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Linked data Crowdsourcing Quality Assessment based on Domain Professionalism

Journal of Physics: Conference Series 2019年第5期1187卷

作者： Lu Yang Li Huang Zhenzhen Liu School of Computer Science and Technology Wuhan University of Science and Technology Wuhan 430065 China Key Laboratory of Intelligent Information Processing and Real-time Industrial System in Hubei Province Wuhan 430065 China Institute of Big Data Science and Engineering Wuhan University of Science and Technology Wuhan 430065 China Key Laboratory of Rich-media Knowledge Organization and Service of Digital Publishing Content National Press and Publication Administration Beijing 100038 China

With the rapid development of Internet technology, crowdsourcing, as a flexible, effective and low-cost problem-solving method, has begun to receive more and more attention. The use of crowdsourcing to evaluate the quality of linked data has also become a research hotspot. This paper proposes the concept of Domain Specialization Test (DST), which uses domain professional testing tasks DSTs to evaluate the professionalism of workers, and combines the idea of Mini-batch Gradient Descent (MBGD) to improve the EM algorithm, and the MBEM algorithm is proposed to achieve efficient and accurate evaluation of task results. The experimental results show that the proposed method can screen out the appropriate workers for the linked data crowdsourcing task and improve the accuracy and iteration efficiency of the results.

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Emergency Event Matching using Hierarchical Blocking Method

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Journal of Physics: Conference Series 2019年第5期1187卷

作者： Chang Wen Yu Liu College of Computer Science and Technology Wuhan University of Science and Technology Wuhan 430065 China Key Laboratory of Intelligent Information Processing and Real-time Industrial System in Hubei Province Wuhan 430065 China Institute of Big Data Science and Engineering Wuhan University of Science and Technology Wuhan 430065 China Key Laboratory of Rich-media Knowledge Organization and Service of Digital Publishing Content National Press and Publication Administration Beijing 100038 China

With the extensive application of the knowledge base (KB), how to complete it is a hot topic on Semantic Web. However, many problems go with the big data, and the event matching is one of these problems, which is finding out the entities referring to the same things in the real world and also the key point in the extending process. To enrich the emergency knowledge base (E-SKB) we constructed before, we need to filter out the news from several web pages and find the same news to avoid data redundancy. In this paper, we proposed a hierarchy blocking method to reduce the times of comparisons and narrow down the scope by extracting the news properties as the blocking keys. The method transforms the event matching problem into a clustering problem. Experimental results show that the proposed method is superior to the existing text clustering algorithm with high precision and less comparison times.

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Global climate

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Bulletin of the American Meteorological Society 2020年第8期101卷 S9-S128页

作者： Dunn, R.J.H. Stanitski, D.M. Gobron, N. Willett, K.M. Met Office Hadley Centre Exeter United Kingdom NOAA/OAR Earth System Research Laboratories Boulder Colorado European Commission Joint Research Centre Ispra Italy Met Office Hadley Centre Exeter United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland Met Office Hadley Centre Exeter United Kingdom University of Reading Reading United Kingdom Department of Atmospheric and Planetary Science Hampton University Hampton Virginia NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina University of Bremen Bremen Germany NOAA/OAR Earth System Research Laboratories Boulder Colorado Centro de Investigaciones sobre Desertificación - Spanish National Research Council Moncada (Valencia) Spain and Regional Climate Group Department of Earth Sciences University of Gothenburg Gothenburg Sweden Instituto de Geografía Pontificia Universidad Católica de Valparaíso Valparaíso Chile NOAA/OAR ESRL Global Monitoring Laboratory Boulder Colorado Department of Civil and Environmental Engineering Princeton University Princeton New Jersey Global Precipitation Climatology Centre Deutscher Wetterdienst Offenbach Germany University of Reading Reading United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom National Oceanography Centre Southampton United Kingdom School of Engineering Newcastle University Newcastle-upon-Tyne United Kingdom Université de Paris Institut de physique du globe de Paris CNRS IGN Paris France and ENSG-Géomatique IGN Marne-la-Vallée France Global Modeling and Assimilation Office NASA Goddard Space Flight Center Greenbelt Maryland Sorbonne Université Paris France Universität Hamburg Hamburg Germany Department of Meteorology University of Reading Reading United Kingdom Geology Department University Centre in Svalbard Longyearbyen Norway Jet Propulsion Laboratory California Institute of Technology Wrightwood Calif

