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arXiv 2022年

作者： Ferreira, André Li, Jianning Alves, Victor Pomykala, Kelsey L. Kleesiek, Jens Egger, Jan Center Algoritmi University of Minho Braga Portugal Computer Algorithms for Medicine Laboratory Graz Austria University Medicine Essen Girardetstraße 2 Essen45131 Germany University Medicine Essen Hufelandstraße 55 Essen45147 Germany Partner Site Essen Hufelandstraße 55 Essen45147 Germany Institute of Computer Graphics and Vision Graz University of Technology Inffeldgasse 16 Graz8010 Austria TU Dortmund University Department of Physics Otto-Hahn-Straße 4 Dortmund44227 Germany Department of Oral and Maxillofacial Surgery University Hospital RWTH Aachen Aachen52074 Germany Institute of Medical Informatics University Hospital RWTH Aachen Aachen52074 Germany

With the massive proliferation of data-driven algorithms, such as deep learning-based approaches, the availability of high-quality data is of great interest. Volumetric data is very important in medicine, as it ranges from disease diagnoses to therapy monitoring. When the dataset is sufficient, models can be trained to help doctors with these tasks. Unfortunately, there are scenarios where large amounts of data is unavailable. For example, rare diseases and privacy issues can lead to restricted data availability. In non-medical fields, the high cost of obtaining enough high-quality data can also be a concern. A solution to these problems can be the generation of realistic synthetic data using Generative Adversarial Networks (GANs). The existence of these mechanisms is a good asset, especially in healthcare, as the data must be of good quality, realistic, and without privacy issues. Therefore, most of the publications on volumetric GANs are within the medical domain. In this review, we provide a summary of works that generate realistic volumetric synthetic data using GANs. We therefore outline GAN-based methods in these areas with common architectures, loss functions and evaluation metrics, including their advantages and disadvantages. We present a novel taxonomy, evaluations, challenges, and research opportunities to provide a holistic overview of the current state of volumetric GANs. Copyright © 2022, The Authors. All rights reserved.

关键词： Generative adversarial networks

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Tumor likelihood estimation on MRI prostate data by utilizing k-Space information

arXiv

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arXiv 2024年

作者： Rempe, Moritz Hörst, Fabian Seibold, Constantin Hadaschik, Boris Schlimbach, Marco Egger, Jan Kröninger, Kevin Breuer, Felix Blaimer, Martin Kleesiek, Jens University Hospital Essen Girardetstraße 2 Essen45131 Germany University Medicine Essen Hufelandstraße 55 Essen45147 Germany Fraunhofer Institute for Integrated Circuits IIS Am Hubland Würzburg97074 Germany Department of Urology University Hospital Essen Hufelandstraße 55 Essen45147 Germany Department of Physics The Technical University Dortmund Otto-Hahn-Straße 4a Dortmund44227 Germany Computer Algorithms for Medicine Laboratory Graz8010 Austria Institute of Computer Graphics and Vision Graz Austria University of Technology Inffeldgasse 16 Graz8010 Austria Partner Site Essen Hufelandstraße 55 Essen45147 Germany

We present a novel preprocessing and prediction pipeline for the classification of magnetic resonance imaging (MRI) that takes advantage of the information rich complex valued k-Space. Using a publicly available MRI raw dataset with 312 subject and a total of 9508 slices, we show the advantage of utilizing the k-Space for better prostate cancer likelihood estimation in comparison to just using the magnitudinal information in the image domain, with an AUROC of 86.1%±1.8%. Additionally, by using high undersampling rates and a simple principal component analysis (PCA) for coil compression, we reduce the time needed for reconstruction by avoiding the time intensive GRAPPA reconstruction algorithm. By using digital undersampling for our experiments, we show that scanning and reconstruction time could be reduced. Even with an undersampling factor of 16, our approach achieves meaningful results, with an AUROC of 71.4%±2.9%, using the PCA coil combination and taking into account the k-Space information. With this study, we were able to show the feasibility of preserving phase and k-Space information, with consistent results. Besides preserving valuable information for further diagnostics, this approach can work without the time intensive ADC and reconstruction calculations, greatly reducing the post processing, as well as potential scanning time, increasing patient comfort and allowing a close to real-time prediction. © 2024, CC BY.

