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Archives of Computational Methods in Engineering 2022年第5期30卷 3467-3467页

作者： Alsalibi, Bisan Mirjalili, Seyedali Abualigah, Laith yahya, Rafaa Ismael Gandomi, Amir H. School of Computer Sciences Universiti Sains Malaysia Penang Malaysia Centre for Artificial Intelligence Research and Optimization Torrens University Australia Adelaide Australia Yonsei Frontier Lab Yonsei University Seoul South Korea Faculty of Computer Sciences and Informatics Amman Arab University Amman Jordan Department of Computer College of Science Mustansiriyah University Baghdad Iraq Faculty of Engineering and Information Technology University of Technology Sydney Ultimo Australia

Cardiac segmentation on late gadolinium enhancement MRI: A benchmark study from multi-sequence cardiac MR segmentation challenge

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arXiv 2020年

作者： Zhuang, Xiahai Xu, Jiahang Luo, Xinzhe Chen, Chen Ouyang, Cheng Rueckert, Daniel Campello, Victor M. Lekadir, Karim Vesal, Sulaiman RaviKumar, Nishant Liu, Yashu Luo, Gongning Chen, Jingkun Li, Hongwei Ly, Buntheng Sermesant, Maxime Roth, Holger Zhu, Wentao Wang, Jiexiang Ding, Xinghao Wang, Xinyue Yang, Sen Li, Lei School of Data Science Fudan University Shanghai China School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China Biomedical Image Analysis Group Imperial College London London United Kingdom Department Mathematics & Computer Science Universitat de Barcelona Barcelona Spain Friedrich-Alexander-Universität Erlangen-Nürnberg Germany School of Computer Science and Technology Harbin Institute of Technology Harbin China Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China Department of Informatics Technical University of Munich Germany INRIA Université Côte d’Azur Sophia Antipolis France NVIDIA Bethesda United States School of Informatics Xiamen University Xiamen China College of Electrical Engineering Sichuan University Chengdu China Tencent AI Lab Shenzhen China

Accurate computing, analysis and modeling of the ventricles and myocardium from medical images are important, especially in the diagnosis and treatment management for patients suffering from myocardial infarction (MI). Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) provides an important protocol to visualize MI. However, automated segmentation of LGE CMR is still challenging, due to the indistinguishable boundaries, heterogeneous intensity distribution and complex enhancement patterns of pathological myocardium from LGE CMR. Furthermore, compared with the other sequences LGE CMR images with gold standard labels are particularly limited, which represents another obstacle for developing novel algorithms for automatic segmentation of LGE CMR. This paper presents the selective results from the Multi-Sequence Cardiac MR (MS-CMR) Segmentation challenge, in conjunction with MICCAI 2019. The challenge offered a data set of paired MS-CMR images, including auxiliary CMR sequences as well as LGE CMR, from 45 patients who underwent cardiomyopathy. It was aimed to develop new algorithms, as well as benchmark existing ones for LGE CMR segmentation and compare them objectively. In addition, the paired MS-CMR images could enable algorithms to combine the complementary information from the other sequences for the segmentation of LGE CMR. Nine representative works were selected for evaluation and comparisons, among which three methods are unsupervised methods and the other six are supervised. The results showed that the average performance of the nine methods was comparable to the inter-observer variations. Particularly, the top-ranking algorithms from both the supervised and unsupervised methods could generate reliable and robust segmentation results. The success of these methods was mainly attributed to the inclusion of the auxiliary sequences from the MS-CMR images, which provide important label information for the training of deep neural networks. The challeng

关键词： Magnetic resonance

Understanding metric-related pitfalls in image analysis validation

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arXiv 2023年

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

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

关键词： computer vision

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

Automatic Intelligent System Using Medical of Things for Multiple Sclerosis Detection

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Computational intelligence and neuroscience 2023年第1期2023卷 4776770页

