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arXiv 2023年

作者： Pignatari, Marco Trueman, Thomas C.L. Womack, Kate A. Gibson, Brad K. Côté, Benoit Turrini, Diego Sneden, Christopher Mojzsis, Stephen J. Stancliffe, Richard J. Fong, Paul Lawson, Thomas V. Keegans, James D. Pilkington, Kate Passy, Jean-Claude Beers, Timothy C. Lugaro, Maria ELKH Konkoly Thege M. út 15–17 BudapestH-1121 Hungary CSFK MTA Centre of Excellence Konkoly Thege Miklós út 15-17. BudapestH-1121 Hungary E. A. Milne Centre for Astrophysics Department of Physics and Mathematics University of Hull HU6 7RX United Kingdom INAF - Turin Astrophysical Observatory Via Osservatorio 20 Pino Torinese10025 Italy INAF - Institute of Space Astrophysics and Planetology Via Fosso del Cavaliere 100 Rome00133 Italy ICSC National Research Centre for High Performance Computing Big Data and Quantum Computing Via Magnanelli 2 Casalecchio di Reno40033 Italy Department of Astronomy and McDonald Observatory The University of Texas AustinTX78712 United States NuGrid Collaboration Joint Institute for Nuclear Astrophysics Center for the Evolution of the Elements United States Department of Physics and Astronomy University of Victoria VictoriaBCV8P 5C2 Canada Pázmány Péter sétány 1/c BudapestH-1117 Hungary H.H. Wills Physics Laboratory University of Bristol Tyndall Avenue BristolBS8 1TL United Kingdom Centre of Excellence for Data Science Artificial Intelligence and Modelling University of Hull HU6 7RX United Kingdom Astrophysics Group Lennard-Jones Laboratories Keele University KeeleST5 5BG United Kingdom School of Physical Sciences The Open University Milton KeynesMK7 6AA United Kingdom Max Planck Institute for Intelligent Systems Tübingen Germany Department of Physics and Astronomy University of Notre Dame Notre DameIN46556 United States ELTE Eötvös Loránd University Institute of Physics Pázmány Péter sétány 1/A Budapest1117 Hungary School of Physics and Astronomy Monash University VIC3800 Australia

Theoretical physical-chemical models for the formation of planetary systems depend on data quality for the Sun’s composition, that of stars in the solar neighbourhood, and of the estimated "pristine" compositions for stellar systems. The effective scatter and the observational uncertainties of elements within a few hundred parsecs from the Sun, even for the most abundant metals like carbon, oxygen and silicon, are still controversial. Here we analyse the stellar production and the chemical evolution of key elements that underpin the formation of rocky (C, O, Mg, Si) and gas/ice giant planets (C, N, O, S). We calculate 198 galactic chemical evolution (GCE) models of the solar neighbourhood to analyse the impact of different sets of stellar yields, of the upper mass limit for massive stars contributing to GCE (Mup) and of supernovae from massive-star progenitors which do not eject the bulk of the iron-peak elements (faint supernovae). Even considering the GCE variation produced via different sets of stellar yields, the observed dispersion of elements reported for stars in the Milky Way disk is not reproduced. Among others, the observed range of super-solar [Mg/Si] ratios, sub-solar [S/N], and the dispersion of up to 0.5 dex for [S/Si] challenge our models. The impact of varying Mup depends on the adopted supernova yields. Thus, observations do not provide a constraint on the Mup parametrization. When including the impact of faint supernova models in GCE calculations, elemental ratios vary by up to 0.1-0.2 dex in the Milky Way disk;this modification better reproduces observations. Copyright © 2023, The Authors. All rights reserved.