关键词： Magnetic resonance imaging

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Comparative Analysis of nnUNet and MedNeXt for Head and Neck Tumor Segmentation in MRI-guided Radiotherapy

arXiv

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arXiv 2024年

作者： Moradi, Nikoo Ferreira, André Puladi, Behrus Kleesiek, Jens Fatemizadeh, Emad Luijten, Gijs Alves, Victor Egger, Jan Department of Electrical Engineering Sharif University of Technology Tehran Iran University Medicine Essen Girardetstraße 2 Essen45131 Germany Center Algoritmi / LASI University of Minho Braga4710-057 Portugal Computer Algorithms for Medicine Laboratory Graz Austria Department of Oral and Maxillofacial Surgery University Hospital RWTH Aachen Aachen Germany Institute of Medical Informatics University Hospital RWTH Aachen Aachen Germany Essen Germany Partner Site Essen Essen Germany Department of Physics TU Dortmund University Dortmund Germany University Medicine Essen Essen Germany Graz University of Technology Inffeldgasse 16/II Graz8010 Austria

Radiation therapy (RT) is essential in treating head and neck cancer (HNC), with magnetic resonance imaging(MRI)-guided RT offering superior soft tissue contrast and functional imaging. However, manual tumor segmentation is time-consuming and complex, and therfore remains a challenge. In this study, we present our solution as team TUMOR to the HNTS-MRG24 MICCAI Challenge which is focused on automated segmentation of primary gross tumor volumes (GTVp) and metastatic lymph node gross tumor volume (GTVn) in pre-RT and mid-RT MRI images. We utilized the HNTS-MRG2024 dataset, which consists of 150 MRI scans from patients diagnosed with HNC, including original and registered pre-RT and mid-RT T2-weighted images with corresponding segmentation masks for GTVp and GTVn. We employed two state-of-the-art models in deep learning, nnUNet and MedNeXt. For Task 1, we pretrained models on pre-RT registered and mid-RT images, followed by fine-tuning on original pre-RT images. For Task 2, we combined registered pre-RT images, registered pre-RT segmentation masks, and mid-RT data as a multi-channel input for training. Our solution for Task 1 achieved 1st place in the final test phase with an aggregated Dice Similarity Coefficient of 0.8254, and our solution for Task 2 ranked 8th with a score of 0.7005. The proposed solution is publicly available at Github Repository. Copyright © 2024, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Generalisation of Segmentation Using Generative Adversarial Networks

Generalisation of Segmentation Using Generative Adversarial ...

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IEEE International Symposium on Biomedical Imaging

作者： André Ferreira Gijs Luijten Behrus Puladi Jens Kleesiek Victor Alves Jan Egger Institute for AI in Medicine (IKIM) University Hospital Essen (AöR) Essen Germany Center Algoritmi / LASI University of Minho Braga Portugal Computer Algorithms for Medicine Laboratory Graz Austria Institute of Medical Informatics University Hospital RWTH Aachen Aachen Germany Department of Oral and Maxillofacial Surgery University Hospital RWTH Aachen Aachen Germany Institute of Computer Graphics and Vision (ICG) Graz University of Technology Graz Austria Cancer Research Center Cologne Essen (CCCE) West German Cancer Center Essen (WTZ) University Hospital Essen (AöR) Essen Germany Partner Site Essen German Cancer Consortium (DKTK) Essen Germany Department of Physics TU Dortmund University Dortmund Germany Center for Virtual and Extended Reality in Medicine (ZvRM) University Hospital Essen Essen Germany

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

State-of-the-art deep learning algorithms are easily biased and evaluated in misleading scenarios, especially in the medical context, where scenarios change rapidly and diseases develop quickly. The BraTS 2024 GoAT challenge aims to evaluate how brain tumour segmentation algorithms can adapt to different circumstances when these are not available for training. Our solution utilises state-of-the-art conditional generative adversarial networks to generate realistic new cases and train a segmentation algorithm that takes advantage of the convolutions and attention mechanisms. Our solution achieved a DSC value of 0.855, 0.863, 0.883 and an HD95 value of 24.83, 24.10 and 21.72 for the enhancing tumour, the tumour core and the whole tumour in the validation set, respectively.

