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arXiv 2022年

作者： Jafari, Mahboobeh Shoeibi, Afshin Khodatars, Marjane Ghassemi, Navid Moridian, Parisa Delfan, Niloufar Alizadehsani, Roohallah Khosravi, Abbas Ling, Sai Ho Zhang, Yu-Dong Wang, Shui-Hua Gorriz, Juan M. Rokny, Hamid Alinejad Acharya, U. Rajendra Internship in BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia Data Science and Computational Intelligence Institute University of Granada Spain Department of Medical Engineering Mashhad Branch Islamic Azad University Mashhad Iran Faculty of Computer Engineering Dept. of Artificial Intelligence Engineering K. N. Toosi University of Technology Tehran Iran Deakin University VIC3217 Australia Australia School of Computing and Mathematical Sciences University of Leicester Leicester United Kingdom Department of Psychiatry University of Cambridge United Kingdom BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia UNSW Data Science Hub The University of New South Wales SydneyNSW2052 Australia Research Centre Macquarie University Sydney2109 Australia Ngee Ann Polytechnic Singapore599489 Singapore Dept. of Biomedical Informatics and Medical Engineering Asia University Taichung Taiwan Dept. of Biomedical Engineering School of Science and Technology Singapore University of Social Sciences Singapore

In recent years, cardiovascular diseases (CVDs) have become one of the leading causes of mortality globally. CVDs appear with minor symptoms and progressively get worse. The majority of people experience symptoms such as exhaustion, shortness of breath, ankle swelling, fluid retention, and other symptoms when starting CVD. Coronary artery disease (CAD), arrhythmia, cardiomyopathy, congenital heart defect (CHD), mitral regurgitation, and angina are the most common CVDs. Clinical methods such as blood tests, electrocardiography (ECG) signals, and medical imaging are the most effective methods used for the detection of CVDs. Among the diagnostic methods, cardiac magnetic resonance imaging (CMR) is increasingly used to diagnose, monitor the disease, plan treatment and predict CVDs. Coupled with all the advantages of CMR data, CVDs diagnosis is challenging for physicians due to many slices of data, low contrast, etc. To address these issues, deep learning (DL) techniques have been employed to the diagnosis of CVDs using CMR data, and much research is currently being conducted in this field. This review provides an overview of the studies performed in CVDs detection using CMR images and DL techniques. The introduction section examined CVDs types, diagnostic methods, and the most important medical imaging techniques. In the following, investigations to detect CVDs using CMR images and the most significant DL methods are presented. Another section discussed the challenges in diagnosing CVDs from CMR data. Next, the discussion section discusses the results of this review, and future work in CVDs diagnosis from CMR images and DL techniques are outlined. The most important findings of this study are presented in the conclusion section. © 2022, CC BY-NC-ND.

关键词： Electrocardiography

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HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation

arXiv

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arXiv 2022年

作者： Heidari, Moein Kazerouni, Amirhossein Soltany, Milad Azad, Reza Aghdam, Ehsan Khodapanah Cohen-Adad, Julien Merhof, Dorit School of Electrical Engineering Iran University of Science and Technology Tehran Iran Institute of Imaging and Computer Vision RWTH Aachen University Aachen Germany Department of Electrical Engineering Shahid Beheshti University Tehran Iran Functional Neuroimaging Unit CRIUGM University of Montreal Canada NeuroPoly Lab Institute of Biomedical Engineering Polytechnique Montreal Canada MILA Quebec AI Institute Montreal Canada Faculty of Informatics and Data Science University of Regensburg Regensburg Germany Fraunhofer Institute for Digital Medicine MEVIS Bremen Germany

Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, quantitative and qualitative results. Our code is publicly available at GitHub. © 2022, CC BY.

