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Correction to: SleepBoost: a multi‑level tree‑based ensemble model for automatic sleep stage classification

Medical & biological engineering & computing 2024年第9期62卷 2785页

作者： Akib Zaman Shiu Kumar Swakkhar Shatabda Iman Dehzangi Alok Sharma Computer Science and Artificial Intelligence Laboratory (CSAIL) Electrical Engineering and Computer Science Department Massachusetts Institute of Technology Cambridge MA USA. School of Electrical & Electronics Engineering Fiji National University Suva Fiji. shiu.kumar@fnu.ac.fj. Centre for Artificial Intelligence and Robotics (CAIR) United International University Dhaka Bangladesh. Department of Computer Science Rutgers University Camden NJ USA. Center for Computational and Integrative Biology Rutgers University Camden USA. Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230‑0045 Japan. Institute for Integrated and Intelligent Systems Griffith University Nathan Brisbane QLD Australia.

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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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Common Limitations of Image Processing Metrics: A Picture Story

arXiv

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arXiv 2021年

作者： Reinke, Annika Tizabi, Minu D. Sudre, Carole H. Eisenmann, Matthias Rädsch, Tim Baumgartner, Michael Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Bankhead, Peter Benis, Arriel Blaschko, Matthew Buettner, Florian Cardoso, M. Jorge Chen, Jianxu Cheplygina, Veronika Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Engelhardt, Sandy Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hamprecht, Fred Hashimoto, Daniel A. Heckmann-Nötzel, Doreen Hirsch, Peter Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kavur, A. Emre Kenngott, Hannes Kleesiek, Jens Kleppe, Andreas Koehler, Sven Kofler, Florian Kopp-Schneider, Annette Kooi, Thijs Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moher, David Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Noyan, M. Alican Petersen, Jens Polat, Gorkem Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Rieke, Nicola Riegler, Michael A. Rivaz, Hassan Saez-Rodriguez, Julio Sánchez, Clara I. Schroeter, Julien Saha, Anindo Selver, M. Alper Sharan, Lalith Shetty, Shravya Smeden, Maarten V.A.N. Stieltjes, Bram Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben V.A.N. Varoquaux, Gaël Wiesenfarth, Manuel Yaniv, Ziv R. Jäger, Paul Maier-Hein, Lena Division of Intelligent Medical Systems and HI Helmholtz Imaging Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Intelligent Medical Systems Heidelberg Germany NCT Heidelberg DKFZ University Medical Center Heidelberg Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Division of Medical Image Computing Heidelberg Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Institute of Genetics and Cancer University of Edinburgh Edinburgh United Kingdom Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Kasteelpark Arenberg 10 - box 2441 Leuven3001 Belgium Frankfurt/Mainz DKFZ UCT Frankfurt-Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany Frankfurt Cancer Insititute Germany Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for St

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide. © 2021, CC BY.

关键词： Medical imaging

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Opening remarks

2016 International Conference on Advances in Human Machine I...

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2016 International Conference on Advances in Human Machine Interaction, HMI 2016 2016年