关键词： Training Knowledge engineering Deep learning Generative adversarial networks Robustness Inference algorithms Tumors

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Ten simple rules for measuring the impact of workshops

arXiv

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arXiv 2018年

作者： Sufi, Shoaib Duckles, Beth Simera, Iveta Nurmikko-Fuller, Terhi Bellis, Louisa Miah, Wadud Wilde, Adriana Nenadic, Aleksandra Silva, Raniere de Beyer, Jennifer A. Struthers, Caroline Emsley, Iain Philippe, Olivier Balzano, Melissa Coelho, Sara Ford, Heather Jones, Catherine Higgins, Vanessa School of Computer Science University of Manchester Manchester United Kingdom Portland State University PortlandOR United States UK EQUATOR Centre Centre for Statistics in Medicine NDORMS University of Oxford Oxford United Kingdom College of Arts and Social Sciences Australian National University Canberra Australia Cancer Research UK Cambridge Centre University of Cambridge Cambridge United Kingdom Numerical Algorithms Group Oxford United Kingdom School of Computer Science University of St Andrews St Andrews United Kingdom Oxford e-Research Centre University of Oxford Oxford United Kingdom Electronics and Computer Science University of Southampton Southampton United Kingdom ELIXIR Hub Wellcome Genome Campus Cambridge United Kingdom EGI Foundation Amsterdam Netherlands School of Media and Communication University of Leeds Leeds United Kingdom Scientific Computing Department Science and Technology Facilities Council Rutherford Appleton Laboratory Didcot United Kingdom School of Social Sciences University of Manchester Manchester United Kingdom

Workshops are used to explore a specific topic, transfer knowledge, solve identified problems or create something new. In funded research projects and other research endeavours, workshops are the mechanism to gather the wider project, community or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops. Copyright © 2018, The Authors. All rights reserved.

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Corrigendum to: GAN-based generation of realistic 3D volumetric data: A systematic review and taxonomy [Medical Image Analysis 93 (2024)]

引用

Medical image analysis 2024年 96卷 103174页

作者： André Ferreira Jianning Li Kelsey L Pomykala Jens Kleesiek Victor Alves Jan Egger Institute for AI in Medicine (IKIM) University Hospital Essen University Duisburg-Essen Girardetstraße 2 Essen 45131 Germany Center Algoritmi/LASI University of Minho Braga 4710-057 Portugal Computer Algorithms for Medicine Laboratory Graz Austria Department of Oral and Maxillofacial Surgery University Hospital RWTH Aachen 52074 Aachen Germany Institute of Medical Informatics University Hospital RWTH Aachen 52074 Aachen Germany. Electronic address: id10656@alunos.uminho.pt. Cancer Research Center Cologne Essen (CCCE) University Medicine Essen Hufelandstraße 55 Essen 45147 Germany. Computer Algorithms for Medicine Laboratory Graz Austria. Cancer Research Center Cologne Essen (CCCE) University Medicine Essen Hufelandstraße 55 Essen 45147 Germany German Cancer Consortium (DKTK) Partner Site Essen Hufelandstraße 55 Essen 45147 Germany TU Dortmund University Department of Physics Otto-Hahn-Straße 4 44227 Dortmund Germany. Institute for AI in Medicine (IKIM) University Hospital Essen University Duisburg-Essen Girardetstraße 2 Essen 45131 Germany. Institute of Computer Graphics and Vision Graz University of Technology Inffeldgasse 16 Graz 801 Austria.

