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Diabetic foot ulcers segmentation challenge report: Benchmark and analysis

Medical image analysis 2024年 94卷 103153页

作者： Moi Hoon Yap Bill Cassidy Michal Byra Ting-Yu Liao Huahui Yi Adrian Galdran Yung-Han Chen Raphael Brüngel Sven Koitka Christoph M Friedrich Yu-Wen Lo Ching-Hui Yang Kang Li Qicheng Lao Miguel A González Ballester Gustavo Carneiro Yi-Jen Ju Juinn-Dar Huang Joseph M Pappachan Neil D Reeves Vishnu Chandrabalan Darren Dancey Connah Kendrick Department of Computing and Mathematics Manchester Metropolitan University John Dalton Building Chester Street Manchester M1 5GD United Kingdom Lancashire Teaching Hospitals NHS Trust Preston PR2 9HT United Kingdom. Electronic address: m.yap@mmu.ac.uk. Department of Computing and Mathematics Manchester Metropolitan University John Dalton Building Chester Street Manchester M1 5GD United Kingdom. Institute of Fundamental Technological Research Polish Academy of Sciences Warsaw Poland RIKEN Center for Brain Science Wako Japan. Department of Computer Science National Tsing Hua University No. 101 Section 2 Kuang-Fu Road Hsinchu Taiwan. West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu China. BCN Medtech Universitat Pompeu Fabra Barcelona Spain AIML University of Adelaide Australia. Institute of Electronics National Yang Ming Chiao Tung University No. 1001 University Road Hsinchu 300 Taiwan. Department of Computer Science University of Applied Sciences and Arts Dortmund (FH Dortmund) Emil-Figge-Str. 42 44227 Dortmund Germany Institute for Medical Informatics Biometry and Epidemiology (IMIBE) University Hospital Essen Zweigertstr. 37 45130 Essen Germany Institute for Artificial Intelligence in Medicine (IKIM) University Hospital Essen Girardetstr. 2 45131 Essen Germany. Institute for Artificial Intelligence in Medicine (IKIM) University Hospital Essen Girardetstr. 2 45131 Essen Germany Institute of Diagnostic and Interventional Radiology and Neuroradiology University Hospital Essen Hufelandstr. 55 45147 Essen Germany. Institute for Medical Informatics Biometry and Epidemiology (IMIBE) University Hospital Essen Zweigertstr. 37 45130 Essen Germany. West China Biomedical Big Data Center West China Hospital Sichuan University Chengdu China Shanghai Artificial Intelligence Laboratory Shanghai China. School of Artificial Intelligence Beijing University of Posts and Telecommunications Beijing China BCN Medtech Universit

Monitoring the healing progress of diabetic foot ulcers is a challenging process. Accurate segmentation of foot ulcers can help podiatrists to quantitatively measure the size of wound regions to assist prediction of healing status. The main challenge in this field is the lack of publicly available manual delineation, which can be time consuming and laborious. Recently, methods based on deep learning have shown excellent results in automatic segmentation of medical images, however, they require large-scale datasets for training, and there is limited consensus on which methods perform the best. The 2022 Diabetic Foot Ulcers segmentation challenge was held in conjunction with the 2022 International Conference on Medical Image computing and Computer Assisted Intervention, which sought to address these issues and stimulate progress in this research domain. A training set of 2000 images exhibiting diabetic foot ulcers was released with corresponding segmentation ground truth masks. Of the 72 (approved) requests from 47 countries, 26 teams used this data to develop fully automated systems to predict the true segmentation masks on a test set of 2000 images, with the corresponding ground truth segmentation masks kept private. Predictions from participating teams were scored and ranked according to their average Dice similarity coefficient of the ground truth masks and prediction masks. The winning team achieved a Dice of 0.7287 for diabetic foot ulcer segmentation. This challenge has now entered a live leaderboard stage where it serves as a challenging benchmark for diabetic foot ulcer segmentation.