作者： Nagaraja, Ch. Swamy, J. Nagendra Rajendra, J. Khan, M.S. Vishwanath Reddy, D.S. Manjunath, N. Dillmann, Ruediger Tarn, Tzyh Jong Zhao, Qianchuan Ammi, Mehdi Zuberek, Wlodek M. Sandhu, P.S. Patthira Newman, K. De Silva Liyanage, Chandratilak Hassan, Sohair Aly Aly Sun, Kien Wen Rahman, Md. Moshiur Ordoño, E. Evangelista Sharma, R.K. Mishra, Preeti Chandel, B.S. Singla, Ekta Petric, Tadej Zhong, Yu Jiglar, Janson Alemzadeh, Kazem Asokan, T. Tripathi, Animesh Tripathi, Manoj Ram, Swaminath Shrma, M.K. Panday, P.N. Kumar, Devendra Hinchey, Mike Stilman, Boris Suraj, Zbigniew Pal, Sankar K. Sasi, Sreela Rajan, Deepu Marshall, Roger G. Abraham, Ajith Peter S, David Paul, Vargheese Gopakumar, V. Dustdar, Schahram Soto, Sebastián Ventura Rausch, Andreas Angelis, Lefteris Nelson, Andrew L. Botzheim, Janos Bernardino, Heder Soares Zboril, Frantisek Ane, Bernadetta Kwintiana Maeda, Toshiyuki Sakalauskas, Virgilijus Hann, Garenth Lim King Samek, Jan Romero Salguero, José Raúl Varghese, Kuruvilla Kriksciuniene, Dalia Mathew, Jimson Reif, Wolfgang Mauri, Giancarlo Cabrerizo Lorite, Francisco Javier Özcan, Ender Cho, Sung-Bae Paily, Roy P. Rezankova, Hana Tudjarov, Boris Hong, Wei-Chiang De Oliveira, José Valente Flores Romero, Juan Jose Oskouei, Rozita Jamili Cicchetti, Antonio Roy, Chanchal Segura, Sergio Samuel, C. Mallet, Frédéric Mernik, Marjan Punnekkat, Sasikumar Waseemulla, A. Sri Devaraj Urs Educational Trust Bangalore India R. L. Jalappa Institute of Technology Doddaballapur Bangalore India Humanoids and Intelligence Systems Lab Kalsruhe Germany Electrical and Systems Engineering Washington University in St. Louis United States Deputy Director of Center for Intelligent and Networked Systems Department of Automation Tsinghua University Beijing China Department of Computer Science CNRS/LIMSI Lab AMI Group France Memorial University St. John'sNL Canada RBIT and Bio-Technology India LR University Thailand University of Colorado at Boulder Boulder United States Faculty of Science University of Brunei Brunei University of Kuala Lumpur Malaysia National Chiao Tung University Taiwan EPR Centre Bangladesh Mapua Institute of Technology Philippines ARO CWC Lucknow India Mpec Kanpur India DSC DBS Kanpu India Indian Institute of Technology Ropar India Jozaf Stefan Institute Department of Automation Biocyernetics and Robotics Ljubljana Slovenia Robotics Institute Carnegie Mellon University Pittsburgh United States Faculty of Engineering University of Bristol United Kingdom Department of Engineering Design Indian Institute of Technology Madras India Lucknow Uni Lucknow India CSJM Uni Kanpur India UPPCB Lucknow India PCB Roorkee India Awadh Uni Faijabad India Agra Uni Agra India Lero University of Limerick Ireland University of Colorado Denver United States University of Rzeszow Poland Indian Statistical Institute Kolkata India Gannon University PA United States Nanyang Technical University Singapore Singapore Plymouth State University NH United States MIR Labs United States Cochin University of Science and Technology India State Project Facilitation Unit TEQIP Kerala India Technical University of Vienna Austria University of Cordoba Spain Clausthal University of Technology Germany Aristotle University of Thessaloniki Greece Androtics LLC TucsonAZ United States Tokyo Metropolitan University Japan Federal Unive

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GardnerNet: An Interpretable Deep Learning Model for Quantitative Human Blastocyst Evaluation - A Retrospective Model Development and Validation Study

SSRN

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SSRN 2024年

作者： Liu, Hang Chen, Longbin Shan, Guanqiao Sun, Chen Liao, Hongqing Lu, Changfu Zhang, Shuoping Dong, Shaonan Xu, Xinxin Yan, Qiuyun Gong, Fei Zhang, Zhuoran Dai, Changsheng Chen, Wenyuan Song, Haocong Chen, Lei Sun, Haixiang Wang, Shanshan Lin, Ge Sun, Yu Gu, Yifan Department of Mechanical and Industrial Engineering University of Toronto 5 King’s College Road TorontoONM5S 3G8 Canada Institute of Reproductive and Stem Cell Engineering School of Basic Medical Science Central South University 172 Tongzipo Road Hunan Province Changsha China Hengyang Nanhua-Xinghui Reproductive Health Hospital 30 Jiefang Road Hunan Province Hengyang China The second Affiliated Hospital Hengyang Medical School University of South China 30 Jiefang Road Hunan Province Hengyang City China Reproductive & Genetic Hospital of CITIC-Xiangya 567 Tongzipo Road Hunan Province Changsha China NHC Key Laboratory of Human Stem Cell and Reproductive Engineering School of Basic Medical Science Central South University 172 Tongzipo Road Hunan Province Changsha China Clinical Research Center for Reproduction and Genetics in Hunan Province Reproductive & Genetic Hospital of CITIC-Xiangya 567 Tongzipo Road Hunan Province Changsha China School of Science and Engineering The Chinese University of Hong Kong-Shenzhen 2001 Longxiang Boulevard Longgang District Shenzhen China Institute of Robotics and Intelligent Systems Dalian University of Technolgy 2 Linggong Road Liaoning Province Dalian China Department of Computer Science University of Toronto 40 St George Street TorontoONM5S 2E4 Canada Center for Reproductive Medicine and Obstetrics and Gynecology Nanjing Drum Tower Hospital Nanjing University Medical School 321 Zhongshan Road Jiangsu Province Nanjing China National Engineering and Research Center of Human Stem Cell 8 Luyun Road Jiangsu Province Changsha China Department of Electrical and Computer Engineering 10 King’s College Road TorontoONM5S 3G8 Canada Institute of Biomedical Engineering University of Toronto 164 College Street TorontoONM5S 3G9 Canada