作者： Sujatha Krishnamoorthy Yaxi Zhang Seifedine Kadry Muhammad Attique Khan Majed Alhaisoni Nasser Mustafa Weifeng Yu Abdullah Alqahtani Zhejiang Bioinformatics International Science and Technology Cooperation Center Wenzhou-Kean University Wenzhou Zhejiang Province China. Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics Wenzhou-Kean University Wenzhou Zhejiang Province China. Department of Neurology Wenzhou Central Hospital Medical Group Wenzhou 325000 China. Department of Applied Data Science Noroff University College Kristiansand Norway. Artificial Intelligence Research Center (AIRC) Ajman University Ajman 346 UAE. Department of Electrical and Computer Engineering Lebanese American University Byblos Lebanon. Department of Computer Science HITEC University Taxila Pakistan. Computer Sciences Department College of Computer and Information Sciences Princess Nourah Bint Abdulrahman University Riyadh 11671 Saudi Arabia. Wenzhou-Kean University School of Science and Technology Wenzhou Zhejiang Province China. College of Computer Engineering and Sciences Prince Sattam Bin Abdulaziz University Al-Kharj Saudi Arabia.

Malfunctions in the immune system cause multiple sclerosis (MS), which initiates mild to severe nerve damage. MS will disturb the signal communication between the brain and other body parts, and early diagnosis will help reduce the harshness of MS in humankind. Magnetic resonance imaging (MRI) supported MS detection is a standard clinical procedure in which the bio-image recorded with a chosen modality is considered to assess the severity of the disease. The proposed research aims to implement a convolutional neural network (CNN) supported scheme to detect MS lesions in the chosen brain MRI slices. The stages of this framework include (i) image collection and resizing, (ii) deep feature mining, (iii) hand-crafted feature mining, (iii) feature optimization with firefly algorithm, and (iv) serial feature integration and classification. In this work, five-fold cross-validation is executed, and the final result is considered for the assessment. The brain MRI slices with/without the skull section are examined separately, presenting the attained results. The experimental outcome of this study confirms that the VGG16 with random forest (RF) classifier offered a classification accuracy of >98% MRI with skull, and VGG16 with K-nearest neighbor (KNN) provided an accuracy of >98% without the skull.

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Data augmentation via dependency tree morphing for low-resource languages

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arXiv 2019年

作者： Gül Şahin, Gözde Steedman, Mark UKP Lab Department of Computer Science Technische Universität Darmstadt Darmstadt Germany School of Informatics University of Edinburgh Edinburgh United Kingdom

Neural NLP systems achieve high scores in the presence of sizable training dataset. Lack of such datasets leads to poor system performances in the case low-resource languages. We present two simple text augmentation techniques using dependency trees, inspired from image processing. We "crop" sentences by removing dependency links, and we "rotate" sentences by moving the tree fragments around the root. We apply these techniques to augment the training sets of low-resource languages in Universal Dependencies project. We implement a character-level sequence tagging model and evaluate the augmented datasets on part-of-speech tagging task. We show that crop and rotate provides improvements over the models trained with non-augmented data for majority of the languages, especially for languages with rich case marking systems. Copyright © 2019, The Authors. All rights reserved.

关键词： Crops

Correction: Health Care Cybersecurity Challenges and Solutions Under the Climate of COVID-19: Scoping Review

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Journal of medical Internet research 2021年第4期23卷 e29877页

作者： Ying He Aliyu Aliyu Mark Evans Cunjin Luo School of Computer Science University of Nottingham Nottingham United Kingdom. School of Computer Science and Informatics De Montfort University Leicester United Kingdom. School of Computer Science and Electronic Engineering University of Essex Colchester United Kingdom. Key Lab of Medical Electrophysiology Ministry of Education Institute of Cardiovascular Research Southwest Medical University Luzhou China.

[This corrects the article DOI: 10.2196/21747.].