关键词： Convolutional neural networks Deep learning Diabetic foot ulcers Metrics Segmentation

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Environment Scan of Generative AI Infrastructure for Clinical and Translational science

arXiv

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arXiv 2024年

作者： Idnay, Betina Xu, Zihan Adams, William G. Adibuzzaman, Mohammad Anderson, Nicholas R. Bahroos, Neil Bell, Douglas S. Bumgardner, Cody Campion, Thomas Castro, Mario Cimino, James J. Cohen, I. Glenn Dorr, David Elkin, Peter L. Fan, Jungwei W. Ferris, Todd Foran, David J. Hanauer, David Hogarth, Mike Huang, Kun Kalpathy-Cramer, Jayashree Kandpal, Manoj Karnik, Niranjan S. Katoch, Avnish Lai, Albert M. Lambert, Christophe G. Li, Lang Lindsell, Christopher Liu, Jinze Lu, Zhiyong Luo, Yuan McGarvey, Peter Mendonca, Eneida A. Mirhaji, Parsa Murphy, Shawn Osborne, John D. Paschalidis, Ioannis C. Harris, Paul A. Prior, Fred Shaheen, Nicholas J. Shara, Nawar Sim, Ida Tachinardi, Umberto Waitman, Lemuel R. Wright, Rosalind J. Zai, Adrian H. Zheng, Kai Lee, Sandra Soo-Jin Malin, Bradley A. Natarajan, Karthik Price, W. Nicholson Zhang, Rui Zhang, Yiye Xu, Hua Bian, Jiang Weng, Chunhua Peng, Yifan Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY United States Department of Population Health Sciences Weill Cornell Medicine New YorkNY United States Department of Pediatrics Boston Medical Center BostonMA United States Chobanian & Avedisian School of Medicine Boston University BostonMA United States Oregon Clinical and Translational Research Institute Oregon Health and Science University PortlandOR United States Department of Public Health Sciences University of California Davis DavisCA United States Keck School of Medicine University of Southern California Los AngelesCA United States Department of Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Pathology and Laboratory Medicine University of Kentucky College of Medicine LexingtonKY United States Division of Pulmonary Critical Care and Sleep Medicine University of Kansas School of Medicine Kansas CityKS United States Department of Biomedical Informatics and Data Science Heersink School of Medicine University of Alabama BirminghamAL United States Harvard Law School Petrie-Flom Center for Health Law Policy Biotechnology and Bioethics Harvard University CambridgeMA United States Department of Biomedical Informatics University at Buffalo BuffaloNY United States Center for Clinical and Translational Science Mayo Clinic RochesterMN United States Technology and Digital Solutions Stanford Medicine Stanford University StanfordCA United States Center for Biomedical Informatics Rutgers Cancer Institute New BrunswickNJ United States Department of Learning Health Sciences University of Michigan Medical School Ann ArborMI United States University of California San Diego La Jolla CA United States Department of Biostatistics and Health Data Science School of Medicine Indiana University IndianapolisIN United States Division of Artificial Medical Intelligence in Ophthalmology Univ

This study reports a comprehensive environmental scan of the generative AI (GenAI) infrastructure in the national network for clinical and translational science across 36 institutions supported by the Clinical and Translational science Award (CTSA) Program led by the National Center for Advancing Translational sciences (NCATS) of the National institutes of Health (NIH) at the United States. With the rapid advancement of GenAI technologies, including large language models (LLMs), healthcare institutions face unprecedented opportunities and challenges. This research explores the current status of GenAI integration, focusing on stakeholder roles, governance structures, and ethical considerations by administering a survey among leaders of health institutions (i.e., representing academic medical centers and health systems) to assess the institutional readiness and approach towards GenAI adoption. Key findings indicate a diverse range of institutional strategies, with most organizations in the experimental phase of GenAI deployment. The study highlights significant variations in governance models, with a strong preference for centralized decision-making but notable gaps in workforce training and ethical oversight. Moreover, the results underscore the need for a more coordinated approach to GenAI governance, emphasizing collaboration among senior leaders, clinicians, information technology staff, and researchers. Our analysis also reveals concerns regarding GenAI bias, data security, and stakeholder trust, which must be addressed to ensure the ethical and effective implementation of GenAI technologies. This study offers valuable insights into the challenges and opportunities of GenAI integration in healthcare, providing a roadmap for institutions aiming to leverage GenAI for improved quality of care and operational efficiency. © 2024, CC BY.

关键词： Electronic health record

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Biomedical image analysis competitions: The state of current participation practice

arXiv

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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Preface

ICMLCA 2021 - 2nd International Conference on Machine Learni...