关键词： Convolution

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Assessing responsible innovation training

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Journal of Responsible Technology 2023年 16卷

作者： Stahl, Bernd Carsten Aicardi, Christine Brooks, Laurence Craigon, Peter J. Cunden, Mayen Burton, Saheli Datta Heaver, Martin De Saille, Stevienna De Dolby, Serena Dowthwaite, Liz Eke, Damian Hughes, Stephen Keene, Paul Kuh, Vivienne Portillo, Virginia Shanley, Danielle Smallman, Melanie Smith, Michael Stilgoe, Jack Ulnicane, Inga Wagner, Christian Webb, Helena School of Computer Science University of Nottingham United Kingdom Dept. of Informatics and School of Biomedical Engineering & Imaging Sciences King's College London United Kingdom Information School University of Sheffield Sheffield United Kingdom Horizon Digital Economy Research School of Computer Science University of Nottingham United Kingdom Independent Researcher Dept of Science and Technology Studies University College London United Kingdom ORBIT RRI limited Leicester United Kingdom Dept of Sociological Studies University of Sheffield Sheffield United Kingdom Centre for Computing and Social Responsibility De Montfort University Leicester United Kingdom School of Chemistry University of Bristol United Kingdom Department of Philosophy Faculty of Arts and Social Sciences Maastricht University Netherlands Biodiversity and Conservation Science Department of Biodiversity Conservation and Attractions Wildlife Research Centre Western Australia De Montfort University United Kingdom Lab for Uncertainty in Data and Decision Making (LUCID) School of Computer Science University of Nottingham United Kingdom

There is broad agreement that one important aspect of responsible innovation (RI) is to provide training on its principles and practices to current and future researchers and innovators, notably including doctoral students. Much less agreement can be observed concerning the question of what this training should consist of, how it should be delivered and how it could be assessed. The increasing institutional embedding of RI leads to calls for the alignment of RI training with training in other subjects. One can therefore observe a push towards the official assessment of RI training, for example in the recent call for proposals for centres for doctoral training by UK Research and Innovation. This editorial article takes its point of departure from the recognition that the RI community will need to react to the call for assessment of RI training. It provides an overview of the background and open questions around RI training and assessment as a background of examples of RI training assessment at doctoral level. There is unlikely to be one right way of assessing RI training across institutions and disciplines, but we expect that the examples provided in this article can help RI scholars and practitioners orient their training and its assessment in ways that are academically viable as well as supportive of the overall aims of RI. © 2023

关键词： Assessment Doctoral training Education Responsible innovation

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Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

SSRN

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SSRN 2024年

作者： Saad Menezes, Maria Clara Hoffman, Alexander F. Tan, Amelia L.M. Nalbandyan, Mariné Omenn, Gilbert S. Mazzotti, Diego R. Hernández-Arango, Alejandro Visweswaran, Shyam Venkatesh, Shruthi Mandl, Kenneth D. Bourgeois, Florence T. Lee, James W.K. Makmur, Andrew Hanauer, David A. Semanik, Michael G. Kerivan, Lauren T. Hill, Terra Forero, Julian Restrepo Castro, Carlos Andrés C.R. Vigna, Matteo Ceriana, Piero Abu-El-rub, Noor Avillach, Paul Bellazzi, Riccardo Callaci, Thomas Gutiérrez-Sacristán, Alba Malovini, Alberto Mathew, Jomol P. Morris, Michele Murthy, Venkatesh Parimbelli, Enea Patel, Lav P. Sáez, Carlos Samayamuthu, Malarkodi Jebathilagam Thompson, Jeffrey A. Tibollo, Valentina Xia, Zongqi Kohane, Isaac S. Harvard Medical School Department of Biomedical Informatics 10 Shattuck Street BostonMA02115 United States School of Medicine and Public Health University of Wisconsin-Madison Office of Informatics and Information Technology 750 Highland Ave MadisonWI53705 United States University of Michigan Department of Computational Medicine & Bioinformatics Internal Medicine Human Genetics Environmental Health 100 Washtenaw Avenue Ann ArborMI48109 United States University of Kansas Medical Center Division of Medical Informatics Division of Pulmonary Critical Care and Sleep Medicine Department of Internal Medicine 3901 Rainbow Blvd Kansas CityKS66160 United States University of Antioquia Hospital Alma Máter de Antioquia Department of Internal Medicine Calle 64 N°51 D - 154 Medellín Colombia University of Pittsburgh Department of Biomedical Informatics 5607 Baum Blvd PittsburghPA15206 United States University of Pittsburgh Department of Neurology 3501 5th Avenue PittsburghPA15206 United States Boston Children's Hospital Computational Health Informatics Program 300 Longwood Avenue BostonMA02115 United States Boston Children's Hospital Department of Pediatrics 300 Longwood Avenue BostonMA02115 United States National University Health System Department of Surgery 1E Kent Ridge Rd Singapore119228 Singapore National University Health System Department of Diagnostic Imaging 1E Kent Ridge Rd Singapore119228 Singapore University of Michigan Department of Learning Health Sciences NCRC 100 2800 Plymouth Road Ann ArborMI48109 United States University of Kansas Medical Center Department of Surgery 3901 Rainbow Blvd Kansas CityKS66160 United States Istituti Clinici Scientifici Maugeri IRCCS Respiratory rehabilitation unit Via Maugeri 10 Pavia27100 Italy University of Kansas Medical Center 3901 Rainbow Blvd Kansas CityKS66160 United States University of Pavia Department of Electrical Computer and Biomedical Engineering via Ferrata 5 Pavia2710

Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the United States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati

关键词： Medical computing

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GSCo: Towards Generalizable AI in Medicine via Generalist-Specialist Collaboration

arXiv

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arXiv 2024年

作者： He, Sunan Nie, Yuxiang Wang, Hongmei Yang, Shu Wang, Yihui Cai, Zhiyuan Chen, Zhixuan Xu, Yingxue Luo, Luyang Xiang, Huiling Lin, Xi Wu, Mingxiang Peng, Yifan Shih, George Xu, Ziyang Wu, Xian Wang, Qiong Chan, Ronald Cheong Kin Vardhanabhuti, Varut Chu, Winnie Chiu Wing Zheng, Yefeng Rajpurkar, Pranav Zhang, Kang Chen, Hao Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong Department of Biomedical Informatics Harvard University Boston United States Department of Ultrasound Sun Yat-sen University Cancer Center Guangzhou China Department of Radiology Shenzhen People’s Hospital Shenzhen China Population Health Sciences Weill Cornell Medicine New York United States Department of Radiology Weill Cornell Medicine New York United States Perelman Department of Dermatology New York Langone Health New York United States Jarvis Research Center Tencent YouTu Lab Shenzhen China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen China Department of Anatomical and Cellular Pathology The Chinese University of Hong Kong Hong Kong State Key Laboratory of Translational Oncology The Chinese University of Hong Kong Hong Kong Department of Diagnostic Radiology The University of Hong Kong Hong Kong Department of Imaging and Interventional Radiology The Chinese University of Hong Kong Hong Kong Medical Artificial Intelligence Laboratory Westlake University Hangzhou China Faculty of Medicine The Macau University of Science and Technology China Department of Chemical and Biological Engineering The Hong Kong University of Science and Technology Hong Kong Division of Life Science The Hong Kong University of Science and Technology Hong Kong State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology Hong Kong Shenzhen-Hong Kong Collaborative Innovation Research Institute The Hong Kong University of Science and Technology Shenzhen China

Generalist foundation models (GFMs) are renowned for their exceptional capability and flexibility in effectively generalizing across diverse tasks and modalities. In the field of medicine, while GFMs exhibit superior generalizability based on their extensive intrinsic knowledge as well as proficiency in instruction following and in-context learning, specialist models excel in precision due to their in-depth domain-specific knowledge. In this work, for the first time, we explore the synergy between the GFM and specialist models, to enable precise medical image analysis on a broader scope. Specifically, we propose a novel cooperative framework, Generalist-Specialist Collaboration (GSCo), which consists of two stages, namely the construction of GFM and specialists, and collaborative inference on downstream tasks. In the construction stage, we develop MedDr, the largest open-source GFM tailored for medicine, showcasing exceptional instruction-following and in-context learning capabilities. Meanwhile, a series of lightweight specialists are crafted for specific downstream tasks with low computational overhead. In the collaborative inference stage, we introduce two cooperative mechanisms, Mixture-of-Expert Diagnosis (MoED) and Retrieval-Augmented Diagnosis (RAD), to harvest the generalist’s in-context learning abilities alongside the specialists’ domain expertise. Concretely, MoED incorporates predictions from specialists as references, while RAD employs specialists to retrieve similar cases, collectively providing MedDr with much more contextual guidance. For a comprehensive evaluation, we curate a large-scale benchmark featuring 28 datasets and about 250,000 images across a wide range of medical modalities, including radiology, pathology, dermatology, ophthalmology, and gastroenterology. Extensive experimental results demonstrate that MedDr consistently outperforms state-of-the-art GFMs on downstream datasets. Furthermore, GSCo exceeds both GFMs and specialists across a