关键词：

Automated Diagnosis of Cardiovascular Diseases from Cardiac Magnetic Resonance Imaging Using Deep Learning Models: A Review

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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

Bias in data-driven AI systems - An introductory survey

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arXiv 2020年

作者： Ntoutsi, Eirini Fafalios, Pavlos Gadiraju, Ujwal Iosifidis, Vasileios Nejdl, Wolfgang Vidal, Maria-Esther Ruggieri, Salvatore Turini, Franco Papadopoulos, Symeon Krasanakis, Emmanouil Kompatsiaris, Ioannis Kinder-Kurlanda, Katharina Wagner, Claudia Karimi, Fariba Fernandez, Miriam Alani, Harith Berendt, Bettina Kruegel, Tina Heinze, Christian Broelemann, Klaus Kasneci, Gjergji Tiropanis, Thanassis Staab, Steffen L3S Research Center Leibniz University Hannover Germany Institute of Computer Science FORTH-ICS Greece TIB Leibniz Information Centre For Science and Tecnhnology Hannover Germany KDDLAB Dipartimento di Informatica Università di Pisa Italy Information Technologies Institute CERTH Thessaloniki Greece GESIS Leibniz Institute for the Social Sciences Cologne Germany Knowledge Media Institute Open University Milton Keynes United Kingdom Faculty of Electrical Engineering and Computer Science TU Berlin Department of Computer Science KU Leuven Germany Institute for Legal Informatics Leibniz University of Hanover Germany Innovation Lab SCHUFA Holding AG Wiesbaden Germany Electronics and Computer Science University of Southampton United Kingdom IPVS Universität Stuttgart Germany

AI-based systems are widely employed nowadays to make decisions that have far-reaching impacts on individuals and society. Their decisions might affect everyone, everywhere and anytime, entailing concerns about potential human rights issues. Therefore, it is necessary to move beyond traditional AI algorithms optimized for predictive performance and embed. Copyright © 2020, The Authors. All rights reserved.

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Automatic optic disc segmentation using a 3D Morphologic Fuzzy Histon Roughness Index

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Research on Biomedical Engineering 2019年第2期35卷 89-102页

作者： Cardoso, Cristiane de Fátima dos Santos Carrijo, Gilberto Arantes Ferreira, Júlio César dos Santos, Jucelino Cardoso Marciano Signal Processing Lab Faculty of Electrical Engineering Federal University of Uberlândia Campus Sta Mônica Av. João Naves de Ávila 2121 Bloco 1N UberlândiaMG38400-000 Brazil Computer Vision Lab Informatics Nucleo Goiano Federal Institute of Education Science and Technology Campus Urutaí Rodovia Geraldo Silva Nascimento km 2.5 Zona Rural Bloco de Informática UrutaíGO75790-000 Brazil

Purpose: Fundus images have become increasingly important due to the growing number of diabetics and their risk of developing diabetic retinopathy. Automated diagnosis of retinal images requires the separation and analysis of retinal elements. Among these elements, the optic nerve head is the most significant since it is used as a reference for detecting other anatomical structures such as the fovea and blood vessels. For this reason, optic disc segmentation is essential. Methods: This paper presents a method for locating and segmenting the optic disc using the circular Hough transform and the roughness index, respectively. We used a location algorithm based on the multiscale energy filter for fast location and the medial Hough transform as the decision criterion. Segmentation was performed with Atanassov’s Intuitionistic Fuzzy Set representation and an algorithm using the 3D roughness index and mathematical morphology to smoothly segmenting. Results: This approach to automatic segmentation was tested on the MESSIDOR database, achieving 99.59% accuracy and 91.56% sensitivity. Other types of roughness indices were also evaluated;however, color correlation within the color space of the object itself produced better results for the proposed algorithm. Conclusion: We hope these findings contribute to the development of reliable automatic diagnostic tools for retinal images. © 2019, Sociedade Brasileira de Engenharia Biomedica.

关键词： Mathematical morphology