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ICMLCA 2021 - 2nd International Conference on Machine Learning and Computer Application 2021年 iii页

作者： Ning, Xiansheng Feng, Yongxin Zhang, Wenbo Yue, Mingkai Du, Ke-Lin Huang, Shutao Zhou, Fang Ba, Shuhong Fu, Chong Shui, Penglang Xu, Shuwen Wu, Sheng Wang, Shushan Du, Zhonghua Gao, Zhijun Fan, Chunlong Li, Yufeng Wang, Yupeng Liu, Qingli Yu, Jingang Yin, Zhenyu Zhang, Deyu Gao, Hongwei Wen, Feng Guo, Cean Hao, Yongping Chan, Yung-Kuan Pavlovich, Vinogradov Gennady Kirpichnikova, Irina Qian, Zhihong Ivanov, Dmitriy V. Zhou, Xueguan Nezamabadi-Pour, Hossein Yang, Qing Zhang, Yongtang Liao, Haibin Huang, Ying Srinivasan, Kathiravan Xu, Zhenghua Pachori, Ram Bilas Zhang, Jialu AlShawabkeh, Mahmoud Guo, Chengjun Chaugule, Archana Ajit Lima, Alberto Sampaio Liu, Huayong Vidal, Jorge Maestre Alrshah, Mohamed A. Ghafoor, Kayhan Zrar Kubicek, Jan Chaugule, Archana Ajit Rodríguez-Pérez, Miguel Kumar, Gulshan Nasri, Mehdi Borrego, Carlos Persico, Valerio Wagh, Sanjeev Yan, Wenjun Yang, Li Yang, Dawei Xing, Yongkang Yang, Huadong Shang, Chengguo Chang, Xingong Shi, Hongbo Li, Aijun Feng, Liping Lv, Yali Liang, Minfu Wang, Kaixuan Bai, Zengliang Liang, Anhui Nan, Zhihong Ji, Suqin Chang, Liwei Zhou, Hongbin Yao, Chunli Cao, Guodong Zhang, Juling School of Information Science and Engineering Shenyang Ligong University China School of Equipment Engineering Shenyang Ligong University China Concordia University Canada School of Automotive and Transportation Shenyang Ligong University China School of Information Science and Engineering Shenyang Ligong University China School of Equipment Engineering Shenyang Ligong University China Northeastern University China Xidian University China Beijing University of Posts and Telecommunications China Beijing Institute of Technology China Nanjing University of Science & Technology China Shenyang Jianzhu University China Shenyang Aerospace University China Dalian University China Shenyang Institute of Computing Technology Chinese Academy of Sciences China Shenyang Ligong University China National Chun Hsing University Taiwan Department of Informatics and Applied Mathematics Russia South Ural State University Russia Jilin University China Samara State University of Transport Russia Naval Universit of Engineering China Shahid Bahonar University of Kermanto Iran Central China Normal University China Guangdong Neusoft Institute China Hubei University of Science and Technology China Liuzhou Railway Vocational Technical College China Vellore Institute of Technology India Hebei University of Technology China Indian Institute of Technology Indore India Xiangnan University China Guangxi Normal University for Nationalities China UESTC China Pimpri-Chinchwad College of Engineering & Research India Federal University of Ceará Brazil Complutense University of Madrid Spain Universiti Putra Malaysia Malaysia Shanghai Jiao Tong University China VŠB - Technical University of Ostrava Cuw Pimpri-Chinchwad College of Engineering & Research Ravet Pune India University of Vigo Spain Division of Research and Development India Islamic Azad University Iran Departament Enginyeria of Information Comunicacions Autonomous University of Barcelona Spain Opportunistic Networks United States Univers

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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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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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NANOGrav 15-year gravitational-wave background methods

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Physical Review D 2024年第10期109卷 103012-103012页

