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arXiv 2023年

作者： Eisenmann, M. Reinke, A. Weru, V. Tizabi, M.D. Isensee, F. Adler, T.J. Ali, S. Andrearczyk, V. Aubreville, M. Baid, U. Bakas, S. Balu, N. Bano, S. Bernal, J. Bodenstedt, S. Casella, A. Cheplygina, V. Daum, M. de Bruijne, M. Depeursinge, A. Dorent, R. Egger, J. Ellis, D.G. Engelhardt, S. Ganz, M. Ghatwary, N. Girard, G. Godau, P. Gupta, A. Hansen, L. Harada, K. Heinrich, M. Heller, N. Hering, A. Huaulmé, A. Jannin, P. Kavur, A.E. Kodym, O. Kozubek, M. Li, J. Li, H. Ma, J. Martín-Isla, C. Menze, B. Noble, A. Oreiller, V. Padoy, N. Pati, S. Payette, K. Rädsch, T. Rafael-Patiño, J. Bawa, V. Singh Speidel, S. Sudre, C.H. van Wijnen, K. Wagner, M. Wei, D. Yamlahi, A. Yap, M.H. Yuan, C. Zenk, M. Zia, A. Zimmerer, D. Aydogan, D. Bhattarai, B. Bloch, L. Brüngel, R. Cho, J. Choi, C. Dou, Q. Ezhov, I. Friedrich, C.M. Fuller, C. Gaire, R.R. Galdran, A. Faura, Á. García Grammatikopoulou, M. Hong, S. Jahanifar, M. Jang, I. Kadkhodamohammadi, A. Kang, I. Kofler, F. Kondo, S. Kuijf, H. Li, M. Luu, M. Martinčič, T. Morais, P. Naser, M.A. Oliveira, B. Owen, D. Pang, S. Park, J. Park, S. Plotka, S. Puybareau, E. Rajpoot, N. Ryu, K. Saeed, N. Shephard, A. Shi, P. Štepec, D. Subedi, R. Tochon, G. Torres, H.R. Urien, H. Vilaça, J.L. Wahid, K.A. Wang, H. Wang, J. Wang, L. Wang, X. Wiestler, B. Wodzinski, M. Xia, F. Xie, J. Xiong, Z. Yang, S. Yang, Y. Zhao, Z. Maier-Hein, K. Jäger, P.F. Kopp-Schneider, A. Maier-Hein, L. Heidelberg Germany Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Germany Heidelberg Germany School of Computing Faculty of Engineering and Physical Sciences University of Leeds Leeds United Kingdom Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington SeattleWA United States Department of Computer Science University College London London United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Biomedical Imaging Group Rotterdam Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam Netherlands Department of Computer Science University of Copenhagen Copenhagen Denmark Sierre Switzerland Harvard Medical School Brigham and Women’s Hospital BostonMA United States School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Essen Germany University of Nebraska Medical Center OmahaNE United States Department of Internal Medicine III Heidelberg University Hospital Heidelberg Germany Neurobiology Research Unit Copenhagen University Hospital Rigshospitalet C

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work. © 2023, CC BY.

关键词： Benchmarking

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

arXiv

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arXiv 2023年

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

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

关键词： Clinical research

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Influence of human engineering on manning levels and human performance on ships

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NAVAL ENGINEERS JOURNAL 1997年第5期109卷 67-76页

作者： Anderson, DE Oberman, FR Malone, TB Baker, CC David E. Anderson:has a bachelor of science degree in environmental engineering from Florida Technological University and a master's degree in environmental engineering from the University of Central Florida. He is a graduate of the Naval Sea Systems Command's Engineer-In-Training (EIT) Program. Mr. Anderson was instrumental in introducing the collective protection system (CPS) in the U.S. Navy developing the initial forward-fit package for the USS Gunston Hall and the engineering change proposal (ECP) for the USS Wasp. In 1990 he joined the Human Systems Integration (HSI) Division (SEA 55W5) where he was task leader for auxiliary ships. He is currently the HSI manager for the future technology variant of the SeaLift ship and the future carrier. Association of Scientists and Engineers 33rdAnnual Technical Symposium 26 April 1996. Fred R. Oberman:has B.A. and M.A. degrees from the University of Chicago and Loyola University (experimental psychology) and an M.S. degree in industrial engineering and operations research from Virginia Polytechnic Institute (VPI). He has more than 30 years experience in HSI management planning research analysis design and testing in government and private sector positions. He is currently responsible for NavSea HSI generic research and tool development efforts. He is responsible for Human Engineering Specifications and Standards (Commercial Hypertext) and is the NavSea 03D7 representative on HSI in Performance Specifications and for integration of HSI within Integrated Logistic Support (ILS). He has served as DoD HSI SubTAG chair and member of the Simulation and Modeling Test and Evaluation Display and Control Systems Human Computer Interaction Specifications and Standards and Systems Design Sub Tags as a member of the Society of Naval Architects and Marine Engineers (SNAME) Systems Safety Panel and a member of NATO RSG 14 on man-machine analysis. Thomas B. Malone: CHFEP received a Ph.D. in experimental psychology from Fordham University in 1964. He is president of Carlow