关键词： Ophthalmology

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Transformers in Medical Image Analysis: A Review

arXiv

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arXiv 2022年

作者： He, Kelei Gan, Chen Li, Zhuoyuan Rekik, Islem Yin, Zihao Ji, Wen Gao, Yang Wang, Qian Zhang, Junfeng Shen, Dinggang Medical School of Nanjing University Nanjing China National Institute of Healthcare Data Science Nanjing University Nanjing China State Key Laboratory for Novel Software Technology Nanjing University Nanjing China BASIRA Lab Faculty of Computer and Informatics Engineering Istanbul Technical University Istanbul Turkey School of Science and Engineering Computing University of Dundee United Kingdom School of Biomedical Engineering ShanghaiTech University Shanghai China Department of Research and Development Shanghai United Imaging Intelligence Co. Ltd. Shanghai China

Transformers have dominated the field of natural language processing, and recently impacted the computer vision area. In the field of medical image analysis, Transformers have also been successfully applied to full-stack clinical applications, including image synthesis/reconstruction, registration, segmentation, detection, and diagnosis. Our paper aims to promote awareness and application of Transformers in the field of medical image analysis. Specifically, we first overview the core concepts of the attention mechanism built into Transformers and other basic components. Second, we review various Transformer architectures tailored for medical image applications and discuss their limitations. Within this review, we investigate key challenges revolving around the use of Transformers in different learning paradigms, improving the model efficiency, and their coupling with other techniques. We hope this review can give a comprehensive picture of Transformers to the readers in the field of medical image analysis. © 2022, CC BY-SA.

关键词： Diagnosis

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An information-theoretic approach to hypergraph psychometrics

arXiv

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arXiv 2022年

作者： Marinazzo, Daniele Van Roozendaal, Jan Rosas, Fernando E. Stella, Massimo Comolatti, Renzo Colenbier, Nigel Stramaglia, Sebastiano Rosseel, Yves Department of Data Analysis Ghent University Belgium Data Science Institute Imperial College London London United Kingdom Centre for Psychedelic Research Imperial College London London United Kingdom Centre for Complexity Science Imperial College London London United Kingdom Department of Informatics University of Sussex Brighton United Kingdom CogNosco Lab Dept. of Computer Science University of Exeter United Kingdom Department of Biomedical and Clinical Sciences "L. Sacco" Università degli Studi di Milano Italy IRCCS San Camillo Hospital Via Alberoni 70 Venice30126 Italy Physics Department Universitá degli Studi di Bari Aldo Moro INFN Sezione di Bari Italy

Psychological network approaches propose to see symptoms or questionnaire items as interconnected nodes, with links between them reflecting pairwise statistical dependencies evaluated on cross-sectional, time-series, or panel data. These networks constitute an established methodology to assess the interactions and relative importance of nodes/indicators, providing an important complement to other approaches such as factor analysis. However, focusing the modelling solely on pairwise relationships can neglect potentially critical information shared by groups of three or more variables in the form of higher-order interdependencies. To overcome this important limitation, here we propose an information-theoretic framework based on hypergraphs as psychometric models. As edges in hypergraphs are capable of encompassing several nodes together, this extension can thus provide a richer representation of the interactions that may exist among sets of psychological variables. Our results show how psychometric hypergraphs can highlight meaningful redundant and synergistic interactions on either simulated or state-of-art, re-analyzed psychometric datasets. Overall, our framework extends current network approaches while leading to new ways of assessing the data that differ at their core from other methods, extending the psychometric toolbox and opening promising avenues for future investigation. © 2022, CC BY.

