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Music, computing, and Health: A Roadmap for the Current and Future Roles of Music Technology for Health Care and Well-Being

引用

Music and Science 2021年 4卷

作者： Agres, Kat R. Schaefer, Rebecca S. Volk, Anja van Hooren, Susan Holzapfel, Andre Dalla Bella, Simone Müller, Meinard de Witte, Martina Herremans, Dorien Ramirez Melendez, Rafael Neerincx, Mark Ruiz, Sebastian Meredith, David Dimitriadis, Theo Magee, Wendy L. Yong Siew Toh Conservatory of Music National University of Singapore Singapore Social and Cognitive Computing Department Institute of High Performance Computing A*STAR Singapore Institute for Psychology Health Medical Neuropsychology Unit Leiden University Leiden Netherlands Leiden Institute for Brain and Cognition Leiden University Leiden Netherlands Academy of Creative and Performing Arts Leiden University Leiden Netherlands Department of Information and Computing Sciences Utrecht University Utrecht Netherlands Faculty of Health care Department of Arts Therapies Zuyd University of Applied Sciences Heerlen Netherlands KenVaK Research Centre for the Arts Therapies and Psychomotricity Heerlen Netherlands Faculty of Psychology Open University of The Netherlands Heerlen Netherlands Division of Media Technology and Interaction Design KTH Royal Institute of Technology Stockholm Sweden International Laboratory for Brain Music and Sound Research (BRAMS) Outremont QC Canada Department of Psychology University of Montreal Montreal QC Canada Centre for Research on Brain Language and Music (CRBLM) Montreal QC Canada University of Economics and Human Sciences in Warsaw Warsaw Poland International Audio Laboratories Erlangen Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen Germany HAN University of Applied Sciences Department of Arts Therapies and Psychological Studies Nijmegen Netherlands University of Amsterdam Research Institute of Child Development and Education Amsterdam Netherlands Treatment Centre for People with Mild Intellectual Disabilities and Psychiatric and Behavioral Disorders Gennep Netherlands Information Systems Technology and Design Singapore University of Technology and Design Singapore Music and Machine Learning Lab Music Technology Group Universitat Pompeu Fabra Barcelona Spain Faculty of EEMCS Interactive Intelligence Group Delft University of Technology Delft Netherlands Centre for Digital Music School of Electronic Engineerin

The fields of music, health, and technology have seen significant interactions in recent years in developing music technology for health care and well-being. In an effort to strengthen the collaboration between the involved disciplines, the workshop “Music, computing, and Health” was held to discuss best practices and state-of-the-art at the intersection of these areas with researchers from music psychology and neuroscience, music therapy, music information retrieval, music technology, medical technology (medtech), and robotics. Following the discussions at the workshop, this article provides an overview of the different methods of the involved disciplines and their potential contributions to developing music technology for health and well-being. Furthermore, the article summarizes the state of the art in music technology that can be applied in various health scenarios and provides a perspective on challenges and opportunities for developing music technology that (1) supports person-centered care and evidence-based treatments, and (2) contributes to developing standardized, large-scale research on music-based interventions in an interdisciplinary manner. The article provides a resource for those seeking to engage in interdisciplinary research using music-based computational methods to develop technology for health care, and aims to inspire future research directions by evaluating the state of the art with respect to the challenges facing each field. © The Author(s) 2021.

关键词： health care interdisciplinarity MedTech music information retrieval (MIR) music neuroscience Music psychology music technology music therapy well-being

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

arXiv

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arXiv 2023年

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

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

关键词： Clinical research

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Why is the Winner the Best?

Why is the Winner the Best?