The objectives of Human Engineering (HE) are generally viewed as increasing human performance, reducing human error, enhancing personnel and equipment safety, and reducing training and related personnel costs. There are other benefits that are thoroughly consistent with the direction of the Navy of the future, chief among these is reduction of required numbers of personnel to operate and maintain Navy ships. The Naval research Advisory Committee (NRAC) report on Man-machine Technology in the Navy estimated that one of the benefits from increased application of man-machine technology to Navy ship design is personnel reduction as well as improving system availability, effectiveness, and safety The objective of this paper is to discuss aspects of the human engineering design of ships and systems that affect manning requirements, and impact human-performance and safety The paper will also discuss how the application of human engineering leads to improved performance, and crew safety, and reduced workload, all of which influence manning levels. Finally, the paper presents a discussion of tools and case studies of good human engineering design practices which reduce manning.

关键词： Human engineering

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TEMPLATES: Characterization of a Merger in the Dusty Lensing SPT0418-47 System

arXiv

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arXiv 2023年

作者： Cathey, Jared Gonzalez, Anthony H. Lower, Sidney Phadke, Kedar A. Spilker, Justin Aravena, Manuel Bayliss, Matthew Birkin, Jack E. Birrer, Simon Chapman, Scott Dahle, Håkon Hayward, Christopher C. Hezaveh, Yashar Hill, Ryley Hutchison, Taylor A. Kim, Keunho J. Mahler, Guillaume Marrone, Daniel P. Narayanan, Desika Navarre, Alexander Reuter, Cassie Rigby, Jane R. Sharon, Keren Solimano, Manuel Sulzenauer, Nikolaus Vieira, Joaquin Vizgan, David Department of Astronomy University of Florida 211 Bryant Space Sciences Center GainesvilleFL32611 United States Department of Astronomy University of Illinois 1002 West Green St. UrbanaIL61801 United States Center for AstroPhysical Surveys National Center for Supercomputing Applications 1205 West Clark Street UrbanaIL61801 United States Department of Physics and Astronomy George P. and Cynthia Woods Mitchell Institute for Fundamental Physics and Astronomy Texas A&M University 4242 TAMU College StationTX77843-4242 United States Núcleo de Astronomía Facultad de Ingeniería y Ciencias Universidad Diego Portales Av. Ejercito 441 Santiago Chile Department of Physics University of Cincinnati CincinnatiOH45221 United States Department of Physics and Astronomy Stony Brook University Stony BrookNY11794 United States Department of Physics and Atmospheric Science Dalhousie University HalifaxNSB3H 4R2 Canada NRC Herzberg Astronomy and Astrophysics 5071 West Saanich Rd VictoriaBCV9E 2E7 Canada Department of Physics and Astronomy University of British Columbia VancouverBCV6T1Z1 Canada Eureka Scientific Inc OaklandCA94602 United States Institute of Theoretical Astrophysics University of Oslo P.O. Box 1029 Blindern OsloNO-0315 Norway Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Physics Université de Montréal Montréal Canada Ciela - Montreal Institute for Astrophysical Data Analysis and Machine Learning Montréal Canada Mila - Quebec Artificial Intelligence Institute Montréal Canada Observational Cosmology Lab NASA Goddard Space Flight Center Code 665 8800 Greenbelt Rd. GreenbeltMD20771 United States Centre for Extragalactic Astronomy Durham University South Road DurhamDH1 3LE United Kingdom Institute for Computational Cosmology Durham University South Road DurhamDH1 3LE United Kingdom Steward Observatory University of Arizona 933 North Cherry Avenue TucsonAZ85721