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Reconstruction of hidden representation for robust feature extraction

arXiv

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arXiv 2017年

作者： Zeng, Y.U. Tianrui, L.I. Ning, Y.U. Yi, P.A.N. Chen, Hongmei Bing, L.I.U. Southwest Jiaotong University School of Information Science and Technology National Engineering Laboratory of Integrated Transportation Big Data Application Technology Chengdu611756 China College at Brockport State University of New York Department of Computing Sciences BrockportNY14420 United States Georgia State University Department of Computer Science AtlantaGA30302 United States University of Illinois at Chicago Department of Computer Science ChicagoIL60607 United States

This paper aims to develop a new and robust approach to feature representation. Motivated by the success of Auto-Encoders, we first theoretically analyze and summarize the general properties of all algorithms that are based on traditional Auto-Encoders: 1) The reconstruction error of the input can not be lower than a lower bound, which can be viewed as a guiding principle for reconstructing the input. Additionally, when the input is corrupted with noises, the reconstruction error of the corrupted input also can not be lower than a lower bound. 2) The reconstruction of a hidden representation achieving its ideal situation is the necessary condition for the reconstruction of the input to reach the ideal state. 3) Minimizing the Frobenius norm of the Jacobian matrix of the hidden representation has a deficiency and may result in a much worse local optimum value. We believe that minimizing the reconstruction error of the hidden representation is more robust than minimizing the Frobenius norm of the Jacobian matrix of the hidden representation. Based on the above analysis, we propose a new model termed Double Denoising Auto-Encoders (DDAEs), which uses corruption and reconstruction on both the input and the hidden representation. We demonstrate that the proposed model is highly flexible and extensible and has a potentially better capability to learn invariant and robust feature representations. We also show that our model is more robust than Denoising Auto-Encoders (DAEs) for dealing with noises or inessential features. Furthermore, we detail how to train DDAEs with two different pre-training methods by optimizing the objective function in a combined and separate manner, respectively. Comparative experiments illustrate that the proposed model is significantly better for representation learning than the state-of-the-art models. Copyright © 2017, The Authors. All rights reserved.

关键词： Jacobian matrices

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Author Correction: Federated learning enables big data for rare cancer boundary detection

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Nature communications 2023年第1期14卷 436页

作者： Sarthak Pati Ujjwal Baid Brandon Edwards Micah Sheller Shih-Han Wang G Anthony Reina Patrick Foley Alexey Gruzdev Deepthi Karkada Christos Davatzikos Chiharu Sako Satyam Ghodasara Michel Bilello Suyash Mohan Philipp Vollmuth Gianluca Brugnara Chandrakanth J Preetha Felix Sahm Klaus Maier-Hein Maximilian Zenk Martin Bendszus Wolfgang Wick Evan Calabrese Jeffrey Rudie Javier Villanueva-Meyer Soonmee Cha Madhura Ingalhalikar Manali Jadhav Umang Pandey Jitender Saini John Garrett Matthew Larson Robert Jeraj Stuart Currie Russell Frood Kavi Fatania Raymond Y Huang Ken Chang Carmen Balaña Jaume Capellades Josep Puig Johannes Trenkler Josef Pichler Georg Necker Andreas Haunschmidt Stephan Meckel Gaurav Shukla Spencer Liem Gregory S Alexander Joseph Lombardo Joshua D Palmer Adam E Flanders Adam P Dicker Haris I Sair Craig K Jones Archana Venkataraman Meirui Jiang Tiffany Y So Cheng Chen Pheng Ann Heng Qi Dou Michal Kozubek Filip Lux Jan Michálek Petr Matula Miloš Keřkovský Tereza Kopřivová Marek Dostál Václav Vybíhal Michael A Vogelbaum J Ross Mitchell Joaquim Farinhas Joseph A Maldjian Chandan Ganesh Bangalore Yogananda Marco C Pinho Divya Reddy James Holcomb Benjamin C Wagner Benjamin M Ellingson Timothy F Cloughesy Catalina Raymond Talia Oughourlian Akifumi Hagiwara Chencai Wang Minh-Son To Sargam Bhardwaj Chee Chong Marc Agzarian Alexandre Xavier Falcão Samuel B Martins Bernardo C A Teixeira Flávia Sprenger David Menotti Diego R Lucio Pamela LaMontagne Daniel Marcus Benedikt Wiestler Florian Kofler Ivan Ezhov Marie Metz Rajan Jain Matthew Lee Yvonne W Lui Richard McKinley Johannes Slotboom Piotr Radojewski Raphael Meier Roland Wiest Derrick Murcia Eric Fu Rourke Haas John Thompson David Ryan Ormond Chaitra Badve Andrew E Sloan Vachan Vadmal Kristin Waite Rivka R Colen Linmin Pei Murat Ak Ashok Srinivasan J Rajiv Bapuraj Arvind Rao Nicholas Wang Ota Yoshiaki Toshio Moritani Sevcan Turk Joonsang Lee Snehal Prabhudesai Fanny Morón Jacob Mandel Konstantinos Kamnitsas Ben Glocker Luke V M Dixon Matthew Williams Peter Zamp Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA. Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Informatics Technical University of Munich Munich Bavaria Germany. Intel Corporation Santa Clara CA USA. Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany. Clinical Cooperation Unit Neuropathology German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Neuropathology Heidelberg University Hospital Heidelberg Germany. Division of Medical Image Computing German Cancer Research Center Heidelberg Germany. Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany. Neurology Clinic Heidelberg University Hospital Heidelberg Germany. Department of Radiology & Biomedical Imaging University of California San Francisco San Francisco CA USA. Symbiosis Center for Medical Image Analysis Symbiosis International University Pune Maharashtra India. Department of Neuroimaging and Interventional Radiology National Institute of Mental Health and Neurosciences Bangalore Karnataka India. Department of Radiology School of Medicine and Public Health University of Wisconsin Madison WI USA. Department of Medical Physics School of Medicine and Public Health University of Wisconsin Madison WI USA. Leeds Teaching Hospitals Trust Department of Radiology Leeds UK. Department of Radiology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. Catalan Institute of Oncology Badalona Spain. Consorci MAR Parc de Salut de Barcelona Catalonia Spain. Department of Radiology (IDI

