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arXiv 2019年

作者： Virtanen, Pauli Gommers, Ralf Oliphant, Travis E. Haberland, Matt Reddy, Tyler Cournapeau, David Burovski, Evgeni Peterson, Pearu Weckesser, Warren Bright, Jonathan van der Walt, Stéfan J. Brett, Matthew Wilson, Joshua Millman, K. Jarrod Mayorov, Nikolay Nelson, Andrew R.J. Jones, Eric Kern, Robert Larson, Eric Carey, C.J. Polat, Ilhan Feng, Yu Moore, Eric W. VanderPlas, Jake Laxalde, Denis Perktold, Josef Cimrman, Robert Henriksen, Ian Quintero, E.A. Harris, Charles R. Archibald, Anne M. Ribeiro, Antônio H. Pedregosa, Fabian van Mulbregt, Paul University of Jyväskylä University of Jyväskylä FI-40014 Finland Quansight LLC AustinTX United States Ultrasound Imaging Mayo Clinic RochesterMN55902 United States Electrical Engineering Brigham Young University ProvoUT84604 United States Enthought Inc. AustinTX78701 United States Anaconda Inc AustinTX78701 United States BioResource and Agricultural Engineering Department California Polytechnic State University San Luis ObispoCA93407 United States Department of Mathematics University of California Los AngelesCA90025 United States Los Alamos National Laboratory Los AlamosNM87544 United States Independent Researcher Higher School of Economics Myasnitskaya 20 Moscow101000 Russia Independent Researcher Saue Estonia Department of Mechanics and Applied Mathematics Institute of Cybernetics Tallinn Technical University Akadeemia Rd 21 Tallinn Estonia Independent Researcher NY United States Berkeley Institute for Data Science University of California BerkeleyCA94720 United States School of Psychology University of Birmingham Edgbaston BirmighamB15 2TT United Kingdom Division of Biostatistics University of California BerkeleyCA94720 United States WayRay LLC Skolkovo Innovation Center Moscow143026 Russia Australian Nuclear Science and Technology Organisation Locked Bag 2001 Kirrawee DCNSW2232 Australia Institute for Learning and Brain Sciences University of Washington SeattleWA98195 United States College of Information and Computing Sciences University of Massachusetts Amherst AmherstMA01002 United States Berkeley Center for Cosmological Physics University of California BerkeleyCA94720 United States Bruker Biospin Corp. 15 Fortune Drive BillericaMA01821 United States University of Washington SeattleWA98195 United States New Technologies - Research Centre University of West Bohemia Univerzitní 8 Plzeň306 14 Czech Republic Oden Institute for Computational Engineering and Sciences University of Texas at Austin AustinTX7

SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments. Copyright © 2019, The Authors. All rights reserved.

关键词： Open source software

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Building a quantum engineering undergraduate program

arXiv

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arXiv 2021年

作者： Asfaw, Abraham Blais, Alexandre Brown, Kenneth R. Candelaria, Jonathan Cantwell, Christopher Carr, Lincoln D. Combes, Joshua Debroy, Dripto M. Donohue, John M. Economou, Sophia E. Edwards, Emily Fox, Michael F.J. Girvin, Steven M. Ho, Alan Hurst, Hilary M. Jacob, Zubin Johnson, Blake R. Johnston-Halperin, Ezekiel Joynt, Robert Kapit, Eliot Klein-Seetharaman, Judith Laforest, Martin Lewandowski, H.J. Lynn, Theresa W. McRae, Corey Rae H. Merzbacher, Celia Michalakis, Spyridon Narang, Prineha Oliver, William D. Palsberg, Jens Pappas, David P. Raymer, Michael G. Reilly, David J. Saffman, Mark Searles, Thomas A. Shapiro, Jeffrey H. Singh, Chandralekha IBM Quantum IBM T. J. Watson Research Center Yorktown HeightsNY United States Institut Quantique Département de Physique Université de Sherbrooke SherbrookeQCJ1K 2R1 Canada Canadian Institute for Advanced Research TorontoONM5G 1M1 Canada The Duke Quantum Center Department of Physics Department of Electrical and Computer Engineering Department of Chemistry Duke University DurhamNC27708 United States SystemX Program Department of Electrical Engineering Stanford University StanfordCA94305 United States Department of Physics and Astronomy University of Southern California Los AngelesCA90089 United States The Quantum Engineering Program Department of Physics Colorado School of Mines GoldenCO80401 United States The Department of Electrical Computer and Energy Engineering University of Colorado Boulder BoulderCO80309 United States The Institute for Quantum Computing University of Waterloo WaterlooONN2L 3G1 Canada The Department of Physics Virginia Tech BlacksburgVA24061 United States The IQUIST University of Illinois Urbana-Champaign UrbanaIL61801 United States JILA National Institute of Standards and Technology The University of Colorado BoulderCO80309 United States Department of Physics University of Colorado Boulder BoulderCO80309 United States The Department of Physics Imperial College London Prince Consort Road LondonSW7 2AZ United Kingdom The Yale Quantum Institute Department of Physics Yale University New HavenCT06520 United States Google Research VeniceCA90291 United States The Department of Physics & Astronomy San José State University San JoséCA95192 United States The School of Electrical and Computer Engineering Purdue University Indiana West Lafayatte47907 United States The Department of Physics The Ohio State University ColumbusOH43210 United States The Department of Physics University of Wisconsin-Madison 1150 University Avenue MadisonWI53706 United States The Quantitative Biosciences and Engineering