作者： Aaron D. Johnson Patrick M. Meyers Paul T. Baker Neil J. Cornish Jeffrey S. Hazboun Tyson B. Littenberg Joseph D. Romano Stephen R. Taylor Michele Vallisneri Sarah J. Vigeland Ken D. Olum Xavier Siemens Justin A. Ellis Rutger van Haasteren Sophie Hourihane Gabriella Agazie Akash Anumarlapudi Anne M. Archibald Zaven Arzoumanian Laura Blecha Adam Brazier Paul R. Brook Sarah Burke-Spolaor Bence Bécsy J. Andrew Casey-Clyde Maria Charisi Shami Chatterjee Katerina Chatziioannou Tyler Cohen James M. Cordes Fronefield Crawford H. Thankful Cromartie Kathryn Crowter Megan E. DeCesar Paul B. Demorest Timothy Dolch Brendan Drachler Elizabeth C. Ferrara William Fiore Emmanuel Fonseca Gabriel E. Freedman Nate Garver-Daniels Peter A. Gentile Joseph Glaser Deborah C. Good Kayhan Gültekin Ross J. Jennings Megan L. Jones Andrew R. Kaiser David L. Kaplan Luke Zoltan Kelley Matthew Kerr Joey S. Key Nima Laal Michael T. Lam William G. Lamb T. Joseph W. Lazio Natalia Lewandowska Tingting Liu Duncan R. Lorimer Jing Luo Ryan S. Lynch Chung-Pei Ma Dustin R. Madison Alexander McEwen James W. McKee Maura A. McLaughlin Natasha McMann Bradley W. Meyers Chiara M. F. Mingarelli Andrea Mitridate Cherry Ng David J. Nice Stella Koch Ocker Timothy T. Pennucci Benetge B. P. Perera Nihan S. Pol Henri A. Radovan Scott M. Ransom Paul S. Ray Shashwat C. Sardesai Carl Schmiedekamp Ann Schmiedekamp Kai Schmitz Brent J. Shapiro-Albert Joseph Simon Magdalena S. Siwek Ingrid H. Stairs Daniel R. Stinebring Kevin Stovall Abhimanyu Susobhanan Joseph K. Swiggum Jacob E. Turner Caner Unal Haley M. Wahl Caitlin A. Witt Olivia Young Center for Gravitation Cosmology and Astrophysics Department of Physics University of Wisconsin-Milwaukee P.O. Box 413 Milwaukee Wisconsin 53201 USA Division of Physics Mathematics and Astronomy California Institute of Technology Pasadena California 91125 USA Department of Physics and Astronomy Widener University One University Place Chester Pennsylvania 19013 USA Department of Physics Montana State University Bozeman Montana 59717 USA Department of Physics Oregon State University Corvallis Oregon 97331 USA NASA Marshall Space Flight Center Huntsville Alabama 35812 USA Department of Physics Texas Tech University Box 41051 Lubbock Texas 79409 USA Department of Physics and Astronomy Vanderbilt University 2301 Vanderbilt Place Nashville Tennessee 37235 USA Jet Propulsion Laboratory California Institute of Technology 4800 Oak Grove Drive Pasadena California 91109 USA Institute of Cosmology Department of Physics and Astronomy Tufts University Medford Massachusetts 02155 USA Department of Astronomy University of Maryland College Park Maryland 20742 Center for Research and Exploration in Space Science and Technology NASA/GSFC Greenbelt Maryland 20771 NASA Goddard Space Flight Center Greenbelt Maryland 20771 USA Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut) Callinstrasse 38 D-30167 Hannover Germany Newcastle University NE1 7RU Newcastle United Kingdom X-Ray Astrophysics Laboratory NASA Goddard Space Flight Center Code 662 Greenbelt Maryland 20771 USA Physics Department University of Florida Gainesville Florida 32611 USA Cornell Center for Astrophysics and Planetary Science and Department of Astronomy Cornell University Ithaca New York 14853 USA Cornell Center for Advanced Computing Cornell University Ithaca New York 14853 USA Institute for Gravitational Wave Astronomy and School of Physics and Astronomy University of Birmingham Edgbaston Birmingham B15 2TT United Kingdom Department of Physics and Astronomy West

Pulsar timing arrays (PTAs) use an array of millisecond pulsars to search for gravitational waves in the nanohertz regime in pulse time of arrival data. This paper presents rigorous tests of PTA methods, examining their consistency across the relevant parameter space. We discuss updates to the 15-year isotropic gravitational-wave background analyses and their corresponding code representations. Descriptions of the internal structure of the flagship algorithms enterprise and ptmcmcsampler are given to facilitate understanding of the PTA likelihood structure, how models are built, and what methods are currently used in sampling the high-dimensional PTA parameter space. We introduce a novel version of the PTA likelihood that uses a two-step marginalization procedure that performs much faster in gravitational wave searches, reducing the required resources facilitating the computation of Bayes factors via thermodynamic integration and sampling a large number of realizations for computing Bayesian false-alarm probabilities. We perform stringent tests of consistency and correctness of the Bayesian and frequentist analysis methods. For the Bayesian analysis, we test prior recovery, simulation recovery, and Bayes factors. For the frequentist analysis, we test that the optimal statistic, when modified to account for a non-negligible gravitational-wave background, accurately recovers the amplitude of the background. We also summarize recent advances and tests performed on the optimal statistic in the literature from both gravitational wave background detection and parameter estimation perspectives. The tests presented here validate current analyses of PTA data.