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Authorship Correction: International Changes in COVID-19 Clinical Trajectories Across 315 Hospitals and 6 Countries: Retrospective Cohort Study

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Journal of medical Internet research 2021年第11期23卷 e34625页

作者： Griffin M Weber Harrison G Zhang Sehi L'Yi Clara-Lea Bonzel Chuan Hong Paul Avillach Alba Gutiérrez-Sacristán Nathan P Palmer Amelia Li Min Tan Xuan Wang William Yuan Nils Gehlenborg Anna Alloni Danilo F Amendola Antonio Bellasi Riccardo Bellazzi Michele Beraghi Mauro Bucalo Luca Chiovato Kelly Cho Arianna Dagliati Hossein Estiri Robert W Follett Noelia García Barrio David A Hanauer Darren W Henderson Yuk-Lam Ho John H Holmes Meghan R Hutch Ramakanth Kavuluru Katie Kirchoff Jeffrey G Klann Ashok K Krishnamurthy Trang T Le Molei Liu Ne Hooi Will Loh Sara Lozano-Zahonero Yuan Luo Sarah Maidlow Adeline Makoudjou Alberto Malovini Marcelo Roberto Martins Bertrand Moal Michele Morris Danielle L Mowery Shawn N Murphy Antoine Neuraz Kee Yuan Ngiam Marina P Okoshi Gilbert S Omenn Lav P Patel Miguel Pedrera Jiménez Robson A Prudente Malarkodi Jebathilagam Samayamuthu Fernando J Sanz Vidorreta Emily R Schriver Petra Schubert Pablo Serrano Balazote Byorn Wl Tan Suzana E Tanni Valentina Tibollo Shyam Visweswaran Kavishwar B Wagholikar Zongqi Xia Daniela Zöller Isaac S Kohane Tianxi Cai Andrew M South Gabriel A Brat Department of Biomedical Informatics Harvard Medical School Boston MA United States. BIOMERIS (BIOMedical Research Informatics Solutions) Pavia Italy. Clinical Research Unit Botucatu Medical School São Paulo State University Botucatu Brazil. Division of Nephrology Department of Medicine Ente Ospedaliero Cantonale Lugano Switzerland. Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy. Information Technology Department Azienda Socio-Sanitaria Territoriale di Pavia Pavia Italy. Unit of Internal Medicine and Endocrinology Istituti Clinici Scientifici Maugeri SpA SB IRCCS Pavia Italy. Massachusetts Veterans Epidemiology Research and Information Center Veterans Affairs Boston Healthcare System Boston MA United States. Department of Electrical Computer and Biomedical Engineering University of Pavia Pavia Italy. Department of Medicine Massachusetts General Hospital Boston MA United States. Department of Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA United States. Health Informatics Hospital Universitario 12 de Octubre Madrid Spain. Department of Learning Health Sciences University of Michigan Medical School Ann Arbor MI United States. Department of Biomedical Informatics University of Kentucky Lexington KY United States. Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine Philadelphia PA United States. Institute for Biomedical Informatics University of Pennsylvania Perelman School of Medicine Philadelphia PA United States. Department of Preventive Medicine Northwestern University Chicago IL United States. Institute for Biomedical Informatics University of Kentucky Lexington KY United States. Medical University of South Carolina Charleston SC United States. Department of Computer Science Renaissance Computing Institute University of North Carolina at Chapel Hill Chapel Hill NC United States. Departm

[This corrects the article DOI: 10.2196/31400.].