关键词： Dispersions

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A strategic review on sustainable approaches in municipal solid waste management andenergy recovery: Role of artificial intelligence,economic stability andlife cycle assessment

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Bioresource technology 2023年 379卷 129044页

作者： Rajendiran Naveenkumar Jayaraj Iyyappan Ravichandran Pravin Seifedine Kadry Jeehoon Han Raveendran Sindhu Mukesh Kumar Awasthi Samuel Lalthazuala Rokhum Gurunathan Baskar Biological Systems Engineering University of Wisconsin-Madison Madison WI 53706 United States Forest Products Laboratory USDA Forest Service Madison WI 53726 United States. Department of Biotechnology Saveetha School of Engineering Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602107 India. Department of Biotechnology St. Joseph's College of Engineering Chennai 600119. India. Department of Applied Data Science Noroff University College Kristiansand Norway Artificial Intelligence Research Center (AIRC) Ajman University Ajman 346 United Arab Emirates Department of Electrical and Computer Engineering Lebanese American University Byblos Lebanon. Department of Chemical Engineering Pohang University of Science and Technology Pohang 37673 Republic of Korea. Department of Food Technology TKM Institute of Technology Kollam Kerala India. College of Natural Resources and Environment Northwest A&F University Yangling Shaanxi Province 712100 China. Department of Chemistry National Institute of Technology Silchar 788010 Assam India. Department of Biotechnology St. Joseph's College of Engineering Chennai 600119. India Department of Applied Data Science Noroff University College Kristiansand Norway. Electronic address: basg2002@***.

The consumption of energy levels has increased in association with economic growth and concurrently increased the energy demand from renewable sources. The need under Sustainable Development Goals (SDG) intends to explore various technological advancements for the utilization of waste to energy. Municipal Solid Waste (MSW) has been reported as constructive feedstock to produce biofuels, biofuel carriers and biochemicals using energy-efficient technologies in risk freeways. The present review contemplates risk assessment and challenges in sorting and transportation of MSW and different aspects of conversion of MSW into energy are critically analysed. The circular bioeconomy of energy production strategies and management of waste are also analysed. The current scenario on MSW and its impacts on the environment are elucidated in conjunction with various policies and amendments equipped for the competent management of MSW in order to fabricate a sustained environment.

关键词： Circular bioeconomy Municipal Solid Waste Risk assessment Sustainable Waste Management

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Recommendations for Successful Development and Implementation of Digital Health Technology Tools

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Journal of medical Internet research 2025年 27卷 e56747页

作者： Rebecca Ting Jiin Loo Francesco Nasta Mirco Macchi Anaïs Baudot Frada Burstein Riley Bove Maike Greve Holger Fröhlich Sara Khalid Arne Küderle Susan L Moore Valerie Storms John Torous Enrico Glaab Biomedical Data Science Group Luxembourg Centre for Systems Biomedicine (LCSB) University of Luxembourg 6 Avenue du Swing Belvaux L-4367 Luxembourg 352 466644 ext 6186. Marseille Medical Genetics (MMG) INSERM Aix Marseille University Marseille France. Department of Human-Centered Computing Faculty of Information Technology Monash University Melbourne Australia. UCSF Weill Institute for Neurosciences University of California San Francisco San Francisco CA United States. Department of Digitalization Copenhagen Business School Frederiksberg Denmark. Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany. Bonn-Aachen International Center for Information Technology (b-it) University of Bonn Bonn Germany. Centre for Statistics in Medicine Botnar Research Centre University of Oxford Oxford United Kingdom. Department of Artificial Intelligence in Biomedical Engineering (AIBE) Friedrich-Alexander-Universität Erlangen-Nürnberg Bayern Germany. Department of Community and Behavioral Health Colorado School of Public Health Aurora CO United States. Independent Patient Expert PEP Matters Hasselt Belgium. Department of Psychiatry Beth Israel Deaconess Medical Center Harvard Medical School Boston MA United States.

