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Generative Adversarial Networks based Skin Lesion Segmentation

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arXiv 2023年

作者： Innani, Shubham Dutande, Prasad Baid, Ujjwal Pokuri, Venu Bakas, Spyridon Talbar, Sanjay Baheti, Bhakti Guntuku, Sharath Chandra Center of Excellence in Signal and Image Processing Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Center for Biomedical Image Computing and Analytics University of Pennsylvania Philadelphia United States Department of Computer and Information Science University of Pennsylvania Philadelphia United States

Skin cancer is a serious condition that requires accurate diagnosis and treatment. One way to assist clinicians in this task is using computer-aided diagnosis (CAD) tools that automatically segment skin lesions from dermoscopic images. We propose a novel adversarial learning-based framework called Efficient-GAN (EGAN) that uses an unsupervised generative network to generate accurate lesion masks. It consists of a generator module with a top-down squeeze excitation-based compound scaled path, an asymmetric lateral connection-based bottom-up path, and a discriminator module that distinguishes between original and synthetic masks. A morphology-based smoothing loss is also implemented to encourage the network to create smooth semantic boundaries of lesions. The framework is evaluated on the International Skin Imaging Collaboration (ISIC) Lesion Dataset 2018. It outperforms the current state-of-the-art skin lesion segmentation approaches with a Dice coefficient, Jaccard similarity, and Accuracy of 90.1%, 83.6%, and 94.5%, respectively. We also design a lightweight segmentation framework (MGAN) that achieves comparable performance as EGAN but with an order of magnitude lower number of training parameters, thus resulting in faster inference times for low compute resource settings. Copyright © 2023, The Authors. All rights reserved.

关键词： Generative adversarial networks

Adapting Machine Learning Diagnostic Models to New Populations Using a Small Amount of Data: Results from Clinical Neuroscience

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arXiv 2023年

作者： Wang, Rongguang Erus, Guray Chaudhari, Pratik Davatzikos, Christos Department of Electrical and Systems Engineering University of Pennsylvania United States Center for AI and Data Science for Integrated Diagnostics University of Pennsylvania United States Center for Biomedical Image Computing and Analytics University of Pennsylvania United States Department of Computer and Information Science University of Pennsylvania United States Department of Radiology Perelman School of Medicine University of Pennsylvania United States Center for Biomedical Image Computing and Analytics University of Pennsylvania 3700 Hamilton Walk 7th Floor PhiladelphiaPA19104 United States

Machine learning (ML) is revolutionizing many areas of engineering and science, including healthcare. However, it is also facing a reproducibility crisis, especially in healthcare. ML models that are carefully constructed from and evaluated on data from one part of the population may not generalize well on data from a different population group, or acquisition instrument settings and acquisition protocols. We tackle this problem in the context of neuroimaging of Alzheimer's disease (AD), schizophrenia (SZ) and brain aging. We develop a weighted empirical risk minimization approach that optimally combines data from a source group, e.g., subjects are stratified by attributes such as sex, age group, race and clinical cohort to make predictions on a target group, e.g., other sex, age group, etc. using a small fraction (10%) of data from the target group. We apply this method to multi-source data of 15,363 individuals from 20 neuroimaging studies to build ML models for diagnosis of AD and SZ, and estimation of brain age. We found that this approach achieves substantially better accuracy than existing domain adaptation techniques: it obtains area under curve greater than 0.95 for AD classification, area under curve greater than 0.7 for SZ classification and mean absolute error less than 5 years for brain age prediction on all target groups, achieving robustness to variations of scanners, protocols, and demographic or clinical characteristics. In some cases, it is even better than training on all data from the target group, because it leverages the diversity and size of a larger training set. We also demonstrate the utility of our models for prognostic tasks such as predicting disease progression in individuals with mild cognitive impairment. Critically, our brain age prediction models lead to new clinical insights regarding correlations with neurophysiological tests. In summary, we present a relatively simple methodology, along with ample experimental evidence, supporting

关键词： Neuroimaging

Bias in Machine Learning Models Can Be Significantly Mitigated by Careful Training: Evidence from Neuroimaging Studies

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arXiv 2022年

作者： Wang, Rongguang Chaudhari, Pratik Davatzikos, Christos Department of Electrical and Systems Engineering University of Pennsylvania United States Center for AI and Data Science for Integrated Diagnostics University of Pennsylvania United States Center for Biomedical Image Computing and Analytics University of Pennsylvania United States Department of Computer and Information Science University of Pennsylvania United States Department of Radiology Perelman School of Medicine University of Pennsylvania United States