The rapidly growing quantum information science and engineering (QISE) industry will require both quantum-aware and quantum-proficient engineers at the bachelor's level. We provide a roadmap for building a quantum engineering education program to satisfy this need. For quantum-aware engineers, we describe how to design a first quantum engineering course accessible to all STEM students. For the education and training of quantum-proficient engineers, we detail both a quantum engineering minor accessible to all STEM majors, and a quantum track directly integrated into individual engineering majors. We propose that such programs typically require only three or four newly developed courses that complement existing engineering and science classes available on most larger campuses. We describe a conceptual quantum information science course for implementation at any post-secondary institution, including community colleges and military schools. QISE presents extraordinary opportunities to work towards rectifying issues of inclusivity and equity that continue to be pervasive within engineering. We present a plan to do so and describe how quantum engineering education presents an excellent set of education research opportunities. Finally, we outline a hands-on training plan on quantum hardware, a key component of any quantum engineering program, with a variety of technologies including optics, atoms and ions, cryogenic and solid-state technologies, nanofabrication, and control and readout electronics. Our recommendations provide a flexible framework that can be tailored for academic institutions ranging from teaching and undergraduate-focused two- and four-year colleges to research-intensive universities. © 2021, CC BY.

关键词： engineering education

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AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

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Immunoinformatics (Amsterdam, Netherlands) 2023年 10卷 100025页

作者： William D Lees Scott Christley Ayelet Peres Justin T Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G Cowell Gur Yaari Martin Corcoran Gunilla B Karlsson Hedestam Mats Ohlin Andrew M Collins Corey T Watson Christian E Busse Institute of Structural and Molecular Biology Birkbeck College London England. Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal. Peter O'Donnell Jr. School of Public Health UT Southwestern Medical Center Dallas TX USA. Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel. Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville KY USA. Department of Biological Sciences Simon Fraser University Burnaby BC Canada. Fred Hutchinson Cancer Research Center Seattle WA USA. Peter O'Donnell Jr. School of Public Health Department of Immunology School of Biomedical Sciences UT Southwestern Medical Center Dallas TX USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Swede. Department of Immunotechnology and SciLifeLab Lund University Lund Sweden. School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia. Division of B Cell Immunology German Cancer Research Center Heidelberg Germany.

Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.

关键词： AIRR-seq Immune receptor Immune receptor germline Immune receptor repertoire Rep-seq

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Harmonized-Multinational qEEG norms (HarMNqEEG)

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NEUROIMAGE 2022年 256卷 119190-119190页