Digital health technology tools (DHTTs) have the potential to transform health care delivery by enabling new forms of participatory and personalized care that fit into patients' daily lives. However, realizing this potential requires careful navigation of numerous challenges. This viewpoint presents the authors' experiences and perspectives on the development and implementation of DHTTs, addressing both established practices and controversial topics. This article offers a practical guide organized into 10 recommendations derived from a multidisciplinary lecture series and associated workshop discussions on "Digital Health and Digital Biomarkers" held at the University of Luxembourg in 2023-2024. Key messages include the need to understand specific health care challenges, form interdisciplinary teams, incorporate patient feedback, select appropriate measurement technologies, ensure data integration and interoperability, apply advanced data science techniques, use scalable designs and open standards, comply with regulatory requirements, and maintain continuous evaluation and improvement. While the guide highlights essential practices, it also addresses contentious issues such as balancing innovation with regulatory compliance, addressing ethical concerns in artificial intelligence adoption, managing privacy versus the need for comprehensive data integration and open science, and managing the financial sustainability of DHTTs. The authors argue that digital health's greatest potential lies in its ability to provide participatory and personalized care, but this requires a delicate balance between technological advances and ethical, legal, and social implications. Overall, this workshop-derived viewpoint aims to help health care professionals, engineers, developers, and researchers not only adopt best practices but also address and resolve the controversial aspects inherent in the development of DHTTs.

关键词： application data interoperability data privacy digital health electronic health record health care technology health monitoring interdisciplinary collaboration mobile health real-time recommendations regulatory compliance technology telehealth user engagement user-centered design wearable

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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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Sparse DNNs with improved adversarial robustness 18

Sparse DNNs with improved adversarial robustness

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Proceedings of the 32nd International Conference on Neural Information Processing systems

作者： Yiwen Guo Chao Zhang Changshui Zhang Yurong Chen Intel Labs China Academy for Advanced Interdisciplinary Studies Center for Data Science Peking University Institute for Artificial Intelligence Tsinghua University (THUAI) State Key Lab of Intelligent Technologies and Systems Beijing National Research Center for Information Science and Technology (BNRis) Department of Automation Tsinghua University

Deep neural networks (DNNs) are computationally/memory-intensive and vulnerable to adversarial attacks, making them prohibitive in some real-world applications. By converting dense models into sparse ones, pruning appears to be a promising solution to reducing the computation/memory cost. This paper studies classification models, especially DNN-based ones, to demonstrate that there exists intrinsic relationships between their sparsity and adversarial robustness. Our analyses reveal, both theoretically and empirically, that nonlinear DNN-based classifiers behave differently under l2 attacks from some linear ones. We further demonstrate that an appropriately higher model sparsity implies better robustness of nonlinear DNNs, whereas over-sparsified models can be more difficult to resist adversarial examples.

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CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer

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Genome biology 2025年第1期26卷 178页

作者： Qifei Wang He Zhu Yiwen Hu Yanjie Chen Yuwei Wang Guochao Li Yun Li Jinfeng Chen Xuegong Zhang James Zou Manolis Kellis Yue Li Dianbo Liu Lan Jiang China National Center for Bioinformation Beijing 100101 China. Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China. University of Chinese Academy of Sciences Beijing 100049 China. School of Computer Science McGill University Montreal QC H3A 0C6 Canada. Mila - Quebec AI Institute Montreal QC H2S 3H1 Canada. Sino-Danish College University of Chinese Academy of Sciences Beijing 100049 China. CAS Key Laboratory of Behavioral Science Institute of Psychology Beijing 100101 China. Department of Psychology University of Chinese Academy of Sciences Beijing 100049 China. International Big-Data Center for Depression Research Institute of Psychology Chinese Academy of Sciences Beijing 100101 China. Department of Automation MOE Key Laboratory of Bioinformatics and Bioinformatics Division BNRIST Tsinghua University Beijing 100084 China. School of Life Sciences and School of Medicine Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China. Department of Computer Science Stanford University Stanford CA 94305 USA. Department of Biomedical Data Science Stanford University School of Medicine Stanford CA 94305 USA. The Broad Institute of MIT and Harvard Cambridge MA 02142 USA. Computer Science and Artificial Intelligence Lab Massachusetts Institute of Technology Cambridge MA 02139 USA. School of Computer Science McGill University Montreal QC H3A 0C6 Canada. yueli@cs.mcgill.ca. Mila - Quebec AI Institute Montreal QC H2S 3H1 Canada. yueli@cs.mcgill.ca. Quantitative Life Science McGill University Montreal QC H3A 1E3 Canada. yueli@cs.mcgill.ca. School of Medicine and College of Design and Engineering National University of Singapore Singapore Singapore. dianbo@nus.edu.sg. China National Center for Bioinformation Beijing 100101 China. jiangl@***. Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China. jiangl@***. University of Chinese Academy of Sciences Beijing 100049 C