Background: Selecting the blastocyst with the highest potential for live birth from a cohort is crucial for the success of in vitro fertilization (IVF). While the Gardner and Schoolcraft morphological grading system, commonly known as the Gardner grading system, is widely used by embryologists worldwide, blastocysts having similar or the same inner cell mass (ICM) and trophectoderm (TE) grades cause challenges for embryologists in decision-making. Furthermore, human assessment is subjective and inconsistent in predicting which blastocysts have higher potential to result in live birth. This study aims to develop an interpretable, quantitative method aligned with the Gardner grading system, providing continuous scores that correlate with live birth outcomes, thereby assisting embryologists in improving blastocyst selection. Methods: In this retrospective study, we developed GardnerNet, an interpretable deep learning model that outputs expansion degree grade and continuous scores quantifying a blastocyst's ICM morphology and TE morphology, based on the Gardner grading system. The continuous ICM and TE scores were calculated by weighting each base grade's predicted probability and summing the predicted probabilities. To represent each blastocyst's overall potential for live birth, we combined the ICM and TE scores using their odds ratios (ORs) for live birth. We further assessed the correlation between the ICM score, TE score, and the OR-combined score (adjusted for expansion degree) with live birth rates by applying GardnerNet to blastocysts with known live birth outcomes. To test its generalizability, we also applied GardnerNet to an external IVF institution, accounting for variations in imaging conditions, live birth rates, and embryologists' experience levels. Findings: GardnerNet was developed using data from 2760 blastocysts with majority-voted grades for expansion degree, ICM, and TE. The model achieved mean area under the receiver operating characteristic curve

关键词： Risk assessment

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Metrics Reloaded: Recommendations for image analysis validation

arXiv

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arXiv 2022年

作者： Maier-Hein, Lena Reinke, Annika Godau, Patrick Tizabi, Minu D. Buettner, Florian Christodoulou, Evangelia Glocker, Ben Isensee, Fabian Kleesiek, Jens Kozubek, Michal Reyes, Mauricio Riegler, Michael A. Wiesenfarth, Manuel Emre Kavur, A. Sudre, Carole H. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Rädsch, Tim Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Jorge Cardoso, M. Cheplygina, Veronika Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian Ginneken, Bram Van Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kofler, Florian Kopp-Schneider, Annette Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rajpoot, Nasir Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Smeden, Maarten Van Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben Van Varoquaux, Gaël Jäger, Paul F. Heidelberg Division of Intelligent Medical Systems and HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt-Marburg Germany Heidelberg Goethe University Frankfurt Germany Department of Medicine Goethe University Frankfurt Germany Department of Informatics Frankfurt Cancer Insititute Germany Department of Computing Imperial College London London United Kingdom Heidelberg Division of Medical Image Computing and HI Applied Computer Vision Lab Germany Institute for AI in Medicine University Medicine Essen Essen Germany Centre for Biomedical Image Analysis Faculty of Informatics Masaryk University Brno Czech Republic ARTORG Center for Biomedical Engineering Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Bern Switzerland Simula Metropolitan Center for Digital Engineering Oslo Norway UiT The Arctic University of Norway Romsø Norway Heidelberg Division of Biostatistics Germany Heidelberg Division of Intelligent Medical Systems Division of Medical Image Computing HI Applied Computer Vision Lab Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Heidelberg Division of Medical Image Computing Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. It was developed by a large international consortium in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint – a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases. © 2022, CC BY.

关键词： Semantic Segmentation

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Understanding metric-related pitfalls in image analysis validation