作者： Li, Min Wang, Ying Lopez-Naranjo, Carlos Hu, Shiang Reyes, Ronaldo Cesar Garcia Paz-Linares, Deirel Areces-Gonzalez, Ariosky Hamid, Aini Ismafairus Abd Evans, Alan C. Savostyanov, Alexander N. Calzada-Reyes, Ana Villringer, Arno Tobon-Quintero, Carlos A. Garcia-Agustin, Daysi Yao, Dezhong Dong, Li Aubert-Vazquez, Eduardo Reza, Faruque Razzaq, Fuleah Abdul Omar, Hazim Abdullah, Jafri Malin Galler, Janina R. Ochoa-Gomez, John F. Prichep, Leslie S. Galan-Garcia, Lidice Morales-Chacon, Lilia Valdes-Sosa, Mitchell J. Trondle, Marius Zulkifly, Mohd Faizal Mohd Rahman, Muhammad Riddha Bin Abdul Milakhina, Natalya S. Langer, Nicolas Rudych, Pavel Koenig, Thomas Virues-Alba, Trinidad A. Lei, Xu Bringas-Vega, Maria L. Bosch-Bayard, Jorge F. Valdes-Sosa, Pedro Antonio [a]The Clinical Hospital of Chengdu Brain Science Institute MOE Key Lab for Neuroinformation School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China [b]Cuban Center for Neurocience La Habana Cuba [c]McGill Centre for Integrative Neuroscience Ludmer Centre for Neuroinformatics and Mental Health Montreal Neurological Institute Canada [d]Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [e]Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [f]Hospital Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [g]Humanitarian Institute Novosibirsk State University Novosibirsk 630090 Russia [h]Laboratory of Psychophysiology of Individual Differences Federal State Budgetary Scientific Institution Scientific Research Institute of Neurosciences and Medicine Novosibirsk 630117 Russia [i]Laboratory of Psychological Genetics at the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia [j]University of Pinar del Río “Hermanos Saiz Montes de Oca” Pinar del Río Cuba [k]Department of Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany [l]Department of Cognitive Neurology University Hospital Leipzig Leipzig Germany [m]Center for Stroke Research Charité-Universitätsmedizin Berlin Berlin Germany [n]Grupo Neuropsicología y Conducta - GRUNECO Faculty of Medicine Universidad de Antioquia Colombia [o]Research Department Institución Prestadora de Servicios de Salud IPS Universitaria Colombia [p]The Cuban center aging longevity and health Havana Cuba [q]Research Unit of NeuroInformation Chinese Academy of Medical Sciences Chengdu 2019RU035 China [r]School of Electrical Engineering Zhengzhou University Zhengzhou 4500

This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects " and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting COVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

关键词： Quantitative EEG EEG cross-spectrum Riemannian geometry Batch effects Z-score Harmonization Malnutrition Covid induced brain dysfunction Developmental Brain Chart

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Abstracts

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JOURNAL OF SPINAL CORD MEDICINE 2021年第SUPPL 1期44卷 S278-S324页

作者： [Anonymous] Department of Medicine Division of Physical Medicine and Rehabilitation University of Toronto Toronto ON CA KITE - Toronto Rehabilitation Institute University Health Network Toronto ON CA Institute for Health Policy Management and Evaluation University of Toronto Toronto ON CA Rehabilitation Sciences Institute University of Toronto Toronto ON CA Institute of Medical Sciences University of Toronto Toronto ON CA. Rehabilitation Sciences Institute University of Toronto ON CA KITE Research Institute-Toronto Rehab-University Health Network Toronto ON CA Physical Therapy Department University of Toronto ON CA Praxis Spinal Cord Institute Vancouver BC Université de Montréal (École de réadaptation) Montreal QC CA Institut de réadaptation Gingras-Linsay-de-Montréal Montreal QC CA Division of Physical Medicine & Rehabilitation Department of Medicine Faculty of Medicine & Dentistry University of Alberta Edmonton AB CA University of Calgary Calgary AB CA Alberta Health Services Centre for Family Medicine Kitchener ON CA McMaster University Department of Family Medicine Hamilton ON CA Dept. of Physical Therapy University of Toronto Toronto ON CA KITE-University Health Network Toronto ON CA Praxis Spinal Cord Institute Vancouver BC CA Center for Interdisciplinary Research in Rehabilitation and Social Integration (CIRRIS) Quebec City QC CA Dept. of Rehabilitation Laval University Quebec City QC CA Institute of Health Policy Management and Evaluation University of Toronto Toronto ON CA School of Rehabilitation Science University of Saskatchewan Saskatoon SK CA Ontario Neurotrauma Foundation Toronto ON CA Canadian Spinal Research Organization Toronto ON CA CIUSSS du Centre-Sud-de-l ‘Île-de-Montréal (Installation Gingras-Lindsay) Montréal QC CA École de réadaptation Université de Montréal Montréal QC CA First Steps Wellness Centre Regina SK CA Stan Cassidy Centre for Rehabilitation Horizon Health Network Fredericton NB CA Departmen

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Quantum Simulation for High-Energy Physics

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PRX Quantum 2023年第2期4卷 027001-027001页