Machine learning methods, especially Transformer architectures, have been widely employed in single-cell omics studies. However, interpretability and accurate representation of out-of-distribution (OOD) cells remains challenging. Inspired by the global workspace theory in cognitive neuroscience, we introduce CellMemory, a bottlenecked Transformer with improved generalizability designed for the hierarchical interpretation of OOD cells. Without pre-training, CellMemory outperforms existing single-cell foundation models and accurately deciphers spatial transcriptomics at high resolution. Leveraging its robust representations, we further elucidate malignant cells and their founder cells across patients, providing reliable characterizations of the cellular changes caused by the disease.

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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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MedShapeNet - A Large-Scale dataset of 3D Medical Shapes for Computer Vision

arXiv

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arXiv 2023年

作者： Li, Jianning Zhou, Zongwei Yang, Jiancheng Pepe, Antonio Gsaxner, Christina Luijten, Gijs Qu, Chongyu Zhang, Tiezheng Chen, Xiaoxi Li, Wenxuan Wodzinski, Marek Friedrich, Paul Xie, Kangxian Jin, Yuan Ambigapathy, Narmada Nasca, Enrico Solak, Naida Melito, Gian Marco Vu, Viet Duc Memon, Afaque R. Schlachta, Christopher De Ribaupierre, Sandrine Patel, Rajnikant Eagleson, Roy Chen, Xiaojun Mächler, Heinrich Kirschke, Jan Stefan de la Rosa, Ezequiel Christ, Patrick Ferdinand Li, Hongwei Bran Ellis, David G. Aizenberg, Michele R. Gatidis, Sergios Küstner, Thomas Shusharina, Nadya Heller, Nicholas Andrearczyk, Vincent Depeursinge, Adrien Hatt, Mathieu Sekuboyina, Anjany Löffler, Maximilian Liebl, Hans Dorent, Reuben Vercauteren, Tom Shapey, Jonathan Kujawa, Aaron Cornelissen, Stefan Langenhuizen, Patrick Ben-Hamadou, Achraf Rekik, Ahmed Pujades, Sergi Boyer, Edmond Bolelli, Federico Grana, Costantino Lumetti, Luca Salehi, Hamidreza Ma, Jun Zhang, Yao Gharleghi, Ramtin Beier, Susann Sowmya, Arcot Garza-Villarreal, Eduardo A. Balducci, Thania Angeles-Valdez, Diego Souza, Roberto Rittner, Leticia Frayne, Richard Ji, Yuanfeng Ferrari, Vincenzo Chatterjee, Soumick Dubost, Florian Schreiber, Stefanie Mattern, Hendrik Speck, Oliver Haehn, Daniel John, Christoph Nürnberger, Andreas Pedrosa, João Ferreira, Carlos Aresta, Guilherme Cunha, António Campilho, Aurélio Suter, Yannick Garcia, Jose Lalande, Alain Vandenbossche, Vicky Van Oevelen, Aline Duquesne, Kate Mekhzoum, Hamza Vandemeulebroucke, Jef Audenaert, Emmanuel Krebs, Claudia van Leeuwen, Timo Vereecke, Evie Heidemeyer, Hauke Röhrig, Rainer Hölzle, Frank Badeli, Vahid Krieger, Kathrin Gunzer, Matthias Chen, Jianxu van Meegdenburg, Timo Dada, Amin Balzer, Miriam Fragemann, Jana Jonske, Frederic Rempe, Moritz Malorodov, Stanislav Bahnsen, Fin H. Seibold, Constantin Jaus, Alexander Marinov, Zdravko Jaeger, Paul F. Stiefelhagen, Rainer Santos, Ana Sofia Lindo, Mariana Ferreira, André Alves, Victor Kamp, Michael Abourayya, Amr Nensa, Felix Hörst, Fabian Brehmer, Alexander Hein Girardetstraße 2 Essen45131 Germany Graz University of Technology Inffeldgasse 16c Graz8010 Austria Graz Austria The Department of Computer Science Johns Hopkins University Malone Hall 3400 N Charles St BaltimoreMD21218 United States Rte Cantonale Lausanne1015 Switzerland The Department of Measurement and Electronics AGH University of Science and Technology Krakow Poland Sierre Switzerland Department of Biomedical Engineering University of Basel Hegenheimermattweg Allschwil167C CH-4123 Switzerland The Boston College 140 Commonwealth Ave Chestnut HillMA02467 United States University Hospital B7-200 339 Windermere Road LondonN6A 5A5 Canada The Department of Radiology Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai200240 China The Research Center for Connected Healthcare Big Data ZhejiangLab Zhejiang Hangzhou311121 China The Faculty of Statistics Technical University Dortmund August-Schmidt-Straße 1 Dortmund44227 Germany The Institute of Mechanics Graz University of Technology Kopernikusgasse 24/IV Graz8010 Austria The Institute of Biomedical Manufacturing and Life Quality Engineering State Key Laboratory of Mechanical System and Vibration School of Mechanical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China The Department of Cardiac Surgery Medical University Graz Auenbruggerplatz 29 Graz8036 Austria The Department of Diagnostic and Interventional Radiology University Hospital Giessen Justus-Liebig-University Giessen Klinikstraße 33 Giessen35392 Germany The Department of Mechanical Engineering Mehran University of Engineering and Technology Jamshoro Sindh76062 Pakistan The Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China The Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie Universitätsklinikum der Technischen Universität München Ismaningerstr. 22 München81675 Germany icometrix Kolonel Be