关键词： Gravitational waves Gravitational wave detection

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Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge

arXiv

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arXiv 2024年

作者： LaBella, Dominic Baid, Ujjwal Khanna, Omaditya McBurney-Lin, Shan McLean, Ryan Nedelec, Pierre Rashid, Arif Tahon, Nourel Hoda Altes, Talissa Bhalerao, Radhika Dhemesh, Yaseen Godfrey, Devon Hilal, Fathi Floyd, Scott Janas, Anastasia Kazerooni, Anahita Fathi Kirkpatrick, John Kent, Collin Kofler, Florian Leu, Kevin Maleki, Nazanin Menze, Bjoern Pajot, Maxence Reitman, Zachary J. Rudie, Jeffrey D. Saluja, Rachit Velichko, Yury Wang, Chunhao Warman, Pranav Adewole, Maruf Albrecht, Jake Anazodo, Udunna Anwar, Syed Muhammad Bergquist, Timothy Chen, Sully Francis Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Khalili, Nastaran Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Liu, Xinyang Mahtabfar, Aria Meier, Zeke Moawad, Ahmed W. Mongan, John Piraud, Marie Shinohara, Russell Takeshi Wiggins, Walter F. Abayazeed, Aly H. Akinola, Rachel Jakab, András Bilello, Michel de Verdier, Maria Correia Crivellaro, Priscila Davatzikos, Christos Farahani, Keyvan Freymann, John Hess, Christopher Huang, Raymond Lohmann, Philipp Moassefi, Mana Pease, Matthew W. Vollmuth, Phillipp Sollmann, Nico Diffley, David Nandolia, Khanak K. Warren, Daniel I. Hussain, Ali Fehringer, Pascal Bronstein, Yulia Deptula, Lisa Stein, Evan G. Taherzadeh, Mahsa de Oliveira, Eduardo Portela Haughey, Aoife Kontzialis, Marinos Saba, Luca Turner, Benjamin Brüßeler, Melanie M.T. Ansari, Shehbaz Gkampenis, Athanasios Weiss, David Maximilian Mansour, Aya Shawali, Islam H. Yordanov, Nikolay Stein, Joel M. Hourani, Roula Moshebah, Mohammed Yahya Abouelatta, Ahmed Magdy Rizvi, Tanvir Willms, Klara Martin, Dann C. Okar, Abdullah D'Anna, Gennaro Taha, Ahmed Sharifi, Yasaman Faghani, Shahriar Kite, Dominic Pinho, Marco Haider, Muhammad Ammar Aristizabal, Alejandro Karargyris, Alexandros Kassem, Hasan Pati, Sarthak Sheller, Micah Alonso-Basanta, Michelle Villanueva-Meyer, Javier Rauschecker, Andreas M. Nada, Ayman Aboian, Mariam Flanders, Adam E. Wiestler, Benedikt Bakas, Spyridon Ca Duke University Medical Center Department of Radiation Oncology DurhamNC United States Division of Computational Pathology Department of Pathology Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Center for Federated Learning in Medicine Indiana University IndianapolisIN United States Department of Neurosurgery Thomas Jefferson University PhiladelphiaPA United States University of California San FranciscoCA United States Yale University New HavenCT United States Department of Radiation Oncology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University of Missouri ColumbiaMO United States Department of Biostatistics and Health Data Science Indiana University School of Medicine IndianapolisIN United States Children's Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Helmholtz AI Helmholtz Munich Germany Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Germany San FranciscoCA United States Biomedical Image Analysis and Machine Learning Department of Quantitative Biomedicine University of Zurich Switzerland Department of Neuroradiology Technical University of Munich Munich Germany University of San Diego CA United States Cornell University IthacaNY United States Department of Radiology Northwestern University EvanstonIL United States Duke University Medical Center School of Medicine DurhamNC United States Lab Crestview Radiology Lagos Nigeria Sage Bionetworks United States McGill University MontrealQC Canada Children's National Hospital WashingtonDC United States George Washington University WashingtonDC United State

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, T2/FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps. © 2024, CC BY.

