarez-Maldonado, I. Astorga, N. Borissova, J. Clocchiatti, A. de Cicco, D. Donoso-Oliva, C. Graham, M.J. Kurtev, R. Mahabal, A. Maureira, J.C. Molina-Ferreiro, R. Moya, A. Palma, W. Prez-Carrasco, M. Protopapas, P. Romero, M. Sabatini-Gacitua, L. Snchez, A. San Martín, J. Sepúlveda-Cobo, C. Vera, E. Vergara, J.R. Center for Mathematical Modeling University of Chile AFB170001 Chile Millennium Institute of Astrophysics Nuncio Monseñor Sótero Sanz 100 Providencia Santiago Chile Departamento de Astronomía Universidad de Chile Casilla 36D Santiago Chile Department of Computer Science University of Concepcin Chile Department of Electrical Engineering Universidad de Chile Av. Tupper 2007 Santiago8320000 Chile Instituto de Astrofísica Facultad de Física Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Department of Engineering and Science Universidad Adolfo Ibaez Av. Diagonal Las Torres 2700 Santiago Chile Centro de Astroingeniería Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Space Science Institute 4750 Walnut Street Suite 205 BoulderCO80301 United States Department of Mathematics and Computer Science Universidad de Santiago de Chile Av. Libertador Bernardo OHiggins 3663 Estación Central Santiago Chile Instituto de Informática Universidad Austral de Chile General Lagos 2086 Valdivia Chile Departamento de Ciencias Físicas Universidad Andres Bello Avda. Republica 252 Santiago Chile Institute of Astronomy University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Instituto de Física y Astronomía Universidad de Valparaíso Av. Gran Bretaña 1111 Playa Ancha Casilla5030 Chile Division of Physics Mathematics and Astronomy California Institute of Technology PasadenaCA91125 United States Center for Data Driven Discovery California Institute of Technology PasadenaCA91125 United States Institute for Applied Computational Science Harvard University CambridgeMA United States Departmento de Informática y Computación Universidad Tecnológica Metropolitana Santiago Chile

We introduce the Automatic Learning for the Rapid Classification of Events (ALeRCE) broker, an astronomical alert broker designed to provide a rapid and self–consistent classification of large etendue telescope alert streams, such as that provided by the Zwicky Transient Facility (ZTF) and, in the future, the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). ALeRCE is a Chilean–led broker run by an interdisciplinary team of astronomers and engineers, working to become intermediaries between survey and follow–up facilities. ALeRCE uses a pipeline which includes the real–time ingestion, aggregation, cross–matching, machine learning (ML) classification, and visualization of the ZTF alert stream. We use two classifiers: a stamp–based classifier, designed for rapid classification, and a light–curve–based classifier, which uses the multi–band flux evolution to achieve a more refined classification. We describe in detail our pipeline, data products, tools and services, which are made public for the community (see https://***). Since we began operating our real–time ML classification of the ZTF alert stream in early 2019, we have grown a large community of active users around the globe. We describe our results to date, including the real–time processing of 9.7×107 alerts, the stamp classification of 1.9 × 107 objects, the light curve classification of 8.5 × 105 objects, the report of 3088 supernova candidates, and different experiments using LSST-like alert streams. Finally, we discuss the challenges ahead to go from a single-stream of alerts such as ZTF to a multi–stream ecosystem dominated by LSST. Copyright © 2020, The Authors. All rights reserved.

关键词： Surveys

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Adaptive resolution molecular dynamics technique: Down to the essential

arXiv

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arXiv 2018年

作者： Krekeler, Christian Agarwal, Animesh Junghans, Christoph Praprotnik, Matej Site, Luigi Delle Institute for Mathematics Freie Universität Berlin Germany Theoretical Biology and Biophysics Group Los Alamos National Laboratory Los AlamosNM87545 United States Computer Computational and Statistical Sciences Division Los Alamos National Laboratory Los AlamosNM87545 United States Laboratory for Molecular Modeling National Institute of Chemistry Hajdrihova 19 LjubljanaSI-1001 Slovenia Department of Physics Faculty of Mathematics and Physics University of Ljubljana Jadranska 19 LjubljanaSI-1000 Slovenia Theoretical Biology and Biophysics Group Los Alamos National Laboratory Los AlamosNM87545 United States

We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region. Copyright © 2018, The Authors. All rights reserved.