Despite the great promise that machine learning has offered in many fields of medicine, it has also raised concerns about potential biases and poor generalization across genders, age distributions, races and ethnicities, hospitals, and data acquisition equipment and protocols. In the current study, and in the context of three brain diseases, we provide evidence which suggests that when properly trained, machine learning models can generalize well across diverse conditions and do not necessarily suffer from bias. Specifically, by using multi-study magnetic resonance imaging consortia for diagnosing Alzheimer's disease, schizophrenia, and autism spectrum disorder, we find that well-trained models have a high area-under-the-curve (AUC) on subjects across different subgroups pertaining to attributes such as gender, age, racial groups, and different clinical studies and are unbiased under multiple fairness metrics such as demographic parity difference, equalized odds difference, equal opportunity difference etc. We find that models that incorporate multi-source data from demographic, clinical, genetic factors and cognitive scores are also unbiased. These models have better predictive AUC across subgroups than those trained only with imaging features but there are also situations when these additional features do not help. © 2022, CC BY.

关键词： Magnetic resonance imaging

Transformer-Based Hierarchical Dynamic Decoders for Salient Object Detection

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SSRN

SSRN 2023年

作者： Zheng, Qingping Zheng, Ling Deng, Jiankang Li, Ying Shang, Changjing Shen, Qiang School of Computer Science National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology Shaanxi Provincial Key Laboratory of Speech & Image Information Processing Northewestern Polytechnical University Shaanxi Xi’an710129 China Fuzhou Institute of Data Technology Fujian350200 China Department of Computing Imperial College London LondonSW7 2AZ United Kingdom

HighlightsTransformer-Based Hierarchical Dynamic Decoders for Salient Object DetectionQingping Zheng, Ling Zheng, Jiankang Deng, Ying Li, Changjing Shang, Qiang Shen• T-HDDNet employs dynamic upsampling and fusion for data-driven salient object detection.• T-HDDNet uses a spatially sensitive loss to learn salient object structures, yielding a high-resolution map.• Our method exceeds benchmarks at 22.19G MACs and 27M Params, reducing costs compared to the top model. © 2023, The Authors. All rights reserved.

关键词： Object detection

Applications of Generative Adversarial Networks in Neuroimaging and Clinical Neuroscience

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arXiv 2022年

作者： Wang, Rongguang Bashyam, Vishnu Yang, Zhijian Yu, Fanyang Tassopoulou, Vasiliki Chintapalli, Sai Spandana Skampardoni, Ioanna Sreepada, Lasya P. Sahoo, Dushyant Nikita, Konstantina Abdulkadir, Ahmed Wen, Junhao Davatzikos, Christos Center for AI and Data Science for Integrated Diagnostics University of Pennsylvania Philadelphia United States Center for Biomedical Image Computing and Analytics University of Pennsylvania Philadelphia United States School of Electrical and Computer Engineering National Technical University of Athens Athens Greece Department of Clinical Neurosciences Lausanne University Hospital University of Lausanne Lausanne Switzerland Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia United States

Generative adversarial networks (GANs) are one powerful type of deep learning models that have been successfully utilized in numerous fields. They belong to the broader family of generative methods, which learn to generate realistic data with a probabilistic model by learning distributions from real samples. In the clinical context, GANs have shown enhanced capabilities in capturing spatially complex, nonlinear, and potentially subtle disease effects compared to traditional generative methods. This review critically appraises the existing literature on the applications of GANs in imaging studies of various neurological conditions, including Alzheimer’s disease, brain tumors, brain aging, and multiple sclerosis. We provide an intuitive explanation of various GAN methods for each application and further discuss the main challenges, open questions, and promising future directions of leveraging GANs in neuroimaging. We aim to bridge the gap between advanced deep learning methods and neurology research by highlighting how GANs can be leveraged to support clinical decision making and contribute to a better understanding of the structural and functional patterns of brain diseases. © 2022, CC BY.