arXiv

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arXiv 2023年

作者： Reinke, Annika Tizabi, Minu D. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Kavur, A. Emre Rädsch, Tim Sudre, Carole H. Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Buettner, Florian Cardoso, M. Jorge Cheplygina, Veronika Chen, Jianxu Christodoulou, Evangelia Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian van Ginneken, Bram Glocker, Ben Godau, Patrick Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Isensee, Fabian Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kleesiek, Jens Kofler, Florian Kooi, Thijs Kopp-Schneider, Annette Kozubek, Michal Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rafelski, Susanne M. Rajpoot, Nasir Reyes, Mauricio Riegler, Michael A. Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. van Calster, Ben Varoquaux, Gaël Yaniv, Ziv R. Jäger, Paul F. Maier-Hein, Lena Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany NCT Heidelberg A Partnership Between DKFZ University Medical Center Heidelberg Germany Heidelberg Division of Medical Image Computing Germany Heidelberg Division of Intelligent Medical Systems Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montreal Canada Division of Computational Pathology Dept of Pathology & Laboratory Medicine Indiana University School of Medicine IU Health Information and Translational Sciences Building Indianapolis United States University of Pennsylvania Richards Medical Research Laboratories FL7 PhiladelphiaPA United States Department of Digital Medical Technologies Holon Institute of Technology Holon Israel European Federation for Medical Informatics Le Mont-sur-Lausanne Switzerland Center for Processing Speech and Images Department of Electrical Engineering KU Leuven Leuven Belgium partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt Marburg Germany Heidelberg Germany Goethe University Frankfurt Department of Medicine Germany Goethe University Frankfurt Department of Informatics Germany and Frankfurt Cancer Insititute Germany Department of Computer Science IT University of Copenhagen Copenhagen Denmark Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V. Dortmund Germany Imaging Platform Broad Institute of MIT and Harvard CambridgeMA United States Centre for Statistics in Medicine University of Oxford Oxford United Kingdom Center for Biomedical In

Validation metrics are key for tracking scientific progress and bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately. While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. While focused on biomedical image analysis, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. The work serves to enhance global comprehension of a key topic in image analysis validation. © 2023, CC BY.

关键词： computer vision

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Energetic electron precipitation driven by electromagnetic ion cyclotron waves from ELFIN’s low altitude perspective

arXiv

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arXiv 2022年

作者： Angelopoulos, V. Zhang, X.-J. Artemyev, A.V. Mourenas, D. Tsai, E. Wilkins, C. Runov, A. Liu, J. Turner, D.L. Li, W. Khurana, K. Wirz, R.E. Sergeev, V.A. Meng, X. Wu, J. Hartinger, M.D. Raita, T. Shen, Y. An, X. Shi, X. Bashir, M.F. Shen, X. Gan, L. Qin, M. Capannolo, L. Ma, Q. Russell, C.L. Masongsong, E.V. Caron, R. He, I. Iglesias, L. Jha, S. King, J. Kumar, S. Le, K. Mao, J. McDermott, A. Nguyen, K. Norris, A. Palla, A. Roosnovo Tam, J. Xie, E. Yap, R.C. Ye, S. Young, C. Adair, L.A. Shaffer, C. Chung, M. Cruce, P. Lawson, M. Leneman, D. Allen, M. Anderson, M. Arreola-Zamora, M. Artinger, J. Asher, J. Branchevsky, D. Cliffe, M. Colton, K. Costello, C. Depe, D. Domae, B.W. Eldin, S. Fitzgibbon, L. Flemming, A. Frederick, D.M. Gilbert, A. Hesford, B. Krieger, R. Lian, K. McKinney, E. Miller, J.P. Pedersen, C. Qu, Z. Rozario, R. Rubly, M. Seaton, R. Subramanian, A. Sundin, S.R. Tan, A. Thomlinson, D. Turner, W. Wing, G. Wong, C. Zarifian, A. Earth Planetary and Space Sciences Department Institute of Geophysics and Planetary Physics University of California Los Angeles Los AngelesCA90095 United States University of Texas at Dallas RichardsonTX75080 United States CEA DAM DIF Arpajon France Atmospheric and Oceanic Sciences Departments University of California Los AngelesCA United States Johns Hopkins University Applied Physics Laboratory LaurelMD United States Department of Astronomy Center for Space Physics Boston University BostonMA United States Mechanical and Aerospace Engineering Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States School of Mechanical Industrial Manufacturing Engineering Oregon State University CorvallisOR97331 United States University of St. Petersburg St. Petersburg Russia Jet Propulsion Laboratory California Institute of Technology PasadenaCA91109 United States Space Science Institute BoulderCO80301 United States Sodankylä Geophysical Observatory University of Oulu Sodankylä Finland Materials Science and Engineering Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States Deloitte Consulting New YorkNY10112 United States Computer Science Department Henry Samueli School of Engineering University of California Los AngelesCA90095 United States Microsoft RedmondWA98052 United States Physics and Astronomy Department University of California Los AngelesCA90095 United States Department of Astronomy and Astrophysics The University of Chicago ChicagoIL60637 United States Raybeam Inc. Mountain ViewCA94041 United States SpaceX HawthorneCA90250 United States Reliable Robotics Corporation Mountain ViewCA94043 United States Los Alamos National Laboratory Los AlamosNM87545 United States Mathematics Department University of California Los AngelesCA90095 United States Planet Labs PBC San FranciscoCA94107 United States KSAT Inc. De