关键词： Ionic liquids

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Correction: CEPC Technical Design Report: Accelerator

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Radiation Detection Technology and Methods 2024年第1期9卷 184-192页

作者： Abdallah, Waleed de Freitas, Tiago CarlosAdorno Afanaciev, Konstantin Ahmad, Shakeel Ahmed, Ijaz Ai, Xiaocong Aleem, Abid Altmannshofer, Wolfgang Alves, Fabio An, Weiming An, Rui Anderle, Daniele Paolo Antusch, Stefan Arai, Yasuo Arbuzov, Andrej Arhrib, Abdesslam Ashry, Mustafa Bai, Sha Bai, Yu Bai, Yang Bairathi, Vipul Balazs, Csaba Bambade, Philip Ban, Yong Bandyopadhyay, Triparno Bao, Shou-Shan Barber, Desmond P. Bat, Ays¸e Batozskaya, Varvara Behera, Subash Chandra Belyaev, Alexander Bertucci, Michele Bi, Xiao-Jun Bi, Yuanjie Bian, Tianjian Bianchi, Fabrizio Bieko¨tter, Thomas Biglietti, Michela Bilanishvili, Shalva Binglin, Deng Bodrov, Denis Bogomyagkov, Anton Bondarenko, Serge Boogert, Stewart Boonekamp, Maarten Borri, Marcello Bosotti, Angelo Boudry, Vincent Boukidi, Mohammed Boyko, Igor Bozovic, Ivanka Bozzi, Giuseppe Brient, Jean-Claude Budzinskaya, Anastasiia Bukhari, Masroor Bytev, Vladimir Cacciapaglia, Giacomo Cai, Hua Cai, Wenyong Cai, Wujun Cai, Yijian Cai, Yizhou Cai, Yuchen Cai, Haiying Cai, Huacheng Calibbi, Lorenzo Cang, Junsong Cao, Guofu Cao, Jianshe Chance, Antoine Chang, Xuejun Chang, Yue Chang, Zhe Chang, Xinyuan Chao, Wei Chatrabhuti, Auttakit Che, Yimin Che, Yuzhi Chen, Bin Chen, Danping Chen, Fuqing Chen, Fusan Chen, Gang Chen, Guoming Chen, Hua-Xing Chen, Huirun Chen, Jinhui Chen, Ji-Yuan Chen, Kai Chen, Mali Chen, Mingjun Chen, Mingshui Chen, Ning Chen, Shanhong Chen, Shanzhen Chen, Shao-Long Chen, Shaomin Chen, Shiqiang Chen, Tianlu Chen, Wei Chen, Xiang Chen, Xiaoyu Chen, Xin Chen, Xun Chen, Xurong Chen, Ye Chen, Ying Chen, Yukai Chen, Zelin Chen, Zilin Chen, Boping Chen, Chunhui Cheng, Hok Chuen Cheng, Huajie Cheng, Shan Cheng, Tongguang Chi, Yunlong Chimenti, Pietro Chiu, Wen Han Cho, Guk Chu, Ming-Chung Chu, Xiaotong Chu, Ziliang Coloretti, Guglielmo Crivellin, Andreas Cui, Hanhua Cui, Xiaohao Cui, Zhaoyuan D’Anzi, Brunella Dai, Ling-Yun Dai, Xinchen Dai, Xuwen De Maria, Antonio De Filippis, Nicola De La Taille, Christophe De Mori, Francesca De Sio, Chiara Del Core, Elisa Deng, Cairo University Giza Egypt Xi’an Jiaotong-Liverpool University Suzhou China Institute of Power Engineering of National Academy of Sciences of Belarus Minsk Belarus Pakistan Institute of Nuclear Science and Technology (PINSTECH) Islamabad Pakistan Applied Physics Department Science and Technology Federal Urdu University of Arts Islamabad Pakistan Zhengzhou University Zhengzhou China Institute of High Energy Physics Chinese Academy of Sciences Beijing China University of California Santa Cruz Santa Cruz USA Nanjing University Nanjing China Beijing Normal University Beijing China Harvard University Cambridge USA South China Normal University Guangzhou China University of Basel Basel Switzerland High Energy Accelerator Research Organization (KEK) Tsukuba Japan Joint Institute for Nuclear Research Dubna Russia Faculty of Sciences and Techniques Université Abdelmalek Essaadi Tangier Morocco Southeast University Nanjing China Department of Physics University of Wisconsin–Madison Madison USA Instituto de Alta Investigación Universidad de Tarapacá Arica Chile Monash University Melbourne Australia Laboratoire de Physique des 2 infinis Irène Joliot-Curie – IJCLab Orsay France Peking University Beijing China Department of Physics and Nanotechnology SRM Institute of Science and Technology Kattankulathur India Shandong University Jinan China University of New Mexico Albuquerque USA Bandirma Onyedi Eylul University Bandırma Turkey National Centre for Nuclear Research Warsaw Poland Indian Institute of Technology Madras (IN) Chennai India University of Southampton Southampton UK INFN Milano - LASA Segrate Italy Sun Yat-Sen University Guangzhou China China Institute of Atomic Energy Beijing China INFN-University of Torino Turin Italy Karlsruhe Institute of Technology Institute for Theoretical Physics Karlsruhe Germany INFN-Sezione di Roma Tre Rome Italy Kutaisi International University Kutaisi Georgia Soochow University Suzhou China Budker Institute