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://***/ and https://***/Jianningli/*** Codes 68T01 © 2023, CC BY.

关键词： Large dataset

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The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

arXiv

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arXiv 2021年

作者： Baheti, Bhakti Chakrabarty, Satrajit Akbari, Hamed Bilello, Michel Wiestler, Benedikt Schwarting, Julian Calabrese, Evan Rudie, Jeffrey Abidi, Syed Mousa, Mina Villanueva-Meyer, Javier Fields, Brandon K.K. Kofler, Florian Shinohara, Russell Takeshi Iglesias, Juan Eugenio Mok, Tony C.W. Chung, Albert C.S. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Grosbröhmer, Christoph Siebert, Hanna Hansen, Lasse Heinrich, Mattias P. Canalini, Luca Klein, Jan Gerken, Annika Heldmann, Stefan Hering, Alessa Hahn, Horst K. Meng, Mingyuan Bi, Lei Feng, Dagan Kim, Jinman Zeineldinal, Ramy A. Karar, Mohamed E. Mathis-Ullrich, Franziska Burgert, Oliver Abderezaei, Javid Pionteck, Aymeric Chopra, Agamdeep Kurt, Mehmet Yan, Kewei Yan, Yonghong Tang, Zhe Ma, Jianqiang Nasser, Sahar Almahfouz Kurian, Nikhil Cherian Meena, Mohit Shamsi, Saqib Sethi, Amit Tustison, Nicholas J. Avants, Brian B. Cook, Philip Gee, James C. Tian, Lin Greer, Hastings Niethammer, Marc Hoopesar, Andrew Hoffmannas, Malte Dalcaar, Adrian V. Christodoulidis, Stergios Estiene, Théo Vakalopoulou, Maria Paragios, Nikos Marcus, Daniel S. Davatzikos, Christos Sotiras, Aristeidis Menze, Bjoern Bakas, Spyridon Waldmannstetter, Diana Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Electrical and Systems Engineering Washington University in St. Louis St. LouisMO United States GE HealthCare San RamonCA United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. LouisMO United States Institute for Informatics Data Science & Biostatistics Washington University School of Medicine St. LouisMO United States Department of Bioengineering Santa Clara University Santa ClaraCA United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Computer Science TUM School of Computation Information and Technology Technical University of Munich Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Munich Germany Department of Nuclear Medicine University Hospital Regensburg Regensburg Germany University Hospital Regensburg Regensburg Germany Department of Radiology & Biomedical Imaging University of California San FranciscoCA United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Radiology University of California San DiegoCA United States Helmholtz AI Helmholtz Munich Neuherberg Germany Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia United States Massachusetts General Hospital Harvard Medical School United States Centre for Medical Imaging Computing University College London United Kingdom The Hong Kong University of Science and Technology Hong Kong University of Applied Sciences West

Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been considerable progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The challenge was conducted in conjunction with both the IEEE International Symposium on Biomedical Imaging (ISBI) 2022 and the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2022. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. The training data with their GT annotations, were publicly released to enable the development of registration algorithms. The validation data, without their GT annotations, were also released to allow for algorithmic evaluation prior to the testing phase, which only allowed submission of containerized algorithms for evaluation on hidden hold-out testing data. Quantitative evaluation and ranking was based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency

关键词： Magnetic resonance imaging

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The leap to ordinal: Detailed functional prognosis after traumatic brain injury with a flexible modelling approach

arXiv

引用

arXiv 2022年

作者： Bhattacharyay, Shubhayu Milosevic, Ioan Wilson, Lindsay Menon, David K. Stevens, Robert D. Steyerberg, Ewout W. Nelson, David W. Ercole, Ari Åkerlund, Cecilia Amrein, Krisztina Andelic, Nada Andreassen, Lasse Anke, Audny Antoni, Anna Audibert, Gérard Azouvi, Philippe Azzolini, Maria Luisa Bartels, Ronald Barzó, Pál Beauvais, Romuald Beer, Ronny Bellander, Bo-Michael Belli, Antonio Benali, Habib Berardino, Maurizio Beretta, Luigi Blaabjerg, Morten Bragge, Peter Brazinova, Alexandra Brinck, Vibeke Brooker, Joanne Brorsson, Camilla Buki, Andras Bullinger, Monika Cabeleira, Manuel Caccioppola, Alessio Calappi, Emiliana Calvi, Maria Rosa Cameron, Peter Lozano, Guillermo Carbayo Carbonara, Marco Cavallo, Simona Chevallard, Giorgio Chieregato, Arturo Citerio, Giuseppe Clusmann, Hans Coburn, Mark Coles, Jonathan Cooper, Jamie D. Correia, Marta Čović, Amra Curry, Nicola Czeiter, Endre Czosnyka, Marek Dahyot-Fizelier, Claire Dark, Paul Dawes, Helen De Keyser, Véronique Degos, Vincent Della Corte, Francesco den Boogert, Hugo Depreitere, Bart Đilvesi, Đula Dixit, Abhishek Donoghue, Emma Dreier, Jens Dulière, Guy-Loup Esser, Patrick Ezer, Erzsébet Fabricius, Martin Feigin, Valery L. Foks, Kelly Frisvold, Shirin Furmanov, Alex Gagliardo, Pablo Galanaud, Damien Gantner, Dashiell Gao, Guoyi George, Pradeep Ghuysen, Alexandre Giga, Lelde Glocker, Ben Golubovic, Jagoš Gomez, Pedro A. Gratz, Johannes Gravesteijn, Benjamin Grossi, Francesca Gruen, Russell L. Gupta, Deepak Haagsma, Juanita A. Haitsma, Iain Helbok, Raimund Helseth, Eirik Horton, Lindsay Huijben, Jilske Hutchinson, Peter J. Jacobs, Bram Jankowski, Stefan Jarrett, Mike Jiang, Ji-Yao Johnson, Faye Jones, Kelly Karan, Mladen Kolias, Angelos G. Kompanje, Erwin Kondziella, Daniel Kornaropoulos, Evgenios Koskinen, Lars-Owe Kovács, Noémi Kowark, Ana Lagares, Alfonso Lanyon, Linda Laureys, Steven Lecky, Fiona Ledoux, Didier Lefering, Rolf Legrand, Valerie Lejeune, Aurelie Levi, Leon Lightfoot, Roger Lingsma, Hester Maas, Andrew I.R. Castaño-León, Ana M. Maegele, Marc Majdan, M Division of Anaesthesia University of Cambridge Addenbrooke's Hospital Cambridge United Kingdom Division of Neurosurgery Department of Clinical Neurosciences Addenbrooke's Hospital University of Cambridge Cambridge United Kingdom Laboratory of Computational Intensive Care Medicine Johns Hopkins University BaltimoreMD United States Division of Psychology University of Stirling Stirling United Kingdom Department of Anesthesiology and Critical Care Medicine Johns Hopkins University BaltimoreMD United States Department of Biomedical Data Sciences Leiden University Medical Center Leiden Netherlands Department of Physiology and Pharmacology Section for Perioperative Medicine and Intensive Care Karolinska Institutet Stockholm Sweden Cambridge Centre for Artificial Intelligence in Medicine Cambridge United Kingdom Division of Surgery and Clinical Neuroscience Department of Physical Medicine and Rehabilitation Oslo University Hospital University of Oslo Oslo Norway Department of Neurosurgery University Hospital Northern Norway Tromso Norway Department of Physical Medicine and Rehabilitation University Hospital Northern Norway Tromso Norway Trauma Surgery Medical University Vienna Vienna Austria Department of Anesthesiology & Intensive Care University Hospital Nancy Nancy France Raymond Poincare Hospital Assistance Publique - Hopitaux de Paris Paris France Department of Anesthesiology & Intensive Care S Raffaele University Hospital Milan Italy Department of Neurosurgery Radboud University Medical Center Nijmegen Netherlands Department of Neurosurgery University of Szeged Szeged Hungary International Projects Management ARTTIC Munchen Germany Department of Neurology Neurological Intensive Care Unit Medical University of Innsbruck Innsbruck Austria Department of Neurosurgery & Anesthesia & Intensive Care Medicine Karolinska University Hospital Stockholm Sweden NIHR Surgical Reconstruction and Microbiology Research Centre Birmingham United Kingdom Anesthesi