关键词： Tumors

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Snowmass 2021 Computational Frontier CompF03 Topical Group Report: Machine Learning

arXiv

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arXiv 2022年

作者： Shanahan, Phiala Terao, Kazuhiro Whiteson, Daniel Aarts, Gert Adelmann, Andreas Akchurin, N. Alexandru, Andrei Amram, Oz Andreassen, Anders Apresyan, Artur Avestruz, Camille Bartoldus, Rainer Bechtol, Keith Benkendorfer, Kees Benelli, Gabriele Bernius, Catrin Bogatskiy, Alexander Bortolato, Blaz Boyda, Denis Brooijmans, Gustaaf Calafiura, Paolo Calì, Salvatore Canelli, Florencia Chachamis, Grigorios Chekanov, S.V. Chen, Deming Chen, Thomas Y. Ćiprijanović, Aleksandra Collins, Jack H. Connolly, Andrew J. Coughlin, Michael Dai, Biwei Damgov, J. DeZoort, Gage Diaz, Daniel Dillon, Barry M. Dinu, Ioan-Mihail Dong, Zhongtian Donini, Julien Duarte, Javier Dugad, S. Dvorkin, Cora Faroughy, D.A. Feickert, Matthew Feng, Yongbin Fenton, Michael Foreman, Sam De Freitas, Felipe F. Funcke, Lena Gc, P. Gandrakota, Abhijith Ganguly, Sanmay Garrison, Lehman H. Gessner, Spencer Ghosh, Aishik Gonsk, Julia Graham, Matthew Gray, Lindsey Grönroos, S. Hackett, Daniel C. Harris, Philip Hauck, Scott Herwig, Christian Holzman, Burt Hopkins, Walter Hsu, Shih-Chieh Huang, Jin Huang, Yi Jin, Xiao-Yong Kagan, Michael Kah, Alan Kamenik, Jernej F. Kansal, Raghav Karagiorgi, Georgia Kasieczka, Gregor Katsavounidis, Erik Khoda, Elham E. Khosa, Charanjit K. Kipf, Thomas Komiske, Patrick Komm, Matthias Kondor, Risi Kourlitis, Evangelos Krause, Claudius Lamichhane, K. Le Pottier, Luc Lin, Meifeng Lin, Yin Liu, Mia Lu, Nan Lucini, Biagio Martinez, J. Martín-Ramiro, Pablo Matevc, Andrej McCormack, William Patrick Metodiev, Eric Mikuni, Vinicius Miller, David W. Mishra-Sharma, Siddharth Mukherjee, Samadrita Murnane, Daniel Nachman, Benjamin Narayan, Gautham Neubauer, Mark Ngadiuba, Jennifer Norberg, Scarlet Nord, Brian Ochoa, Inês Offermann, Jan T. Park, Sang Eon Pedro, Kevin Peña, Cristían Perloff, Alexx Pettee, Mariel Pierini, Maurizio Quast, T. Rankin, Dylan Ren, Yihui Rieger, Marcel Vlimant, Jean-Roch Roy, Avik Sanz, Veronica Sarda, Nilai Savard, Claire Scheinker, Alexander Seljak, Uroš Sheldon, Brian Shih, David Shimmin, Chase Smolkovic, Aleks Ste Swansea University SwanseaSA2 8PP United Kingdom Villazzano38123 Italy Paul Scherrer Institute PSI Villigen5232 Switzerland Texas Tech University LubbockTX79409 United States The George Washington University WashingtonDC20052 United States University of Maryland College ParkMD20742 United States The Johns Hopkins University BaltimoreMD21211 United States Google Mountain ViewCA94043 United States Fermi National Accelerator Laboratory BataviaIL60510 United States University of Michigan Ann ArborMI48109 United States SLAC National Accelerator Laboratory StanfordCA94309 United States University of Wisconsin-Madison 1150 University Avenue MadisonWI53706-1390 United States Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Reed College PortlandOR97202 United States Flatiron Institute 162 5th Avenue New YorkNY10010 United States Jožef Stefan Institute Jamova 39 Ljubljana1000 Slovenia Argonne National Laboratory ArgonneIL60439 United States The NSF AI Institute for Artificial Intelligence and Fundamental Interactions United States Nevis Laboratories Columbia University 136 S Broadway IrvingtonNY United States Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States University of Zurich Winterthurerstrasse 190 Zurich8057 Switzerland Switzerland University of Illinois at Urbana-Champaign ChampaignIL61820 United States University of Washington SeattleWA98195 United States University of Minnesota MinneapolisMN55455 United States Berkeley Center for Cosmological Physics University of California Berkeley United States Princeton University PrincetonNJ08544 United States University of California La Jolla San DiegoCA92093 United States University of Heidelberg Heidelberg Germany University of Kansas 1251 Wescoe Hall Dr. LawrenceKS66045 United States Université Clermont Auvergne France Tata Institute of Fundamental Research Mumbai400005 India Harvard University