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The importance of transparency and reproducibility in artificial intelligence research

arXiv

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arXiv 2020年

作者： Haibe-Kains, Benjamin Adam, George Alexandru Hosny, Ahmed Khodakarami, Farnoosh Waldron, Levi Wang, Bo McIntosh, Chris Kundaje, Anshul Greene, Casey S. Hoffman, Michael M. Leek, Jeffrey T. Huber, Wolfgang Brazma, Alvis Pineau, Joelle Tibshirani, Robert Hastie, Trevor Ioannidis, John P.A. Quackenbush, John Aerts, Hugo J.W.L. Princess Margaret Cancer Centre University Health Network TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada Ontario Institute for Cancer Research TorontoON Canada Vector Institute for Artificial Intelligence TorontoON Canada Program Brigham and Women's Hospital Harvard Medical School BostonMA United States Radiation Oncology and Radiology Dana-Farber Cancer Institute Brigham and Women's Department of Epidemiology and Biostatistics Institute for Implementation Science in Population Health CUNY Graduate School of Public Health and Health Policy New YorkNY United States Peter Munk Cardiac Centre University Health Network TorontoON Canada Hospital Harvard Medical School BostonMA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Dept. of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Childhood Cancer Data Lab Alex's Lemonade Stand Foundation PhiladelphiaPA United States Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany European Molecular Biology Laboratory European Bioinformatics Institute EMBL-EBI Hinxton United Kingdom McGill University MontrealQC Canada Montreal Institute for Learning Algorithms QC Canada StanfordCA United States Department of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Departments of Medicine of Health Research and Policy and of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Department of Statistics Stanford University School of Humanities and Sciences StanfordCA United States Department of Biostatistics Harvard T.H Chan School of Public Health BostonMA Un

In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines its scientific value. We identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al and provide solutions with implications for the broader field. Copyright © 2020, The Authors. All rights reserved.

关键词： Artificial intelligence

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Aortic Vessel Tree Segmentation for Cardiovascular Diseases Treatment: Status Quo

引用

ACM Computing Surveys 1000年

作者： Yuan Jin Antonio Pepe Jianning Li Christina Gsaxner Yuxuan Chen Behrus Puladi Fen-hua Zhao Kelsey Pomykala Jens Kleesiek Alejandro Frangi Jan Egger Institute of Computer Graphics and Vision Graz University of Technology Graz Austria Research Centre for Frontier Fundamental Studies Zhejiang Lab Hangzhou China Institute of Computer Graphics and Vision Graz University of Technology Graz Austria Institute for Artificial Intelligence in Medicine Essen University Hospital (AöR) Essen Germany Zhejiang Laboratory of Philosophy and Social Sciences - Laboratory of Intelligent Society and Governance Zhejiang Lab Hangzhou China Institute of Medical Informatics RWTH Aachen University Aachen Germany Wenzhou Medical University Affiliated Dongyang Hospital Dongyang China Cancer Research Center Cologne Essen Essen Germany German Cancer Consortium Heidelberg Germany Christabel Pankhurst Institute The University of Manchester Manchester United Kingdom of Great Britain and Northern Ireland School of Health Sciences The University of Manchester Division of Informatics Imaging and Data Sciences Manchester United Kingdom of Great Britain and Northern Ireland The University of Manchester School of Computer Science Manchester United Kingdom of Great Britain and Northern Ireland Manchester University NHS Foundation Trust Manchester United Kingdom of Great Britain and Northern Ireland Insitute of Artificial Intelligence in Medicine Essen University Hospital (AöR) Essen Germany Computer Algorithms for Medicine Laboratory Graz Austria Cancer Research Center Cologne Essen (CCCE) Essen Germany

