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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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A framework and resource for global collaboration in non-human primate neuroscience

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Current Research in Neurobiology 2023年 4卷 100079页

作者： Hartig, Renée Klink, P. Christiaan Polyakova, Zlata Dehaqani, Mohammad-Reza A. Bondar, Igor Merchant, Hugo Vanduffel, Wim Roe, Anna Wang Nambu, Atsushi Thirumala, M. Shmuel, Amir Kapoor, Vishal Gothard, Katalin M. Evrard, Henry C. Basso, Michele A. Petkov, Christopher I. Mitchell, Anna S. Max Planck Institute for Biological Cybernetics Max-Planck-Ring 11 Tübingen 72076 Germany Functional and Comparative Neuroanatomy Laboratory Werner Reichardt Centre for Integrative Neuroscience Eberhard Karls University of Tübingen Otfried-Müller-Straße 25 Tübingen 72076 Germany Department of Psychiatry and Psychotherapy University Medical Center Johannes Gutenberg-University Mainz 55131 Germany Nathan S. Kline Institute for Psychiatric Research Center for Biomedical Imaging and Neuromodulation Orangeburg New York 10962 United States Department of Vision and Cognition Netherlands Institute for Neuroscience Royal Netherlands Academy of Arts and Sciences Meibergdreef 47 Amsterdam 1105 BA Netherlands Laboratory of Visual Brain Therapy Sorbonne Université Institut National de la Santé et de la Recherche Médicale Centre National de la Recherche Scientifique Institut de la Vision Paris F-75012 France Experimental Psychology Helmholtz institute Utrecht University Heidelberglaan 1 Utrecht 3584 CS Netherlands Center for Human Nature Artificial Intelligence and Neuroscience Hokkaido University Sapporo 060-0812 Japan School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran School of Cognitive Sciences Institute for Research in Fundamental Sciences (IPM) Tehran Iran Department of Brain and Cognitive Sciences Cell Science Research Center Royan Institute for Stem Cell Biology and Technology ACECR Tehran Iran Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences Moscow Russian Federation Institute of Neurobiology Universidad Nacional Autónoma de México Campus Juriquilla Department of Neurophysiology Querétaro 76230 Mexico Laboratory for Neuro- and Psychophysiology Department of Neurosciences KU Leuven Medical School Leuven 3000 Belgium Leuven Brain Institute KU Leuven Leuven 3000 Belgium Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlest

As science and technology evolve, there is an increasing need for promotion of international scientific exchange. Collaborations, while offering substantial opportunities for scientists and benefit to society, also present challenges for those working with animal models, such as non-human primates (NHPs). Diversity in regulation of animal research is sometimes mistaken for the absence of common international welfare standards. Here, the ethical and regulatory protocols for 13 countries that have guidelines in place for biomedical research involving NHPs were assessed with a focus on neuroscience. Review of the variability and similarity in trans-national NHP welfare regulations extended to countries in Asia, Europe and North America. A tabulated resource was established to advance solution-oriented discussions and scientific collaborations across borders. Our aim is to better inform the public and other stakeholders. Through cooperative efforts to identify and analyze information with reference to evidence-based discussion, the proposed key ingredients may help to shape and support a more informed, open framework. This framework and resource can be expanded further for biomedical research in other countries. © 2023

关键词： Ethics Macaque Marmoset Regulations Requirements Welfare

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A Hardware Trojan Attack on FPGA-Based Cryptographic Key Generation: Impact and Detection

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Journal of Hardware and Systems Security 2018年第3期2卷 225-239页

作者： Vidya Govindan Rajat Subhra Chakraborty Pranesh Santikellur Aditya Kumar Chaudhary Secured Embedded Architecture Laboratory (SEAL) Department of Computer Science and Engineering Indian Institute of Technology Kharagpur Kharagpur India Centre for Artificial Intelligence and Robotics DRDO Complex Bangalore India

True Random Number Generator (TRNG) circuits are important components of cryptographic systems. Lack of statistical randomness in the generated bitstreams from a TRNG can result in compromised keys, leading to serious security breaches. In this paper, we describe a Hardware Trojan Horse (HTH)-based attack on the TRNG of an FPGA-based cryptosystem, that results in reduced entropy and increased predictability of the generated keys. The proposed HTH does not cause any functional failure in the cryptosystem, and its impact is undetectable by analysis of the compromised bitstream using standard statistical randomness testing software suites (NIST, two enhanced versions of NIST Dieharder, and LIL-tests), and by a circuit-level HTH detection technique using Transition Effect Ring Oscillator (TERO). Finally, we show that the impact of the HTH can be detected by applying Wavelet Transform on the compromised bitstream.