引用

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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DeePMD-kit v2: A software package for Deep Potential models

arXiv

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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AIROGS: ARTIFICIAL INTELLIGENCE FOR ROBUST GLAUCOMA SCREENING CHALLENGE

arXiv

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arXiv 2023年

作者： De Vente, Coen Vermeer, Koenraad A. Jaccard, Nicolas Wang, He Sun, Hongyi Khader, Firas Truhn, Daniel Aimyshev, Temirgali Zhanibekuly, Yerkebulan Le, Tien-Dung Galdran, Adrian Ballester, Miguel Ángel González Carneiro, Gustavo Devika, R.G. Hrishikesh, P.S. Puthussery, Densen Liu, Hong Yang, Zekang Kondo, Satoshi Kasai, Satoshi Wang, Edward Durvasula, Ashritha Heras, Jónathan Zapata, Miguel Ángel Araújo, Teresa Aresta, Guilherme Bogunović, Hrvoje Arikan, Mustafa Lee, Yeong Chan Cho, Hyun Bin Choi, Yoon Ho Qayyum, Abdul Razzak, Imran Van Ginneken, Bram Lemij, Hans G. Sánchez, Clara I. Group Informatics Institute Universiteit Van Amsterdam Noord-Holland Amsterdam Netherlands The Department of Biomedical Engineering and Physics Amsterdam Umc Locatie Amc Noord-Holland Amsterdam Netherlands Department of Radiology and Nuclear Medicine Radboudumc Gelderland Nijmegen Netherlands The Rotterdam Ophthalmic Institute Rotterdam Eye Hospital Rotterdam Netherlands Project Orbis International Inc. New York United States The Peking Union Medical College Hospital Beijing China The Xuanwu Hospital Capital Medical University Beijing100053 China The Tsinghua University Beijing China The Department of Diagnostic and Interventional Radiology University Hospital Aachen Aachen Germany Cmc Technologies Llp Nur-Sultan Kazakhstan Kbc Belgium Universitat Pompeu Fabra Barcelona Spain The Australian Institute for Machine Learning Aiml University of Adelaide Australia Icrea Barcelona Spain The Centre for Vision Speech and Signal Processing University of Surrey United Kingdom The College of Engineering Trivandrum India Founding Minds Software India The Institute of Computing Technology Chinese Academy of Sciences China The Muroran Institute of Technology Japan The Niigata University of Health and Welfare Japan The Schulich School of Medicine and Dentistry University of Western Ontario London Canada The Department of Mathematics and Computer Science University of la Rioja Spain Hospital Vall Hebron Passeig Roser 126 Sant Cugat del Vallès Barcelona08195 Spain UPRetina Barcelona Spain The Christian Doppler Laboratory for Artificial Intelligence in Retina Department of Ophthalmology and Optometry Medical University of Vienna Vienna Austria The Institute of Ophthalmology University College London London United Kingdom The Research Institute for Future Medicine Samsung Medical Center Seoul Korea Republic of Sungkyunkwan University Samsung Medical Center Seoul Korea Republic of The Department of Artificial Intelligence and Informatics Mayo Clinic Jacks

The early detection of glaucoma is essential in preventing visual impairment. Artificial intelligence (AI) can be used to analyze color fundus photographs (CFPs) in a cost-effective manner, making glaucoma screening more accessible. While AI models for glaucoma screening from CFPs have shown promising results in laboratory settings, their performance decreases significantly in realworld scenarios due to the presence of out-of-distribution and low-quality images. To address this issue, we propose the Artificial Intelligence for Robust Glaucoma Screening (AIROGS) challenge. This challenge includes a large dataset of around 113,000 images from about 60,000 patients and 500 different screening centers, and encourages the development of algorithms that are robust to ungradable and unexpected input data. We evaluated solutions from 14 teams in this paper, and found that the best teams performed similarly to a set of 20 expert ophthalmologists and optometrists. The highest-scoring team achieved an area under the receiver operating characteristic curve of 0.99 (95% CI: 0.98-0.99) for detecting ungradable images on-the-fly. Additionally, many of the algorithms showed robust performance when tested on three other publicly available datasets. These results demonstrate the feasibility of robust AI-enabled glaucoma screening. Copyright © 2023, The Authors. All rights reserved.

