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WHITE MATTER HYPERINTENSITIES IN RELATION TO PATTERNS OF ACCELERATED BRAIN AGING, AD-LIKE ATROPHY AND AMYLOID BURDEN: RESULTS FROM THE ISTAGING CONSORTIUM ON MACHINE LEARNING AND LARGE-SCALE IMAGING analytics

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Alzheimer's & Dementia 2019年第7期15卷 P904-P905页

作者： Mohamad Habes Raymond Pomponio Haochang Shou Jimit Doshi Aristeidis Sotiras Guray Erus Lenore J. Launer Elizabeth Mamourian Murat Bilgel Kristine Yaffe Dhivya Srinivasan Mark A. Espeland Ilya M. Nasrallah Christopher C. Rowe Henry Voelzke Sterling C. Johnson Marilyn S. Albert Nick Bryan Hans J. Grabe Susan M. Resnick Christos Davatzikos University of Pennsylvania Philadelphia PA USA Department of Neurology and Penn Memory Center University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics and Department of Radiology University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics University of Pennsylvania Philadelphia PA USA National Institute on Aging Bethesda MD USA National Institute on Aging NIH Baltimore MD USA Department of Epidemiology & Biostatistics University of California San Francisco San Francisco CA USA Wake Forest School of Medicine Winston-Salem NC USA Department of Molecular Imaging and Therapy Centre for PET Austin Health Heidelberg Australia Institute for Community Medicine University Medicine Greifswald Greifswald Germany Wisconsin Alzheimer's Institute University of Wisconsin School of Medicine and Public Health Madison WI USA Johns Hopkins University School of Medicine Baltimore MD USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA University of Texas at Austin Austin TX USA Department of Psychiatry University Medicine Greifswald and German Center for Neurodegenerative Disease (DZNE) Rostock/Greifswald Greifswald Germany

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***: Dissemination platform for deep learning models

arXiv

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arXiv 2019年

作者： Hosny, Ahmed Schwier, Michael Berger, Christoph Örnek, Evin P. Turan, Mehmet Tran, Phi V. Weninger, Leon Isensee, Fabian Maier-Hein, Klaus H. McKinley, Richard Lu, Michael T. Hoffmann, Udo Menze, Bjoern Bakas, Spyridon Fedorov, Andriy Aerts, Hugo J.W.L. Program Brigham and Women's Hospital Harvard Medical School BostonMA United States Department of Radiation Oncology Dana-Farber Cancer Institute Harvard Medical School BostonMA United States Department of Radiology Brigham and Women's Hospital Dana-Farber Cancer Institute Harvard Medical School BostonMA United States Harvard Medical School BostonMA United States Institute for Advanced Study Department of Informatics Technical University of Munich Munich Germany Max Planck Institute for Intelligent Systems Stuttgart Germany Booz Allen Hamilton McLeanVA United States Institute of Imaging & Computer Vision RWTH Aachen University Aachen Germany Heidelberg Germany Support Centre for Advanced Neuroimaging University Institute of Diagnostic Interventional Neuroradiology Inselspital Bern University Hospital Bern Switzerland Cardiovascular Imaging Research Center Massachusetts General Hospital Harvard Medical School Boston United States Cardiac MR PET CT Program Department of Radiology Massachusetts General Hospital BostonMA United States Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Radiology & Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Radiology and Nuclear Medicine GROW CARIM Maastricht University Maastricht Netherlands

Recent advances in artificial intelligence research have led to a profusion of studies that apply deep learning to problems in image analysis and natural language processing among others. Additionally, the availability of open-source computational frameworks has lowered the barriers to implementing state-of-the-art methods across multiple domains. Albeit leading to major performance breakthroughs in some tasks, effective dissemination of deep learning algorithms remains challenging, inhibiting reproducibility and benchmarking studies, impeding further validation, and ultimately hindering their effectiveness in the cumulative scientific progress. In developing a platform for sharing research outputs, we present *** (***), a community-driven container-based software engine and platform for the structured dissemination of deep learning models. For contributors, the engine controls data flow throughout the inference cycle, while the contributor-facing standard template exposes model-specific functions including inference, as well as pre- and post-processing. Python and RESTful Application programming interfaces (APIs) enable users to interact with models hosted on *** and allows both researchers and developers to utilize models out-of-the-box. *** is domain-, data-, and framework-agnostic, catering to different workflows and contributors' preferences. Copyright © 2019, The Authors. All rights reserved.

关键词： Containers

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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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