We review comprehensive observations of electromagnetic ion cyclotron (EMIC) wave-driven energetic electron precipitation using data from the energetic electron detector on the Electron Losses and Fields InvestigatioN (ELFIN) mission, two polar-orbiting low-altitude spinning CubeSats, measuring 50-5000 keV electrons with good pitch-angle and energy resolution. EMIC wave-driven precipitation exhibits a distinct signature in energy-spectrograms of the precipitating-to-trapped flux ratio: peaks at >0.5 MeV which are abrupt (bursty) (lasting ∼17s, or ∆L ∼ 0.56) with significant substructure (occasionally down to sub-second timescale). We attribute the bursty nature of the precipitation to the spatial extent and structuredness of the wave field at the equator. Multiple ELFIN passes over the same MLT sector allow us to study the spatial and temporal evolution of the EMIC wave - electron interaction region. Case studies employing conjugate ground-based or equatorial observations of the EMIC waves reveal that the energy of moderate and strong precipitation at ELFIN approximately agrees with theoretical expectations for cyclotron resonant interactions in a cold plasma. Using 2 years of ELFIN data uniformly distributed in local time, we assemble a statistical database of ∼50 events of strong EMIC wave-driven precipitation. Most reside at L ∼ 5 − 7 at dusk, while a smaller subset exists at L ∼ 8 − 12 at post-midnight. The energies of the peak-precipitation ratio and of the half-peak precipitation ratio (our proxy for the minimum resonance energy) exhibit an L-shell dependence in good agreement with theoretical estimates based on prior statistical observations of EMIC wave power spectra. The precipitation ratio’s spectral shape for the most intense events has an exponential falloff away from the peak (i.e., on either side of ∼ 1.45 MeV). It too agrees well with quasi-linear diffusion theory based on prior statistics of wave spectra. It should be noted though that this diffusive

关键词： Radiation belts

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK 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 Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

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 post-processing (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.

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MODELING AND CONTROL OF ELEVATORS BY STATECHARTS

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Asian Journal of Control 2008年第2期6卷

作者： Yi-Sheng Huang Sheng-Luen Chung Mu-Der Jeng Department of Aeronautical Engineering Chung Cheng Institute of Technology National Defense University Tashi Taoyuan 335 Taiwan R.O.C. Department of Electrical Engineering National Taiwan University of Science and Technology Taipei 106 Taiwan R.O.C. Department of Electrical Engineering National Taiwan Ocean University Kellung 202 Taiwan R.O.C. MuDer Jeng received the Ph.D. degree in computer and systems engineering from Rensselaer Polytechnic Institute Troy NY in 1992. Since August 1992 Dr. Jeng has been with National Taiwan Ocean University Keelung Taiwan where he is currently a full Professor at the Department of Electrical Engineering. His current research interests include Petri nets discrete event systems computer integrated manufacturing semiconductor factory automation embedded systems. Dr. Jeng is the author/co-author of over 120 book chapters journal papers and conference papers. Dr. Jeng received the Franklin V. Taylor Outstanding Paper Award from the IEEE Systems Man and Cybernetics Society in 1993. He was granted the Research Award by the National Science Council of Taiwan annually from 1994 to 2000. He is an Associate Editor for IEEE Transactions on Systems Man and Cybernetics-Part A IEEE Transactions on Robotics and Automation IEEE Transactions on Robotics and serves on the Editorial Board of International Journal of Computer Integrated Manufacturing. He has been a Guest Editor for eight leading journals. Dr. Jeng is the Chair of the Technical Committee on Discrete Event Systems of the IEEE SMC Society and the Founding Chair of the Technical Committee on Semiconductor Factory Automation of the IEEE Robotics and Automation Society. He served as the Exhibitions Chair of 2003 IEEE International Conference on Robotics and Automation and the Special Sessions Chair of 2004 IEEE International Conference on Networking Sensing and Control. He serves as a Program Co-Chair of 2005 IEEE International Conference on Networking Sensing and Control and the Organization Commit

Statechart has been utilized as a visual formalism for the modeling of complex and interactive systems for its illuminating features on describing properties of causality, concurrency, and synchronization. This paper presents the application of satechart to the modeling, design and implementation of an elevator system, whose system behavior involves aggregating complexity of state descriptions, and imposition of underlying control policy. Based on the operational flow of an elevator, we derive the associated statechart model by looking into the inherent hierarchical structure of the elevator. The advantage of the proposed approach is the clear presentation of system behavior in terms of conditions and events that cause the transitions in system dynamics. Implementation of the controlled elevator based on the modeled statechart is also presented.

关键词： Statechart interactive systems elevator

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