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Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals (vol 52, pg 1314, 2020)

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NATURE GENETICS 2021年第5期53卷 762-762页

作者： Surendran, Praveen Feofanova, Elena V. Lahrouchi, Najim Ntalla, Ioanna Karthikeyan, Savita Cook, James Chen, Lingyan Mifsud, Borbala Yao, Chen Kraja, Aldi T. Cartwright, James H. Hellwege, Jacklyn N. Giri, Ayush Tragante, Vinicius Thorleifsson, Gudmar Liu, Dajiang J. Prins, Bram P. Stewart, Isobel D. Cabrera, Claudia P. Eales, James M. Akbarov, Artur Auer, Paul L. Bielak, Lawrence F. Bis, Joshua C. Braithwaite, Vickie S. Brody, Jennifer A. Daw, E. Warwick Warren, Helen R. Drenos, Fotios Nielsen, Sune Fallgaard Faul, Jessica D. Fauman, Eric B. Fava, Cristiano Ferreira, Teresa Foley, Christopher N. Franceschini, Nora Gao, He Giannakopoulou, Olga Giulianini, Franco Gudbjartsson, Daniel F. Guo, Xiuqing Harris, Sarah E. Havulinna, Aki S. Helgadottir, Anna Huffman, Jennifer E. Hwang, Shih-Jen Kanoni, Stavroula Kontto, Jukka Larson, Martin G. Li-Gao, Ruifang Lindstrom, Jaana Lotta, Luca A. Lu, Yingchang Luan, Jian'an Mahajan, Anubha Malerba, Giovanni Masca, Nicholas G. D. Mei, Hao Menni, Cristina Mook-Kanamori, Dennis O. Mosen-Ansorena, David Muller-Nurasyid, Martina Pare, Guillaume Paul, Dirk S. Perola, Markus Poveda, Alaitz Rauramaa, Rainer Richard, Melissa Richardson, Tom G. Sepulveda, Nuno Sim, Xueling Smith, Albert V. Smith, Jennifer A. Staley, James R. Stanakova, Alena Sulem, Patrick Theriault, Sebastien Thorsteinsdottir, Unnur Trompet, Stella Varga, Tibor V. Velez Edwards, Digna R. Veronesi, Giovanni Weiss, Stefan Willems, Sara M. Yao, Jie Young, Robin Yu, Bing Zhang, Weihua Zhao, Jing-Hua Zhao, Wei Zhao, Wei Evangelou, Evangelos Aeschbacher, Stefanie Asllanaj, Eralda Blankenberg, Stefan Bonnycastle, Lori L. Bork-Jensen, Jette Brandslund, Ivan Braund, Peter S. Burgess, Stephen Cho, Kelly Christensen, Cramer Connell, John de Mutsert, Renee Dominiczak, Anna F. Dorr, Marcus Eiriksdottir, Gudny Farmaki, Aliki-Eleni Gaziano, J. Michael Grarup, Niels Grove, Megan L. Hallmans, Goran Hansen, Torben Have, Christian T. Heiss, Gerardo Jorgensen, Marit E. Jousilahti, Pekka Kajantie, Eero Kamat, Mihir Karajamaki, AnneMari Kar British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care University of Cambridge Cambridge UK British Heart Foundation Centre of Research Excellence University of Cambridge Cambridge UK Health Data Research UK Cambridge Wellcome Genome Campus and University of Cambridge Cambridge UK Rutherford Fund Fellow Department of Public Health and Primary Care University of Cambridge Cambridge UK MRC Biostatistics Unit University of Cambridge Cambridge UK National Institute for Health Research Cambridge Biomedical Research Centre University of Cambridge and Cambridge University Hospitals Cambridge UK MRC Integrative Epidemiology Unit (IEU) Population Health Sciences Bristol Medical School University of Bristol Bristol UK Robertson Centre for Biostatistics University of Glasgow Glasgow UK MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge UK Department of Immunology and Inflammation Imperial College London London UK Centre for Non-communicable Disease Research (CNCR) Dhaka Bangladesh National Institute for Health Research (NIHR) Blood and Transplant Research Unit (BTRU) in Donor Health and Genomics at the University of Cambridge Cambridge UK Department of Human Genetics Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge UK Department of Biostatistics and Epidemiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Center for Non-Communicable Diseases Karachi Pakistan Department of Genetics Novo Nordisk Research Centre Oxford Oxford UK Human Genetics Center Department of Epidemiology Human Genetics and Environmental Sciences School of Public Health University of Texas Health Science Center at Houston Houston TX USA Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Cardiovascular Research Center Center for Genomic Medicine

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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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