The aortic vessel tree, composed of the aorta and its branches, is crucial for blood supply to the body. Aortic diseases, such as aneurysms and dissections, can lead to life-threatening ruptures, often requiring open surgery. Therefore, patients commonly undergo treatment under constant monitoring, which requires regular inspections of the vessels through medical imaging techniques. Overlapping and comparing aortic vessel tree geometries from consecutive images allows for tracking changes in both the aorta and its branches. Manual reconstruction of the vessel tree is time-consuming and impractical in clinical settings. In contrast, automatic or semi-automatic segmentation algorithms can perform this task much faster, making them suitable for routine clinical use. This paper systematically reviews methods for the automatic and semi-automatic segmentation of the aortic vessel tree, concluding with a discussion on their clinical applicability, the current research landscape, and ongoing challenges.

关键词： Aorta Vessel Tree Machine Learning Deep Learning Segmentation Analysis Cardiovascular Disease Aneurysm Dissection Computed Tomography.

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Perspectives on adaptive dynamical systems

arXiv

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arXiv 2023年

作者： Sawicki, Jakub Berner, Rico Loos, Sarah A.M. Anvari, Mehrnaz Bader, Rolf Barfuss, Wolfram Botta, Nicola Brede, Nuria Franović, Igor Gauthier, Daniel J. Goldt, Sebastian Hajizadeh, Aida Hövel, Philipp Karin, Omer Lorenz-Spreen, Philipp Miehl, Christoph Mölter, Jan Olmi, Simona Schöll, Eckehard Seif, Alireza Tass, Peter A. Volpe, Giovanni Yanchuk, Serhiy Kurths, Jürgen Potsdam Institute for Climate Impact Research Telegrafenberg Potsdam14473 Germany Fachhochschule Nordwestschweiz FHNW Leonhardsstrasse 6 Basel4009 Switzerland Department of Physics Humboldt-Universität zu Berlin Newtonstraße 15 Berlin12489 Germany DAMTP University of Cambridge Wilberforce Road CambridgeCB3 0WA United Kingdom Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt-Augustin53757 Germany Institute of Systematic Musicology University of Hamburg Germany Transdisciplinary Research Area: Sustainable Futures University of Bonn Bonn53113 Germany University of Bonn Bonn53113 Germany Department of Computer Science and Engineering Chalmers University of Technology Göteborg412 96 Sweden Department of Computer Science University of Potsdam An der Bahn 2 Potsdam14476 Germany Scientific Computing Laboratory Center for the Study of Complex Systems Institute of Physics Belgrade University of Belgrade Pregrevica 118 Belgrade11080 Serbia The Ohio State University Department of Physics and Electrical and Computer Engineering 191 West Woodruff Ave ColumbusOH43210 United States ResCon Technologies LLC 1275 Kinnear Rd. Suite 239 ColumbusOH43212 United States Trieste Italy Research Group Comparative Neuroscience Leibniz Institute for Neurobiology Magdeburg Germany Theoretical Physics Saarland University Saarbrücken66123 Germany Center for Biophysics Saarland University Saarbrücken66123 Germany Department of Mathematics Imperial College London United Kingdom Center for Adaptive Rationality Max Planck Institute for Human Development Lentzeallee 94 Berlin14195 Germany Max Planck Institute for Brain Research Max-von-Laue-Straße 4 Frankfurt am Main60438 Germany Technical University of Munich School of Life Sciences Alte Akademie 8 Freising85354 Germany Department of Mathematics School of Computation Information and Technology Technical University of Munich Boltzmannstraße 3 Garching bei München8574

Adaptivity is a dynamical feature that is omnipresent in nature, socio-economics, and technology. For example, adaptive couplings appear in various real-world systems like the power grid, social, and neural networks, and they form the backbone of closed-loop control strategies and machine learning algorithms. In this article, we provide an interdisciplinary perspective on adaptive systems. We reflect on the notion and terminology of adaptivity in different disciplines and discuss which role adaptivity plays for various fields. We highlight common open challenges, and give perspectives on future research directions, looking to inspire interdisciplinary approaches. Copyright © 2023, The Authors. All rights reserved.

关键词： Dynamical systems

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