关键词： Information theory

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QUBIQ: Uncertainty Quantification for biomedical Image Segmentation Challenge

arXiv

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arXiv 2024年

作者： Li, Hongwei Bran Navarro, Fernando Ezhov, Ivan Bayat, Amirhossein Das, Dhritiman Kofler, Florian Shit, Suprosanna Waldmannstetter, diana Paetzold, Johannes C. Hu, Xiaobin Wiestler, Benedikt Zimmer, Lucas Amiranashvili, Tamaz Prabhakar, Chinmay Berger, Christoph Weidner, Jonas Alonso-Basanta, Michelle Rashid, Arif Baid, Ujjwal Adel, Wesam Alis, Deniz Baheti, Bhakti Bai, Yingbin Bhat, Ishaan Cetindag, Sabri Can Chen, Wenting Cheng, Li Dutande, Prasad Dular, Lara Elattar, Mustafa A. Feng, Ming Gao, Shengbo Huisman, Henkjan Hu, Weifeng Innani, Shubham Ji, Wei Karimi, Davood Kuijf, Hugo J. Kwak, Jin Tae Le, Hoang Long Li, Xiang Lin, Huiyan Liu, Tongliang Ma, Jun Ma, Kai Ma, Ting Oksuz, Ilkay Holland, Robbie Oliveira, Arlindo L. Pal, Jimut Bahan Pei, Xuan Qiao, Maoying Saha, Anindo Selvan, Raghavendra Shen, Linlin Silva, Joao Lourenco Spiclin, Ziga Talbar, Sanjay Wang, Dadong Wang, Wei Wang, Xiong Wang, Yin Xi, Ruiling Xu, Kele Yang, Yanwu Yergin, Mert Yu, Shuang Zeng, Lingxi Zhang, YingLin Zhao, Jiachen Zheng, Yefeng Zukovec, Martin Do, Richard Becker, Anton Simpson, Amber Konukoglu, Ender Jakab, Andras Bakas, Spyridon Joskowicz, Leo Menze, Bjoern Department of Informatics Technical University of Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Department of Quantitative Biomedicine University of Zurich Switzerland University Children’s Hospital Zurich University of Zurich Switzerland Department of Radioncology and Radiation Theraphy Klinikum rechts der Isar Technical University of Munich Germany Department of Information Technology and Electrical Engineering ETH-Zurich Switzerland Department of Radiology Memorial Sloan Kettering Cancer Center New York City United States Department of Biomedical and Molecular Sciences Queen’s University Canada TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany McGovern Institute Massachusetts Institute of Technology United States Institute for Diagnostic and Interventional Radiology Unveristy Zurich Hospital Switzerland BioMedIA Imperial College London United Kingdom Department of Radiation Oncology University of Pennsylvania PA United States University of Pennsylvania PA United States Department of Radiation Oncology Winship Cancer Institute of Emory University Georgia United States Nile University Cairo Egypt Department of Medical Sciences Acibadem University Istanbul Turkey Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Trustworthy Machine Learning Lab University of Sydney Australia Image Sciences Institute University Medical Center Utrecht Netherlands Computer Engineering Department Istanbul Technical University Istanbul Turkey School of Computer Science Shenzhen University Shenzhen China University of Alberta United States University of Ljubljana Faculty of Electrical Engineering Ljubljana Slovenia Tongji University Shanghai China OPPO Research Institute Shanghai China School of Biological and Medical Engineering Beihang University Beijing China Harvard Medical School Boston

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT;various organs such as the brain, prostate, kidney, and pancreas;and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks. © 2024, CC BY-NC-ND.

关键词： Image segmentation

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P-012 Investigating the potential role of microRNAs as biomarkers in idiopathic non-obstructive azoospermia: A systematic review and in-silico analysis of the affected pathways

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Human Reproduction 2022年第SUPPLEMENT_1期37卷

作者： Pantou, A Grigoriadis, S Karagkouni, D Pantos, K Maziotis, E Tomara, P Hatzigeorgiou, A Agarwal, A Sfakianoudis, K Simopoulou, M Genesis Genoma Lab Department of Genetic Diagnosis- Clinical Genetics & Research Athens Greece National and Kapodistrian University of Athens Laboratory of Physiology- Medical School Athens Greece University of Thessaly DIANA-Lab- Department of Computer Science and Biomedical Informatics Lamia Greece Genesis Athens Clinic Centre for Human Reproduction Athens Greece Cleveland Clinic American Center for Reproductive Medicine Cleveland Greece

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on computer Vision and Pattern Recognition (CVPR)

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

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

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