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Propagating Confidences through CNNs for Sparse Data Regression

arXiv

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arXiv 2018年

作者： Eldesokey, Abdelrahman Felsberg, Michael Khan, Fahad Shahbaz Computer Vision Laboratory Department of Electrical Engineering Linköping University Linköping Sweden Inception Institute of Artificial Intelligence Abu Dhabi United Arab Emirates

In most computer vision applications, convolutional neural networks (CNNs) operate on dense image data generated by ordinary cameras. Designing CNNs for sparse and irregularly spaced input data is still an open problem with numerous applications in autonomous driving, robotics, and surveillance. To tackle this challenging problem, we introduce an algebraically-constrained convolution layer for CNNs with sparse input and demonstrate its capabilities for the scene depth completion task. We propose novel strategies for determining the confidence from the convolution operation and propagating it to consecutive layers. Furthermore, we propose an objective function that simultaneously minimizes the data error while maximizing the output confidence. Comprehensive experiments are performed on the KITTI depth benchmark and the results clearly demonstrate that the proposed approach achieves superior performance while requiring three times fewer parameters than the state-of-the-art methods. Moreover, our approach produces a continuous pixel-wise confidence map enabling information fusion, state inference, and decision support. Copyright © 2018, The Authors. All rights reserved.

关键词： Convolution

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A Generative Appearance Model for End-to-end Video Object Segmentation

arXiv

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arXiv 2018年

作者： Johnander, Joakim Danelljan, Martin Brissman, Emil Khan, Fahad Shahbaz Felsberg, Michael Computer Vision Laboratory Department of Electrical Engineering Linköping University Inception Institute of Artificial Intelligence Abu Dhabi United Arab Emirates Saab Sweden Zenuity Sweden

One of the fundamental challenges in video object segmentation is to find an effective representation of the target and background appearance. The best performing approaches resort to extensive fine-tuning of a convolutional neural network for this purpose. Besides being prohibitively expensive, this strategy cannot be truly trained end-to-end since the online fine-tuning procedure is not integrated into the offline training of the *** address these issues, we propose a network architecture that learns a powerful representation of the target and background appearance in a single forward pass. The introduced appearance module learns a probabilistic generative model of target and background feature distributions. Given a new image, it predicts the posterior class probabilities, providing a highly discriminative cue, which is processed in later network modules. Both the learning and prediction stages of our appearance module are fully differentiable, enabling true end-to-end training of the entire segmentation pipeline. Comprehensive experiments demonstrate the effectiveness of the proposed approach on three video object segmentation benchmarks. We close the gap to approaches based on online fine-tuning on DAVIS17, while operating at 15 FPS on a single GPU. Furthermore, our method outperforms all published approaches on the large-scale YouTube-VOS dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Network architecture

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Automated sequence and motion planning for robotic spatial extrusion of 3D trusses

arXiv

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arXiv 2018年

作者： Huang, Yijiang Garrett, Caelan R. Mueller, Caitlin T. Building Technology Program Department of Architecture Massachusetts Institute of Technology CambridgeMA02139 United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA02139 United States

While robotic spatial extrusion has demonstrated a new and efficient means to fabricate 3D truss structures in architectural scale, a major challenge remains in automatically planning extrusion sequence and robotic motion for trusses with unconstrained topologies. This paper presents the first attempt in the field to rigorously formulate the extrusion sequence and motion planning (SAMP) problem, using a CSP encoding. Furthermore, this research proposes a new hierarchical planning framework to solve the extrusion SAMP problems that usually have a long planning horizon and 3D configuration complexity. By decoupling sequence and motion planning, the planning framework is able to efficiently solve the extrusion sequence, end-effector poses, joint configurations, and transition trajectories for spatial trusses with nonstandard topologies. This paper also presents the first detailed computation data to reveal the runtime bottleneck on solving SAMP problems, which provides insight and comparing baseline for future algorithmic development. Together with the algorithmic results, this paper also presents an open-source and modularized software implementation called Choreo that is machine-agnostic. To demonstrate the power of this algorithmic framework, three case studies, including real fabrication and simulation results, are presented. Copyright © 2018, The Authors. All rights reserved.