关键词： Diagnosis

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Biomedical image analysis competitions: The state of current participation practice

arXiv

引用

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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The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

arXiv

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arXiv 2024年

作者： Lyu, Jun Qin, Chen Wang, Shuo Wang, Fanwen Li, Yan Wang, Zi Guo, Kunyuan Ouyang, Cheng Tänzer, Michael Liu, Meng Sun, Longyu Sun, Mengting Li, Qin Shi, Zhang Hua, Sha Li, Hao Chen, Zhensen Zhang, Zhenlin Xin, Bingyu Metaxas, Dimitris N. Yiasemis, George Teuwen, Jonas Zhang, Liping Chen, Weitian Pang, Yanwei Liu, Xiaohan Razumov, Artem Dylov, Dmitry V. Dou, Quan Yan, Kang Xue, Yuyang Du, Yuning Dietlmeier, Julia Garcia-Cabrera, Carles Hemidi, Ziad Al-Haj Vogt, Nora Xu, Ziqiang Zhang, Yajing Chu, Ying-Hua Chen, Weibo Bai, Wenjia Zhuang, Xiahai Qin, Jing Wu, Lianmin Yang, Guang Qu, Xiaobo Wang, He Wang, Chengyan Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School 399 Revolution Drive BostonMA02215 United States Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Bioengineering & I-X Imperial College London LondonW12 7SL United Kingdom Cardiovascular Magnetic Resonance Unit Royal Brompton Hospital Guy’s and St Thomas’ NHS Foundation Trust LondonSW3 6NP United Kingdom Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen361102 China Department of Computing Department of Brain Sciences Imperial College London LondonSW7 2AZ United Kingdom Human Phenome Institute Fudan University 825 Zhangheng Road Pudong New District Shanghai201203 China Department of Radiology Zhongshan Hospital Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Department of Computer Science Rutgers University PiscatawayNJ08854 United States AI for Oncology Netherlands Cancer Institute Plesmanlaan 121 Amsterdam1066 CX Netherlands Department of Imaging and Interventional Radiology The Chinese University of Hong Kong Hong Kong TJK-BIIT Lab School of Electrical and Information Engineering Tianjin University Tianjin300072 China Skolkovo Institute Of Science And Technology Center for Artificial Intelligence Technology 30/1 Bolshoy blvd. Moscow121205 Russia Department of Biomedical Engineering University of Virginia

Cardiac magnetic resonance imaging (MRI) provides detailed and quantitative evaluation of the heart’s structure, function, and tissue characteristics with high-resolution spatial-temporal imaging. However, its slow imaging speed and motion artifacts are notable limitations. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on Medical Image computing and Computer-Assisted Intervention (MICCAI). CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techn

关键词： Mapping

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Why is the winner the best?

arXiv

引用

arXiv 2023年

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

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

关键词： Benchmarking

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Recent developments in the PySCF program package

arXiv

引用

arXiv 2020年

作者： Sun, Qiming Zhang, Xing Banerjee, Samragni Bao, Peng Barbry, Marc Blunt, Nick S. Bogdanov, Nikolay A. Booth, George H. Chen, Jia Cui, Zhi-Hao Eriksen, Janus Juul Gao, Yang Guo, Sheng Hermann, Jan Hermes, Matthew R. Koh, Kevin Koval, Peter Lehtola, Susi Li, Zhendong Liu, Junzi Mardirossian, Narbe McClain, James D. Motta, Mario Mussard, Bastien Pham, Hung Q. Pulkin, Artem Purwanto, Wirawan Robinson, Paul J. Ronca, Enrico Sayfutyarova, Elvira Scheurer, Maximilian Schurkus, Henry F. Smith, James E.T. Sun, Chong Sun, Shi-Ning Upadhyay, Shiv Wagner, Lucas K. Wang, Xiao White, Alec Whitfield, James Daniel Williamson, Mark J. Wouters, Sebastian Yang, Jun Yu, Jason M. Zhu, Tianyu Berkelbach, Timothy C. Sharma, Sandeep Sokolov, Alexander Yu. Chan, Garnet Kin-Lic AxiomQuant Investment Management LLC Shanghai200120 China Division of Chemistry and Chemical Engineering California Institute of Technology PasadenaCA91125 United States Department of Chemistry and Biochemistry The Ohio State University ColumbusOH43210 United States Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing100190 China Simbeyond B.V. P.O. Box 513 EindhovenNL-5600 MB Netherlands Department of Chemistry Lensfield Road CambridgeCB2 1EW United Kingdom Max Planck Institute for Solid State Research Heisenbergstraße 1 Stuttgart70569 Germany Department of Physics King's College London Strand LondonWC2R 2LS United Kingdom Department of Physics University of Florida GainesvilleFL32611 United States Quantum Theory Project University of Florida GainesvilleFL32611 United States School of Chemistry University of Bristol Cantock's Close BristolBS8 1TS United Kingdom Division of Engineering and Applied Science California Institute of Technology PasadenaCA91125 United States Google Inc. Mountain ViewCA94043 United States FU Berlin Department of Mathematics and Computer Science Arnimallee 6 Berlin14195 Germany TU Berlin Machine Learning Group Marchstr. 23 Berlin10587 Germany Department of Chemistry Chemical Theory Center Supercomputing Institute University of Minnesota 207 Pleasant Street SE MinneapolisMN55455 United States Department of Chemistry and Biochemistry The University of Notre Dame du Lac 251 Nieuwland Science Hall Notre DameIN46556 United States Simune Atomistics S.L. Avenida Tolosa 76 Donostia-San Sebastian Spain HelsinkiFI-00014 Finland Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing100875 China Department of Chemistry The Johns Hopkins University BaltimoreMD21218 United States AMGEN

PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows. The present paper explains the design and philosophy behind PYSCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PYSCF as a development environment. We then summarize the capabilities of PYSCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PYSCF across the domains of quantum chemistry, materials science, machine learning and quantum information science. Copyright © 2020, The Authors. All rights reserved.

关键词： Python

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Constructing Impactful machine learning research for Astronomy: Best Practices for researchers and Reviewers

arXiv

引用

arXiv 2023年

作者： Huppenkothen, Daniela Ntampaka, Michelle Ho, Matthew Fouesneau, Morgan Nord, Brian Peek, J.E.G. Walmsley, Mike Wu, John F. Avestruz, C. Buck, Tobias Brescia, Massimo Finkbeiner, Douglas P. Goulding, Andy D. Kacprzak, T. Melchior, Peter Pasquato, Mario Ramachandra, Nesar Ting, Yuan-Sen van de Ven, Glenn Villar, Soledad Villar, V.A. Zinger, Elad SRON Netherlands Institute for Space Research Niels Bohrweg 4 Leiden2333CA Netherlands Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Space Telescope Science Institute BaltimoreMD21218 United States Department of Physics & Astronomy Johns Hopkins University BaltimoreMD21218 United States UMR 7095 98 bis bd Arago ParisF-75014 France Königstuhl 17 HeidelbergD-69117 Germany Fermi National Accelerator Laboratory P. O. Box 500 BataviaIL60510 United States Kavli Institute for Cosmological Physics University of Chicago ChicagoIL60637 United States Department of Astronomy and Astrophysics University of Chicago ChicagoIL60637 United States Jodrell Bank Centre for Astrophysics Department of Physics & Astronomy University of Manchester ManchesterM13 9PL United Kingdom Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Leinweber Center for Theoretical Physics University of Michigan Ann ArborMI48109 United States Department of Physics University of Michigan Ann ArborMI48109 United States Universität Heidelberg Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Im Neuenheimer Feld 205 Heidelberg69120 Germany Universität Heidelberg Zentrum für Astronomie Institut für Theoretische Astrophysik Albert-Ueberle-Straße 2 Heidelberg69120 Germany Department of Physics "E. Pancini " University Federico II of Napoli Via Cinthia 21 NapoliI-80126 Italy INAF Astronomical Observatory of Capodimonte Salita Moiariello 16 NapoliI-80131 Italy Department of Physics Harvard University 17 Oxford St. CambridgeMA02138 United States Harvard-Smithsonian Center for Astrophysics 60 Garden St. CambridgeMA02138 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States Swiss Data Science Center Paul Scherrer Institute Villigen5303 Switzerland Center for Statistics & Machine Learn

machine learning has rapidly become a tool of choice for the astronomical community. It is being applied across a wide range of wavelengths and problems, from the classification of transients to neural network emulators of cosmological simulations, and is shifting paradigms about how we generate and report scientific results. At the same time, this class of method comes with its own set of best practices, challenges, and drawbacks, which, at present, are often reported on incompletely in the astrophysical literature. With this paper, we aim to provide a primer to the astronomical community, including authors, reviewers, and editors, on how to implement machine learning models and report their results in a way that ensures the accuracy of the results, reproducibility of the findings, and usefulness of the method. Copyright © 2023, The Authors. All rights reserved.

关键词： machine learning

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