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Metrics Reloaded: Recommendations for image analysis validation

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arXiv 2022年

作者： Maier-Hein, Lena Reinke, Annika Godau, Patrick Tizabi, Minu D. Buettner, Florian Christodoulou, Evangelia Glocker, Ben Isensee, Fabian Kleesiek, Jens Kozubek, Michal Reyes, Mauricio Riegler, Michael A. Wiesenfarth, Manuel Emre Kavur, A. Sudre, Carole H. Baumgartner, Michael Eisenmann, Matthias Heckmann-Nötzel, Doreen Rädsch, Tim Acion, Laura Antonelli, Michela Arbel, Tal Bakas, Spyridon Benis, Arriel Blaschko, Matthew B. Jorge Cardoso, M. Cheplygina, Veronika Cimini, Beth A. Collins, Gary S. Farahani, Keyvan Ferrer, Luciana Galdran, Adrian Ginneken, Bram Van Haase, Robert Hashimoto, Daniel A. Hoffman, Michael M. Huisman, Merel Jannin, Pierre Kahn, Charles E. Kainmueller, Dagmar Kainz, Bernhard Karargyris, Alexandros Karthikesalingam, Alan Kenngott, Hannes Kofler, Florian Kopp-Schneider, Annette Kreshuk, Anna Kurc, Tahsin Landman, Bennett A. Litjens, Geert Madani, Amin Maier-Hein, Klaus Martel, Anne L. Mattson, Peter Meijering, Erik Menze, Bjoern Moons, Karel G.M. Müller, Henning Nichyporuk, Brennan Nickel, Felix Petersen, Jens Rajpoot, Nasir Rieke, Nicola Saez-Rodriguez, Julio Sánchez, Clara I. Shetty, Shravya Smeden, Maarten Van Summers, Ronald M. Taha, Abdel A. Tiulpin, Aleksei Tsaftaris, Sotirios A. Calster, Ben Van Varoquaux, Gaël Jäger, Paul F. Heidelberg Division of Intelligent Medical Systems and HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg a partnership between DKFZ University Medical Center Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Intelligent Medical Systems Germany partner site Frankfurt/Mainz a partnership between DKFZ and UCT Frankfurt-Marburg Germany Heidelberg Goethe University Frankfurt Germany Department of Medicine Goethe University Frankfurt Germany Department of Informatics Frankfurt Cancer Insititute Germany Department of Computing Imperial College London London United Kingdom Heidelberg Division of Medical Image Computing and HI Applied Computer Vision Lab Germany Institute for AI in Medicine University Medicine Essen Essen Germany Centre for Biomedical Image Analysis Faculty of Informatics Masaryk University Brno Czech Republic ARTORG Center for Biomedical Engineering Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Bern Switzerland Simula Metropolitan Center for Digital Engineering Oslo Norway UiT The Arctic University of Norway Romsø Norway Heidelberg Division of Biostatistics Germany Heidelberg Division of Intelligent Medical Systems Division of Medical Image Computing HI Applied Computer Vision Lab Germany MRC Unit for Lifelong Health and Ageing UCL Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom School of Biomedical Engineering and Imaging Science King’s College London London United Kingdom Heidelberg Division of Medical Image Computing Germany Instituto de Cálculo CONICET – Universidad de Buenos Aires Buenos Aires Argentina Centre for Medical Image Computing University College London London United Kingdom McGill University Montréal

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, we created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. It was developed by a large international consortium in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint – a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. Its applicability is demonstrated for various biomedical use cases. © 2022, CC BY.

关键词： Semantic Segmentation

A Topic-Triggered Translation Model for Statistical Machine Translation

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Chinese Journal of Electronics 2017年第1期26卷 65-72页

作者： SU Jinsong WANG Zhihao WU Qingqiang YAO Junfeng LONG Fei ZHANG Haiying Software School Xiamen University Provincial Key Laboratory for Computer Information Processing Technology Soochow University Automation Department Xiamen University

Translation model containing translation rules with probabilities plays a crucial role in statistical machine translation. Conventional method estimates translation probabilities with only the consideration of cooccurrence frequencies of bilingual translation units, while ignoring document-level context information. In this paper, we extend the conventional translation model to a topic-triggered one. Specifically, we estimate topic-specific translation probabilities of translation rules by leveraging topical context information, and online score selected translation rules according to topic posterior distributions of translated sentences. As compared with the conventional model, our model allows for more fine-grained distinction among different translations. Experiment results on large data set demonstrate the effectiveness of our model.

关键词： Statistical machine translation Topictriggered translation model Topical context information

Learning tubule-sensitive CNNs for pulmonary airway and artery-vein segmentation in CT

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arXiv 2020年

作者： Qin, Yulei Zheng, Hao Gu, Yun Huang, Xiaolin Yang, Jie Wang, Lihui Yao, Feng Zhu, Yue-Min Yang, Guang-Zhong Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province School of Computer Science and Technology Guizhou University Guiyang China Department of Thoracic Surgery Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China Université de Lyon INSA Lyon CREATIS CNRS INSERM UMR 5220 VilleurbanneU1206 France Institute of Medical Robotics School of Biomedical Engineering Shanghai Jiao Tong University Shanghai China

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://***/News/56. © 2020, CC BY.