We present JWST and ALMA results for the lensing system SPT0418−47, which includes a strongly-lensed, dusty star-forming galaxy at redshift z = 4.225 and an associated multiply-imaged companion. JWST NIRCam and MIRI imaging observations presented in this paper were acquired as part of the Early Release Science program Targeting Extremely Magnified Panchromatic Lensed Arcs and Their Extended Star Formation (TEMPLATES). This data set provides robust, mutiwavelength detection of stellar light in both the main (SPT0418A) and companion (SPT0418B) galaxies, while the ALMA detection of [C II] emission confirms that SPT0418B lies at the same redshift as SPT0418A. From a source plane reconstruction, we infer that the projected physical separation of the two galaxies is 4.42 ±0.05 kpc. We derive total magnifications of µ = 29.5 ±1.2 and µ = 4.2 ±0.9 for SPT0418A and SPT0418B, respectively. We use both cigale and prospector to derive stellar masses. The stellar mass ratio of SPT0418A and SPT0418B is approximately 4 to 1 (4.5 ± 1.0 for cigale and 4.2+1.9−1.6 for prospector). We also see evidence of extended structure associated with SPT0418A in the lensing reconstruction that is suggestive of a tidal feature. Interestingly, the star formation rates and stellar masses of both galaxies are consistent with the main sequence of star-forming galaxies at this epoch, indicating that this ongoing interaction has not noticeably elevated the star formation levels. © 2023, CC BY.

关键词： Galaxies

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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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Correction to: Gait variability as digital biomarker of disease severity in Huntington's disease

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Journal of neurology 2020年第6期267卷 1602页

作者： Heiko Gaßner Dennis Jensen Franz Marxreiter Anja Kletsch Stefan Bohlen Robin Schubert Lisa M Muratori Bjoern Eskofier Jochen Klucken Jürgen Winkler Ralf Reilmann Zacharias Kohl Department of Molecular Neurology University Hospital Erlangen Friedrich-Alexander University Erlangen-Nürnberg (FAU) Schwabachanlage 6 91054 Erlangen Germany. George-Huntington Institute (GHI) GmbH Münster Germany. Rehabilitation Research and Movement Performance Laboratory (RRAMP Lab) Stony Brook University Stony Brook NY USA. Machine Learning and Data Analytics Lab Friedrich-Alexander University Erlangen-Nürnberg (FAU) Erlangen Germany. Medical Valley-Digital Health Application Center GmbH Bamberg Germany. Fraunhofer Institute for Integrated Circuits IIS Erlangen Germany. Department of Radiology University of Muenster Muenster Germany. Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research University of Tuebingen Tuebingen Germany. Department of Molecular Neurology University Hospital Erlangen Friedrich-Alexander University Erlangen-Nürnberg (FAU) Schwabachanlage 6 91054 Erlangen Germany. Zacharias.Kohl@klinik.uni-regensburg.de. Center for Rare Diseases Erlangen University Hospital Erlangen Erlangen Germany. Zacharias.Kohl@klinik.uni-regensburg.de. Department of Neurology University of Regensburg Regensburg Germany. Zacharias.Kohl@klinik.uni-regensburg.de.

The original version of this article unfortunately contained a mistake. The name of one author is not presented correctly in the author group.

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

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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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Quantum computing at the frontiers of biological sciences