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Randomized reference models for temporal networks

arXiv

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arXiv 2018年

作者： Gauvin, Laetitia Génois, Mathieu Karsai, Márton Kivelä, Mikko Takaguchi, Taro Valdano, Eugenio Vestergaard, Christian L. Data Science Lab ISI Foundation Turin Italy Aix Marseille Univ. Univ. Toulon CNRS CPT Marseille France Department of Network and Data Science Central European University Vienna1100 Austria Université de Lyon ENS de Lyon INRIA CNRS LIP UMR 5668 IXXI Lyon69364 Cedex 07 France Alfréd Rényi Insititute of Mathematics BudapestH-1053 Hungary Department of Computer Science Aalto University School of Science P.O. Box 12200 AaltoFI-00076 Finland National Institute of Information and Communications Technology 4-2-1 Nukui-Kitamachi Koganei Tokyo184-8795 Japan Center for Biomedical Modeling The Semel Institute for Neuroscience and Human Behavior David Geffen School of Medicine University of California Los Angeles 760 Westwood Plaza Los AngelesCA90024 United States Decision and Bayesian Computation Department of Computational Biology Department of Neuroscience CNRS USR 3756 UMR 3571 Institut Pasteur 25 rue du Docteur Roux Paris75015 France

Many dynamical systems can be successfully analyzed by representing them as networks. Empirically measured networks and dynamic processes that take place in these situations show heterogeneous, non-Markovian, and intrinsically correlated topologies and dynamics. This makes their analysis particularly challenging. Randomized reference models (RRMs) have emerged as a general and versatile toolbox for studying such systems. Defined as random networks with given features constrained to match those of an input (empirical) network, they may for example be used to identify important features of empirical networks and their effects on dynamical processes unfolding in the network. RRMs are typically implemented as procedures that reshuffle an empirical network, making them very generally applicable. However, the effects of most shuffling procedures on network features remain poorly understood, rendering their use non-trivial and susceptible to misinterpretation. Here we propose a unified framework for classifying and understanding microcanonical RRMs (MRRMs) that sample networks with uniform probability. Focusing on temporal networks, we survey applications of MRRMs found in literature, and we use this framework to build a taxonomy of MRRMs that proposes a canonical naming convention, classifies them, and deduces their effects on a range of important network features. We furthermore show that certain classes of MRRMs may be applied in sequential composition to generate new MRRMs from the existing ones surveyed in this article. We finally provide a tutorial showing how to apply a series of MRRMs to analyze how different network features affect a dynamic process in an empirical temporal network. Our taxonomy provides a reference for the use of MRRMs, and the theoretical foundations laid here may further serve as a base for the development of a principled and automatized way to generate and apply randomized reference models for the study of networked systems. Copyright © 2018,

关键词： Taxonomies

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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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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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