When a patient is admitted to the intensive care unit (ICU) after a traumatic brain injury (TBI), an early prognosis is essential for baseline risk adjustment and shared decision making. TBI outcomes are commonly categorised by the Glasgow Outcome Scale - Extended (GOSE) into eight, ordered levels of functional recovery at 6 months after injury. Existing ICU prognostic models predict binary outcomes at a certain threshold of GOSE (e.g., prediction of survival [GOSE > 1]). We aimed to develop ordinal prediction models that concurrently predict probabilities of each GOSE score. From a prospective cohort (n = 1,550, 65 centres) in the ICU stratum of the Collaborative European NeuroTrauma Effectiveness research in TBI (center-TBI) patient dataset, we extracted all clinical information within 24 hours of ICU admission (1,151 predictors) and 6-month GOSE scores. We analysed the effect of two design elements on ordinal model performance: (1) the baseline predictor set, ranging from a concise set of ten validated predictors to a token-embedded representation of all possible predictors, and (2) the modelling strategy, from ordinal logistic regression to multinomial deep learning. With repeated k-fold cross-validation, we found that expanding the baseline predictor set significantly improved ordinal prediction performance while increasing analytical complexity did not. Half of these gains could be achieved with the addition of eight high-impact predictors to the concise set. At best, ordinal models achieved 0.76 (95% CI: 0.74 - 0.77) ordinal discrimination ability (ordinal c-index) and 57% (95% CI: 54% - 60%) explanation of ordinal variation in 6-month GOSE (Somers' Dxy). Model performance and the effect of expanding the predictor set decreased at higher GOSE thresholds, indicating the difficulty of predicting better functional outcomes shortly after ICU admission. Our results motivate the search for informative predictors that improve confidence in prognosis of higher GOSE a

关键词： Neural network models

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