The rapidly-developing intersection of machine learning (ML) with high-energy physics (HEP) presents both opportunities and challenges to our community. Far beyond applications of standard ML tools to HEP problems, genuinely new and potentially revolutionary approaches are being developed by a generation of talent literate in both fields. There is an urgent need to support the needs of the interdisciplinary community driving these developments, including funding dedicated research at the intersection of the two fields, investing in high-performance computing at universities and tailoring allocation policies to support this work, developing of community tools and standards, and providing education and career paths for young researchers attracted by the intellectual vitality of machine learning for high energy physics. © 2022, CC BY.

关键词： High energy physics

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Correction: Assessing real-world gait with digital technology? Validation, insights and recommendations from the Mobilise-D consortium

引用

Journal of neuroengineering and rehabilitation 2024年第1期21卷 71页

作者： M Encarna Micó-Amigo Tecla Bonci Anisoara Paraschiv-Ionescu Martin Ullrich Cameron Kirk Abolfazl Soltani Arne Küderle Eran Gazit Francesca Salis Lisa Alcock Kamiar Aminian Clemens Becker Stefano Bertuletti Philip Brown Ellen Buckley Alma Cantu Anne-Elie Carsin Marco Caruso Brian Caulfield Andrea Cereatti Lorenzo Chiari Ilaria D'Ascanio Bjoern Eskofier Sara Fernstad Marcel Froehlich Judith Garcia-Aymerich Clint Hansen Jeffrey M Hausdorff Hugo Hiden Emily Hume Alison Keogh Felix Kluge Sarah Koch Walter Maetzler Dimitrios Megaritis Arne Mueller Martijn Niessen Luca Palmerini Lars Schwickert Kirsty Scott Basil Sharrack Henrik Sillén David Singleton Beatrix Vereijken Ioannis Vogiatzis Alison J Yarnall Lynn Rochester Claudia Mazzà Silvia Del Din Translational and Clinical Research Institute Faculty of Medical Sciences Newcastle University Newcastle Upon Tyne UK. Department of Mechanical Engineering and Insigneo Institute for in Silico Medicine The University of Sheffield Sheffield UK. Laboratory of Movement Analysis and Measurement Ecole Polytechnique Federale de Lausanne Lausanne Switzerland. Machine Learning and Data Analytics Lab Department of Artificial Intelligence in Biomedical Engineering Friedrich-Alexander-Universität Erlangen Nürnberg Erlangen Germany. Center for the Study of Movement Cognition and Mobility Neurological Institute Tel Aviv Sourasky Medical Center Tel Aviv Israel. Department of Biomedical Sciences University of Sassari Sassari Italy. Department of Electronics and Telecommunications Politecnico di Torino Turin Italy. National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre (BRC) Newcastle University and The Newcastle Upon Tyne Hospitals NHS Foundation Trust Newcastle Upon Tyne UK. Robert Bosch Gesellschaft für Medizinische Forschung Stuttgart Germany. The Newcastle Upon Tyne Hospitals NHS Foundation Trust Newcastle Upon Tyne UK. School of Computing Newcastle University Newcastle Upon Tyne UK. Barcelona Institute for Global Health (ISGlobal) Barcelona Spain. Universitat Pompeu Fabra Barcelona Catalonia Spain. CIBER Epidemiología y Salud Pública (CIBERESP) Madrid Spain. Insight Centre for Data Analytics University College Dublin Dublin Ireland. School of Public Health Physiotherapy and Sports Science University College Dublin Dublin Ireland. Department of Electrical Electronic and Information Engineering «Guglielmo Marconi» University of Bologna Bologna Italy. Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV) University of Bologna Bologna Italy. Grünenthal GmbH Aachen Germany. Department of Neurology University Medical Center Schleswig-Holstein Campus Kiel Kiel Germany. Sagol School of Neuroscien

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