arXiv

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arXiv 2019年

作者： Emani, Prashant S. Warrell, Jonathan Anticevic, Alan Bekiranov, Stefan Gandal, Michael McConnell, Michael J. Sapiro, Guillermo Aspuru-Guzik, Alán Baker, Justin Bastiani, Matteo McClure, Patrick Murray, John Sotiropoulos, Stamatios N. Taylor, Jacob Senthil, Geetha Lehner, Thomas Gerstein, Mark B. Harrow, Aram W. Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Yale School of Medicine Department of Psychiatry New HavenCT06511 United States University of Virginia School of Medicine Department of Biochemistry and Molecular Genetics CharlottesvilleVA22903 United States Department of Psychiatry Semel Institute David Geffen School of Medicine University of California–Los Angeles 695 Charles E. Young Drive South Los AngelesCA90095 United States Univ. of Virginia School of Medicine Department of Neuroscience CharlottesvilleVA22903 United States Department of Electrical and Computer Engineering Duke University DurhamNC27708 United States Department of Chemistry University of Toronto 80 St. George Street TorontoONM5S 3H6 Canada TorontoONM5S 1M1 Canada CIFAR Artificial Intelligence Research Chair Vector Institute TorontoONM5S 1M1 Canada Department of Computer Science University of Toronto 40 St. George Street TorontoONM5S 2E4 Canada Schizophrenia and Bipolar Disorder Program McLean Hospital BelmontMA02478 United States Department of Psychiatry Harvard Medical School BostonMA02114 United States Sir Peter Mansfield Imaging Centre School of Medicine University of Nottingham NottinghamNG7 2RD United Kingdom Machine Learning Team National Institute of Mental Health BethesdaMD20892 United States Section on Functional Imaging Methods National Institute of Mental Health BethesdaMD20892 United States Department of Psychiatry Yale University School of Medicine New HavenCT06511 United States Department of Physics Yale University New HavenCT06511 United States Joint Center for Quantum Information and Computer Science University of Maryland College ParkMD20742 United States National Institute of Standards and Technology GaithersburgMD20899 United States Office of Genomics Research Coordination N

The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems. Innovation in massively parallel, classical computing hardware and algorithms continues to address many of these challenges, but there is a need to simultaneously consider new paradigms to circumvent current barriers to processing speed. Accordingly, we articulate a view towards quantum computation and quantum information science, where algorithms have demonstrated potential polynomial and exponential computational speedups in certain applications, such as machine learning. The maturation of the field of quantum computing, in hardware and algorithm development, also coincides with the growth of several collaborative efforts to address questions across length and time scales, and scientific disciplines. We use this coincidence to explore the potential for quantum computing to aid in one such endeavor: the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. By examining joint opportunities for computational innovation across fields, we highlight the need for a common language between biological data analysis and quantum computing. Ultimately, we consider current and future prospects for the employment of quantum computing algorithms in the biological sciences. Copyright © 2019, The Authors. All rights reserved.

关键词： machine learning

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

引用

Nature chemical biology 2018年第9期14卷 901-901页

作者： Kiryl D Piatkevich Erica E Jung Christoph Straub Changyang Linghu Demian Park HoJun Suk Daniel R Hochbaum Daniel Goodwin Eftychios Pnevmatikakis Nikita Pak Takashi Kawashima ChaoTsung Yang Jeffrey L Rhoades Or Shemesh Shoh Asano YoungGyu Yoon Limor Freifeld Jessica L Saulnier Clemens Riegler Florian Engert Thom Hughes Mikhail Drobizhev Balint Szabo Misha B Ahrens Steven W Flavell Bernardo L Sabatini Edward S Boyden Media Lab Massachusetts Institute of Technology (MIT) Cambridge MA USA. Howard Hughes Medical Institute Department of Neurobiology Harvard Medical School Boston MA USA. Department of Electrical Engineering and Computer Science MIT Cambridge MA USA. Harvard-MIT Division of Health Sciences and Technology MIT Cambridge MA USA. Simons Center Data Analysis Simons Foundation New York NY USA. Department of Mechanical Engineering MIT Cambridge MA USA. Janelia Research Campus Howard Hughes Medical Institute Ashburn Virginia USA. Picower Institute for Learning & Memory and Department of Brain & Cognitive Sciences MIT Cambridge MA USA. Department of Molecular and Cellular Biology and Center for Brain Science Harvard University Cambridge MA USA. Department of Neurobiology Faculty of Life Sciences University of Vienna Wien Austria. Department of Cell Biology and Neuroscience Montana State University Bozeman Montana USA. Department of Biological Physics Eotvos University Budapest Hungary. Media Lab Massachusetts Institute of Technology (MIT) Cambridge MA USA. esb@media.mit.edu. Department of Biological Engineering MIT Cambridge MA USA. esb@media.mit.edu. MIT Center for Neurobiological Engineering MIT Cambridge MA USA. esb@media.mit.edu. Department of Brain and Cognitive Sciences MIT Cambridge MA USA. esb@media.mit.edu. MIT McGovern Institute for Brain Research MIT Cambridge MA USA. esb@media.mit.edu.

In the version of this article originally published, the bottom of Figure 4f,g was partially truncated in the PDF. The error has been corrected in the PDF version of this article.

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