关键词： computerized tomography

Protecting privacy of users in brain-computer interface applications

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arXiv 2019年

作者： Agarwal, Anisha Dowsley, Rafael McKinney, Nicholas D. Wu, Dongrui Lin, Chin-Teng De Cock, Martine Nascimento, Anderson C.A. School of Engineering and Technology University of Washington TacomaWA98402 United States Department of Computer Science Bar-Ilan University Israel School of Engineering and Technology University of Washington TacomaWA98402 United States Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Automation Huazhong University of Science and Technology Wuhan China School of Software University of Technology Sydney Australia Department of Applied Mathematics Computer Science and Statistics Ghent University Ghent9000 Belgium

Machine learning (ML) is revolutionizing research and industry. Many ML applications rely on the use of large amounts of personal data for training and inference. Among the most intimate exploited data sources is electroencephalogram (EEG) data, a kind of data that is so rich with information that application developers can easily gain knowledge beyond the professed scope from unprotected EEG signals, including passwords, ATM PINs, and other intimate data. The challenge we address is how to engage in meaningful ML with EEG data while protecting the privacy of users. Hence, we propose cryptographic protocols based on Secure Multiparty Computation (SMC) to perform linear regression over EEG signals from many users in a fully privacy-preserving (PP) fashion, i.e. such that each individual's EEG signals are not revealed to anyone else. To illustrate the potential of our secure framework, we show how it allows estimating the drowsiness of drivers from their EEG signals as would be possible in the unencrypted case, and at a very reasonable computational cost. Our solution is the first application of commodity-based SMC to EEG data, as well as the largest documented experiment of secret sharing based SMC in general, namely with 15 players involved in all the computations. Copyright © 2019, The Authors. All rights reserved.

关键词： Machine learning

AIROGS: ARTIFICIAL INTELLIGENCE FOR ROBUST GLAUCOMA SCREENING CHALLENGE

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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

An improved convex programming model for the inverse problem in intensity-modulated radiation therapy

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International Journal of Performability Engineering 2018年第5期14卷 871-884页

作者： Lan, Yihua Zhang, Xingang Zhang, Jianyang Wang, Yang Hung, Chih-Cheng School of Computer and Information Technology Nanyang Normal University Nanyang473061 China Institute of Image Processing and Pattern Recognition Nanyang Normal University Nanyang473061 China Radiology Department Central Hospital of Nanyang Nanyang473061 China Laboratory for Machine Vision and Security Research College of Computing and Software Engineering Kennesaw State University - Marietta Campus 1100 South Marietta Parkway MariettaGA30067-2896 United States

Intensity modulated radiation therapy technology (IMRT) is one of the main approaches in cancer treatment because it can guarantee the killing of cancer cells while optimally protecting normal tissue from complications. Inverse planning, which is the core component of the entire IMRT system, is mainly based on accurate mathematical modeling and associated fast solving methods. In inverse planning, the fluence map optimization, which considers the multi-leaf collimator (MLC) modulation, is the current research focus. Although the hitting constrain problem with the unidirectional movement of leaf-sweeping has been solved, our goal is to solve the hitting constrain problem with the bidirectional movement of leaf-sweeping. In this study, we propose a non-synchronized type to solve the hitting constrain problem with the bidirectional movement of leaf-sweeping schemes for IMRT. In solving this problem, a new mathematical model is proposed under the framework of convex programming. The advantage of the convex model is to avoid the uncertainty and inaccuracy that occurs in the non-convex programming solving process. Experimental results for two clinical testing cases show that under the same condition of total number of monitoring units, the new proposed model produces better dose distribution than those of the total variance and quadratic models. © 2018 Totem Publisher, Inc. All rights reserved.

关键词： Convex optimization

A review of uncertainty quantification in deep learning: Techniques, applications and challenges

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arXiv 2020年

作者： Abdar, Moloud Pourpanah, Farhad Hussain, Sadiq Rezazadegan, Dana Liu, Li Ghavamzadeh, Mohammad Fieguth, Paul Cao, Xiaochun Khosravi, Abbas Rajendra Acharya, U. Makarenkov, Vladimir Nahavandi, Saeid Deakin University Australia College of Mathematics and Statistics Guangdong Key Lab. of Intelligent Information Processing Shenzhen University Shenzhen518060 China Dibrugarh University Dibrugarh India Department of Computer Science and Software Engineering Swinburne University of Technology Melbourne Australia Center for Machine Vision and Signal Analysis University of Oulu Oulu Finland Google research United States Department of Systems Design Engineering University of Waterloo Waterloo Canada State Key Laboratory of Information Security Institute of Information Engineering Chinese Academy of Sciences Beijing China Department of Electronics and Computer Engineering Ngee Ann Polytechnic Clementi Singapore Department of Computer Science University of Quebec in Montreal MontrealQC Canada