作者： Christian W. Bauer Zohreh Davoudi A. Baha Balantekin Tanmoy Bhattacharya Marcela Carena Wibe A. de Jong Patrick Draper Aida El-Khadra Nate Gemelke Masanori Hanada Dmitri Kharzeev Henry Lamm Ying-Ying Li Junyu Liu Mikhail Lukin Yannick Meurice Christopher Monroe Benjamin Nachman Guido Pagano John Preskill Enrico Rinaldi Alessandro Roggero David I. Santiago Martin J. Savage Irfan Siddiqi George Siopsis David Van Zanten Nathan Wiebe Yukari Yamauchi Kübra Yeter-Aydeniz Silvia Zorzetti Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics Maryland Center for Fundamental Physics and the NSF Institute for Robust Quantum Simulation University of Maryland College Park Maryland 20742 USA Department of Physics University of Wisconsin Madison Wisconsin 53706 USA T-2 Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Fermi National Accelerator Laboratory Batavia Illinois 60510 USA Enrico Fermi Institute University of Chicago Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago Chicago Illinois 60637 USA Department of Physics University of Chicago Chicago Illinois 60637 USA Department of Physics and Illinois Center for the Advanced Study of the Universe and Illinois Quantum Information Science and Technology Center University of Illinois Urbana Illinois 61801 USA QuEra Computing Inc Boston Massachusetts 02135 USA Department of Mathematics University of Surrey Guildford Surrey GU2 7XH United Kingdom Center for Nuclear Theory Department of Physics and Astronomy Stony Brook University New York 11794-3800 USA Department of Physics Brookhaven National Laboratory Upton New York 11973 USA Peng Huanwu Center for Fundamental Theory Hefei Anhui 230026 China Interdisciplinary Center for Theoretical Study University of Science and Technology of China Hefei Anhui 230026 China Pritzker School of Molecular Engineering Chicago Quantum Exchange and Kadanoff Center for Theoretical Physics University of Chicago Illinois 60637 USA qBraid Co. Harper Court 5235 Chicago Illinois 60615 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Department of Physics and Astronomy University of Iowa Iowa City Iowa 52242 USA Duke Quantum Center Duke University Durham North Carolina 27701 USA Department of Electrical and Computer Engineering Duke University Durham North Carolina 27708 USA Department of Physics Duke University

It is for the first time that quantum simulation for high-energy physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in quantum information sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This Roadmap is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.

关键词： Quantum simulation

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

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Nature computational science 2023年第7期3卷 658页

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

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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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Body appreciation around the world: Measurement invariance of the Body Appreciation Scale-2 (BAS-2) across 65 nations, 40 languages, gender identities, and age

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Body image 2023年 46卷 449-466页