关键词： Generative adversarial networks

Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge

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arXiv 2025年

作者： Imran, Muhammad Krebs, Jonathan R. Sivaraman, Vishal Balaji Zhang, Teng Kumar, Amarjeet Ueland, Walker R. Fassler, Michael J. Huang, Jinlong Sun, Xiao Wang, Lisheng Shi, Pengcheng Rokuss, Maximilian Baumgartner, Michael Kirchhof, Yannick Maier-Hein, Klaus H. Isensee, Fabian Liu, Shuolin Han, Bing Nguyen, Bong Thanh Shin, Dong-Jin Ji-Woo, Park Choi, Mathew Uhm, Kwang-Hyun Ko, Sung-Jea Lee, Chanwoong Chun, Jaehee Kim, Jin Sung Zhang, Minghui Zhang, Hanxiao You, Xin Gu, Yun Pan, Zhaohong Liu, Xuan Liang, Xiaokun Tiefenthaler, Markus Almar-Munoz, Enrique Schwab, Matthias Kotyushev, Mikhail Epifanov, Rostislav Wodzinski, Marek Müller, Henning Qayyum, Abdul Mazher, Moona Niederer, Steven A. Wang, Zhiwei Yang, Kaixiang Ren, Jintao Korreman, Stine Sofia Gao, Yuchong Zeng, Hongye Zheng, Haoyu Zheng, Rui Yue, Jinghua Zhou, Fugen Liu, Bo Cosman, Alexander Liang, Muxuan Zhao, Chang Upchurch, Gilbert R. Ma, Jun Zhou, Yuyin Cooper, Michol A. Shao, Wei Department of Medicine University of Florida GainesvilleFL32611 United States Department of Surgery University of Florida GainesvilleFL32611 United States Department of Electrical and Computer Engineering University of Florida GainesvilleFL32611 United States Department of Computer Information Science and Engineering University of Florida GainesvilleFL32611 United States Shanghai Jiao Tong University Shanghai China Electronic & Information Engineering School Harbin Institute of Technology [Shenzhen Shenzhen China Division of Medical Image Computing German Cancer Research Center [DKFZ Heidelberg Germany CO. LTD Beijing China MedAI Seoul Korea Republic of Korea University Seoul Korea Republic of Department of Radiation Oncology Yonsei Cancer Center Heavy Ion Therapy Research Institute Yonsei University College of Medicine Seoul Korea Republic of Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Medical University of Innsbruck Innsbruck Austria Novosibirsk State University Novosibirsk Russia AGH University of Krakow Krakow Poland Sierre Switzerland University of Geneva Geneva Switzerland The Sense Innovation and Research Center Sion Switzerland National Heart and Lung Institute Faculty of Medicine Imperial College London London United Kingdom Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology Hubei Wuhan China Aarhus University Department of Clinical Medicine Nordre Palle Juul-Jensens Blvd. 11 Aarhus8200 Denmark Shanghaitech University Pudong Shanghai China Image Processing Center Beihang University Beijing China Department of Computer Science and Engineering University of California Santa CruzCA95064 United States Department of Biostatistics University of Florida GainesvilleFL32611 United States University Health Network ON Canada Agronomy Department University of F

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://***. © 2025, CC BY-NC-SA.

关键词： computerized tomography

Why is the Winner the Best?

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Why is the Winner the Best?

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.

关键词：

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

The effect of data augmentation on classification of atrial fibrillation in short single-lead ecg signals using deep neural networks

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arXiv 2020年

作者： Hatamian, Faezeh Nejati Ravikumar, Nishant Vesal, Sulaiman Kemeth, Felix P. Struck, Matthias Maier, Andreas Department of Image Processing and Medical Technology Fraunhofer Institute for Integrated Circuits IIS Erlangen Germany Pattern Recognition Lab Department of Computer Science Friedrich-Alexander University Erlangen-Nrnberg Erlangen Germany School of Computing LICAMM Leeds Institute of Cardiovascular and Metabolic Medicine School of Medicine University of Leeds United Kingdom

Cardiovascular diseases are the most common cause of mortality worldwide. Detection of atrial fibrillation (AF) in the asymptomatic stage can help prevent strokes. It also improves clinical decision making through the delivery of suitable treatment such as, anticoagulant therapy, in a timely manner. The clinical significance of such early detection of AF in electrocardiogram (ECG) signals has inspired numerous studies in recent years, of which many aim to solve this task by leveraging machine learning algorithms. ECG datasets containing AF samples, however, usually suffer from severe class imbalance, which if unaccounted for, affects the performance of classification algorithms. Data augmentation is a popular solution to tackle this problem. In this study, we investigate the impact of various data augmentation algorithms, e.g., oversampling, Gaussian Mixture Models (GMMs) and Generative Adversarial Networks (GANs), on solving the class imbalance problem. These algorithms are quantitatively and qualitatively evaluated, compared and discussed in detail. The results show that deep learning-based AF signal classification methods benefit more from data augmentation using GANs and GMMs, than oversampling. Furthermore, the GAN results in circa 3% better AF classification accuracy in average while performing comparably to the GMM in terms of f1-score. Copyright © 2020, The Authors. All rights reserved.

关键词： Diseases