—Uncertainty quantification (UQ) plays a pivotal role in the reduction of uncertainties during both optimization and decision making, applied to solve a variety of real-world applications in science and engineering. Bayesian approximation and ensemble learning techniques are two of the most widely-used UQ methods in the literature. In this regard, researchers have proposed different UQ methods and examined their performance in a variety of applications such as computer vision (e.g., self-driving cars and object detection), image processing (e.g., image restoration), medical image analysis (e.g., medical image classification and segmentation), natural language processing (e.g., text classification, social media texts and recidivism risk-scoring), bioinformatics, etc. This study reviews recent advances in UQ methods used in deep learning, investigates the application of these methods in reinforcement learning, and highlight the fundamental research challenges and directions associated with the UQ field. Copyright © 2020, The Authors. All rights reserved.

关键词： image segmentation

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Network Resilience

arXiv 2020年

作者： Liu, Xueming Li, Daqing Ma, Manqing Szymanski, Boleslaw K. Eugene Stanley, H. Gao, Jianxi Key Laboratory of Image Information Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Hubei Wuhan430074 China School of Reliability and Systems Engineering Beihang University Beijing100191 China College of Safety Science and Engineering Civil Aviation University of China Tianjin 300300 China Department of Computer Science Rensselaer Polytechnic Institute TroyNY12180 United States Network Science and Technology Center Rensselaer Polytechnic Institute TroyNY12180 United States Center for Polymer Studies Department of Physics Boston University BostonMA02215 United States

Many systems on our planet shift abruptly and irreversibly from the desired state to an undesired state when forced across a "tipping point". Some examples are mass extinctions within ecosystems, cascading failures in infrastructure systems, and changes in human and animal social networks. The ability to avoid such regime shifts or to recover quickly from such a non-resilient state demonstrates a system's resilience;system resilience is a quality that enables a system to adjust its activities to retain its basic functionality when errors and failures occur. In the past 50 years, attention has been paid almost exclusively to low-dimensional systems;scholars have focused on the calibration of the resilience functions of such systems and the identification of indicators of early warning signals based on two to three connected components. In recent years, taking advantage of network theory and the availability of lavish real datasets, network scientists have begun to explore real-world complex networked multidimensional systems, as well as their resilience functions and early warning indicators. This report presents a comprehensive review of resilience functions and regime shifts in complex systems in domains such as ecology, biology, society, and infrastructure. The research approach includes empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also review the definitions of some ambiguous terms, including robustness, resilience, and stability. Copyright © 2020, The Authors. All rights reserved.

关键词： Complex networks

Overview of the CCKS 2019 knowledge graph evaluation track: Entity, relation, event and QA

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arXiv 2020年

作者： Han, Xianpei Wang, Zhichun Zhang, Jiangtao Wen, Qinghua Li, Wenqi Tang, Buzhou Wang, Qi Feng, Zhifan Zhang, Yang Lu, Yajuan Wang, Haitao Chen, Wenliang Shao, Hao Chen, Yubo Liu, Kang Zhao, Jun Wang, Taifeng Zhang, Kezun Wang, Meng Jiang, Yinlin Qi, Guilin Zou, Lei Hu, Sen Zhang, Minhao Lin, Yinnian Chinese Information Processing Laboratory Institute of Software Chinese Academy of Sciences Beijing100190 China School of Artificial Intelligence Beijing Normal University Beijing100875 China 305 Hospital of People’s Liberation Army Beijing100017 China Department of Computer Science and Technology Tsinghua University Beijing100084 China Yidu Cloud Beijing100000 China Harbin Institute of Technology Shenzhen Guangdong518055 China Baidu Beijing100193 China School of Computer Science & Technology Soochow University Suzhou Jiangsu215006 China Gowild Suzhou Jiangsu215002 China National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing100190 China School of Artificial Intelligence University of Chinese Academy of Sciences Beijing100049 China Ant Financial Hangzhou Zhejiang310000 China School of Computer Science and Engineering Southeast University Nanjing Jiangsu211189 China Key Laboratory of Computer Network Information Integration Southeast University Nanjing Jiangsu211189 China Peking University Beijing100871 China

Knowledge graph models world knowledge as concepts, entities, and the relationships between them, which has been widely used in many real-world tasks. CCKS 2019 held an evaluation track with 6 tasks and attracted more than 1,600 teams. In this paper we give an overview of the knowledge graph evaluation tract at CCKS 2019. By reviewing the task definition, successful methods, useful resources, good strategies and research challenges associated with each task in CCKS 2019, this paper can provide a helpful reference for developing knowledge graph applications and conducting future knowledge graph researches. Copyright © 2020, The Authors. All rights reserved.

关键词： Knowledge graph