作者： Viren Swami Ulrich S Tran Stefan Stieger Toivo Aavik Hamed Abdollahpour Ranjbar Sulaiman Olanrewaju Adebayo Reza Afhami Oli Ahmed Annie Aimé Marwan Akel Hussam Al Halbusi George Alexias Khawla F Ali Nursel Alp-Dal Anas B Alsalhani Sara Álvares-Solas Ana Carolina Soares Amaral Sonny Andrianto Trefor Aspden Marios Argyrides John Jamir Benzon R Aruta Stephen Atkin Olusola Ayandele Migle Baceviciene Radvan Bahbouh Andrea Ballesio David Barron Ashleigh Bellard Sóley Sesselja Bender Kerime Derya Beydağ Gorana Birovljević Marie-Ève Blackburn Teresita Borja-Alvarez Joanna Borowiec Miroslava Bozogáňová Solfrid Bratland-Sanda Matthew H E M Browning Anna Brytek-Matera Marina Burakova Yeliz Çakır-Koçak Pablo Camacho Vittorio Emanuele Camilleri Valentina Cazzato Silvia Cerea Apitchaya Chaiwutikornwanich Trawin Chaleeraktrakoon Tim Chambers Qing-Wei Chen Xin Chen Chin-Lung Chien Phatthanakit Chobthamkit Bovornpot Choompunuch Emilio J Compte Jennifer Corrigan Getrude Cosmas Richard G Cowden Kamila Czepczor-Bernat Marcin Czub Wanderson Roberto da Silva Mahboubeh Dadfar Simon E Dalley Lionel Dany Jesus Alfonso D Datu Pedro Henrique Berbert de Carvalho Gabriel Lins de Holanda Coelho Avila Odia S De Jesus Sonia Harzallah Debbabi Sandesh Dhakal Francesca Di Bernardo Donka D Dimitrova Jacinthe Dion Barnaby Dixson Stacey M Donofrio Marius Drysch Hongfei Du Angel M Dzhambov Claire El-Jor Violeta Enea Mehmet Eskin Farinaz Farbod Lorleen Farrugia Leonie Fian Maryanne L Fisher Michał Folwarczny David A Frederick Matthew Fuller-Tyszkiewicz Adrian Furnham Antonio Alías García Shulamit Geller Marta Ghisi Alireza Ghorbani Maria Angeles Gomez Martinez Sarah Gradidge Sylvie Graf Caterina Grano Gyöngyvér Gyene Souheil Hallit Motasem Hamdan Jonathan E Handelzalts Paul H P Hanel Steven R Hawks Issa Hekmati Mai Helmy Tetiana Hill Farah Hina Geraldine Holenweger Martina Hřebíčková Olasupo Augustine Ijabadeniyi Asma Imam Başak İnce Natalia Irrazabal Rasa Jankauskiene Ding-Yu Jiang Micaela Jiménez-Borja Verónica Jiménez-Borja Evan M Johnson Veljko Jov School of Psychology and Sport Science Anglia Ruskin University Cambridge United Kingdom Centre for Psychological Medicine Perdana University Kuala Lumpur Malaysia. Electronic address: viren.swami@aru.ac.uk. Department of Cognition Emotion and Methods in Psychology Faculty of Psychology University of Vienna Vienna Austria. Department of Psychology and Psychodynamics Karl Landsteiner University of Health Sciences Krems an der Donau Austria. Institute of Psychology University of Tartu Tartu Estonia. Department of Psychology Koç University Istanbul Turkiye. Department of Psychology and Behavioural Studies Ekiti State University Ado-Ekiti Nigeria. Department of Art Studies Tarbiat Modares University Tehran Iran. Department of Psychology University of Chittagong Chattogram Bangladesh. Department of Psychoeducation and Psychology Université du Québec en Outaouais Saint-Jérôme Canada. INSPECT-LB: National Institute of Public Health Clinical Epidemiology and Toxicology Beirut Lebanon School of Pharmacy Lebanese International University Beirut Lebanon. Department of Management Ahmed Bin Mohammad Military College Doha Qatar. Faculty of Psychology Panteion University of Social and Political Sciences Athens Greece. Royal College of Surgeons Ireland-Bahrain Adliya Bahrain. Department of Midwifery Faculty of Health Sciences Munzur University Tunceli Turkiya. Department of Oral Medicine and Diagnostic Sciences Vision College of Dentistry and Nursing Vision Colleges Riyadh Saudi Arabia. Facultad de Ciencias de la Vida Universidad Regional Amazónica Ikiam Muyuna Ecuador. Federal Institute of Education Science and Technology of Southeast Minas Gerais Barbacena Brazil. Department of Psychology Universitas Islam Indonesia Yogyakarta Indonesia. Department of Psychology Aberystwyth University Ceredigion United Kingdom. Department of Psychology Neapolis University Pafos Paphos Cyprus. Department of Psychology De La Salle University Phillippines. Department of Gen

The Body Appreciation Scale-2 (BAS-2) is a widely used measure of a core facet of the positive body image construct. However, extant research concerning measurement invariance of the BAS-2 across a large number of nations remains limited. Here, we utilised the Body Image in Nature (BINS) dataset - with data collected between 2020 and 2022 - to assess measurement invariance of the BAS-2 across 65 nations, 40 languages, gender identities, and age groups. Multi-group confirmatory factor analysis indicated that full scalar invariance was upheld across all nations, languages, gender identities, and age groups, suggesting that the unidimensional BAS-2 model has widespread applicability. There were large differences across nations and languages in latent body appreciation, while differences across gender identities and age groups were negligible-to-small. Additionally, greater body appreciation was significantly associated with higher life satisfaction, being single (versus being married or in a committed relationship), and greater rurality (versus urbanicity). Across a subset of nations where nation-level data were available, greater body appreciation was also significantly associated with greater cultural distance from the United States and greater relative income inequality. These findings suggest that the BAS-2 likely captures a near-universal conceptualisation of the body appreciation construct, which should facilitate further cross-cultural research.

关键词： Body appreciation Body appreciation Scale-2 (BAS-2) Cross-cultural Measurement invariance Multi-group confirmatory factor analysis (MG-CFA) Psychometrics Structural analysis

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