关键词： Motion planning

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QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

arXiv

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arXiv 2021年

作者： Mehta, Raghav Filos, Angelos Baid, Ujjwal Sako, Chiharu McKinley, Richard Rebsamen, Michael Dätwyler, Katrin Meier, Raphael Radojewski, Piotr Murugesan, Gowtham Krishnan Nalawade, Sahil Ganesh, Chandan Wagner, Ben Yu, Fang F. Fei, Baowei Madhuranthakam, Ananth J. Maldjian, Joseph A. Daza, Laura Gómez, Catalina Arbeláez, Pablo Dai, Chengliang Wang, Shuo Reynaud, Hadrien Mo, Yuanhan Angelini, Elsa Guo, Yike Bai, Wenjia Banerjee, Subhashis Pei, Linmin Murat, A.K. Rosas-González, Sarahi Zemmoura, Ilyess Tauber, Clovis Vu, Minh H. Nyholm, Tufve Löfstedt, Tommy Ballestar, Laura Mora Vilaplana, Veronica McHugh, Hugh Talou, Gonzalo Maso Wang, Alan Patel, Jay Chang, Ken Hoebel, Katharina Gidwani, Mishka Arun, Nishanth Gupta, Sharut Aggarwal, Mehak Singh, Praveer Gerstner, Elizabeth R. Kalpathy-Cramer, Jayashree Boutry, Nicolas Huard, Alexis Vidyaratne, Lasitha Rahman, Md Monibor Iftekharuddin, Khan M. Chazalon, Joseph Puybareau, Elodie Tochon, Guillaume Ma, Jun Cabezas, Mariano Llado, Xavier Oliver, Arnau Valencia, Liliana Valverde, Sergi Amian, Mehdi Soltaninejad, Mohammadreza Myronenko, Andriy Hatamizadeh, Ali Feng, Xue Dou, Quan Tustison, Nicholas Meyer, Craig Shah, Nisarg A. Talbar, Sanjay Weber, Marc-André Mahajan, Abhishek Jakab, Andras Wiest, Roland Fathallah-Shaykh, Hassan M. Nazeri, Arash Milchenko, Mikhail Marcus, Daniel Kotrotsou, Aikaterini Colen, Rivka Freymann, John Kirby, Justin Davatzikos, Christos Menze, Bjoern Bakas, Spyridon Gal, Yarin Arbel, Tal McGill University MontrealQC Canada Group University of Oxford Oxford United Kingdom University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine The University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University Institute of Diagnostic and Interventional Neuroradiology University of Bern Inselspital Bern University Hospital Bern Switzerland Department of Radiology University of Texas Southwestern Medical Center DallasTX United States Department of Bioengineering University of Texas DallasTX United States Advanced Imaging Research Center University of Texas Southwestern Medical Center DallasTX United States Universidad de los Andes Bogotá Colombia Data Science Institute Imperial College London London United Kingdom NIHR Imperial BRC ITMAT Data Science Group Imperial College London London United Kingdom Department of Brain Sciences Imperial College London London United Kingdom Machine Intelligence Unit Indian Statistical Institute Kolkata India Department of CSE University of Calcutta Kolkata India Department of Information Technology Uppsala University Uppsala Sweden Department of Diagnostic Radiology The University of Pittsburgh Medical Center PittsburghPA United States UMR U1253 iBrain Université de Tours Inserm Tours France Department of Radiation Sciences Umeå University Umeå Sweden Department of Computing Science Umeå University Umeå Sweden Signal Theory and Communications Department Universitat Politècnica de Catalunya Barcelona Tech Barcelona Spain Faculty of Medical and Health Sciences University of Auckland Auckland New Zealand Radiology Department Auckland City Hospital Auckland New Zealand Auckland Bioengineering Institute University of Auckland New Zealand Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://***/RagMeh11/QU-BraTS. © 2021, CC BY.

关键词： Benchmarking

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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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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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Publisher Correction: Global estimates on the number of people blind or visually impaired by cataract: a meta-analysis from 2000 to 2020

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Eye (London, England) 2024年第11期38卷 2229-2231页

作者： Konrad Pesudovs Hugh R. Taylor Tabassom Sedighi Rupert R. A. Bourne Shahina Pardhan Van Charles Lansingh John H. Kempen Ian Tapply Arthur G. Fernandes Maria Vittoria Cicinelli Alessandro Arrigo Nicolas Leveziel Serge Resnikoff Seth Flaxman Mukkharram M. Bikbov Tasanee Braithwaite Alain Bron Ching-Yu Cheng Monte A. Del Monte Joshua R. Ehrlich Leon B. Ellwein David Friedman João M. Furtado Gus Gazzard Ronnie George M. Elizabeth Hartnett Jost B. Jonas Rim Kahloun Moncef Khairallah Rohit C. Khanna Janet Leasher Julie-Anne Little Vinay Nangia Michal Nowak Tunde Peto Pradeep Ramulu Fotis Topouzis Mitiadis Tsilimbaris Ya Xing Wang Ningli Wang Paul Svitil Briant Theo Vos Katrin Burkart Kaleb Coberly Xiaochen Dai Stephen S. Lim Tomislav Mestrovic Ali H. Mokdad Christopher J. L. Murray Jaimie D. Steinmetz Awoke Misganaw Yohannes Habtegiorgis Abate Mohammad Abdollahi Mozhan Abdollahi Ayele Mamo Abebe Olumide Abiodun Richard Gyan Aboagye Woldu Aberhe Abrha Hasan Abualruz Hiwa Abubaker Ali Eman Abu-Gharbieh Salahdein Aburuz Tadele Girum Girum Adal Mesafint Molla Adane Isaac Yeboah Addo Qorinah Estiningtyas Sakilah Adnani Muhammad Sohail Afzal Muhammad Umair Shahin Aghamiri Bright Opoku Ahinkorah Aqeel Ahmad Sajjad Ahmad Ali Ahmadi Siamak Sabour Ayman Ahmed Haroon Ahmed Ahmad Samir Alfaar Abid Ali Syed Shujait Shujait Ali Awais Altaf Hubert Amu Emmanuel Manu Sofia Androudi Rodrigo Anguita Abhishek Anil Rimple Jeet Kaur Muhammad Aaqib Shamim Saeid Anvari Anayochukwu Edward Anyasodor Francis Appiah Jalal Arabloo Haleh Ayatollahi Mosab Arafat Damelash Areda Reza Arefnezhad Brhane Berhe Aregawi Akeza Awealom Asgedom Tahira Ashraf Seyyed Shamsadin Athari Bantalem Tilaye Tilaye Atinafu Birhan Tsegaw Taye Maha Moh’d Wahbi Atout Alok Atreya Ahmed Y. Azzam Hassan Babamohamadi Sara Bagherieh Yogesh Bahurupi Atif Amin Baig Shumaila Nargus Biswajit Banik Mainak Bardhan Saurav Basu Kavita Batra Nebiyou Simegnew Bayileyegn Fatemeh Bazvand Addisu Shunu Beyene Awoke Masrie Asrat Derese Devidas S. Bhagat Akshaya Srikanth Bhagavathula Pankaj Bh Medicine & Health University of New South Wales Sydney NSW Australia School of Optometry and Vision Science University of New South Wales Sydney NSW Australia School of Population and Global Health University of Melbourne Carlton VIC Australia Vision and Eye Research Institute Anglia Ruskin University Cambridge UK HelpMeSee Instituto Mexicano de Oftalmologia Santiago de Querétaro Mexico University of Miami Gables FL USA University of Utah Salt Lake City UT USA Chief Medical Office HelpMeSee New York NY USA Mexican Institute of Ophthalmology Queretaro Mexico Department of Ophthalmology Massachusetts Eye and Ear/Shepens Eye Research Institute/Harvard Medical School Boston MA USA Eye Unit MyungSung Christian Medical Center (MCM) Comprehensive Specialized Hospital and MyungSun Medical College Addis Ababa Ethiopia Department of Ophthalmology Addis Ababa University Addis Ababa Ethiopia Sight for Souls Bellevue WA USA Department of Ophthalmology Harvard University Boston MA USA Eye Unit MyungSung Medical College Addis Ababa Ethiopia Addenbrooke’s Hospital Cambridge UK Department of Ophthalmology Cambridge University Hospitals Cambridge UK Federal University of Sao Paolo Sao Paolo SP Brazil University of Calgary Calgary AB Canada Department of Ophthalmology and Visual Sciences Federal University of São Paulo Sao Paulo Brazil School of Medicine Vita-Salute San Raffaele University Milan Italy Department of Ophthalmology IRCCS San Raffaele Scientific Institute Milan Italy Department of Ophthalmology San Raffaele Scientific Institute Milano Italy IRCCS San Raffaele Scientific Institute Vita-Salute University Milan Italy Scientific Institute San Raffaele Hospital Vita-Salute University Milan Italy University of Poitiers Poitiers France CHU de Poitiers Poitiers France Ophthalmology Department CHU de Poitiers (Poitiers University Hospital) Poitiers France Unité 1084 National Institute of Health and Medical Research (INSERM) Poitiers France

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