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arXiv 2023年

作者： Lee, Edward H. Kelly, Brendan Altinmakas, Emre Dogan, Hakan Mohammadzadeh, Maryam Colak, Errol Fu, Steve Choudhury, Olivia Ratan, Ujjwal Kitamura, Felipe Chaves, Hernan Zheng, Jimmy Said, Mourad Reis, Eduardo Lim, Jaekwang Yokoo, Patrícia Mitchell, Courtney Houshmand, Golnaz Ghassemi, Marzyeh Killeen, Ronan Qiu, Wendy Hayden, Joel Rafiee, Farnaz Klochko, Chad Bevins, Nicholas Sazgara, Faeze Wong, S. Simon Moseley, Michael Halabi, Safwan Yeom, Kristen W. School of Medicine Stanford University United States Insight Centre for Data Analytics University College Dublin Ireland Icahn School of Medicine at Mount Sinai United States Koç University School of Medicine Turkey Division of Neuroradiology Amiralam Hospital Tehran University of Medical Sciences Iran Unity Health Toronto St. Michael’s Hospital University of Toronto Canada Amazon Web Services United States Universidade Federal de São Paulo Brazil Fleni Argentina Radiology Department Centre International Carthage Médicale Monastir Tunisia Hospital Israelita Albert Einstein SP São Paulo Brazil Department of Radiology Kyungpook National University Hospital Korea Republic of Department of Radiology St. Joseph’s Hospital and Medical Center United States Rajaie Cardiovascular Medical and Research Center Iran University of Medical Sciences Iran Dept. of Electrical Engineering and Computer Science at MIT United States Department of Radiology Henry Ford Health System DetroitMI United States Department of Radiology Guilan University of Medical Sciences Iran Department of Electrical Engineering Stanford University United States Ann & Robert H. Lurie Children's Hospital of Chicago United States

While it is well known that population differences from genetics, sex, race, and environmental factors contribute to disease, AI studies in medicine have largely focused on locoregional patient cohorts with less diverse data sources. Such limitation stems from barriers to large-scale data share and ethical concerns over data privacy. Federated learning (FL) is one potential pathway for AI development that enables learning across hospitals without data share. In this study, we show the results of various FL strategies on one of the largest and most diverse COVID-19 chest CT datasets: 21 participating hospitals across five continents that comprise >10,000 patients with >1 million images. We also propose an FL strategy that leverages synthetically generated data to overcome class and size imbalances. We also describe the sources of data heterogeneity in the context of FL, and show how even among the correctly labeled populations, disparities can arise due to these biases. Copyright © 2023, The Authors. All rights reserved.

关键词： Hospitals

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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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PennyLane: Automatic differentiation of hybrid quantum-classical computations

arXiv

引用

arXiv 2018年

作者： Bergholm, Ville Izaac, Josh Schuld, Maria Gogolin, Christian Ahmed, Shahnawaz Ajith, Vishnu Alam, M. Sohaib Alonso-Linaje, Guillermo AkashNarayanan, B. Asadi, Ali Arrazola, Juan Miguel Azad, Utkarsh Banning, Sam Blank, Carsten Bromley, Thomas R. Cordier, Benjamin A. Ceroni, Jack Delgado, Alain Matteo, Olivia Di Dusko, Amintor Garg, Tanya Guala, Diego Hayes, Anthony Hill, Ryan Ijaz, Aroosa Isacsson, Theodor Ittah, David Jahangiri, Soran Jain, Prateek Jiang, Edward Khandelwal, Ankit Kottmann, Korbinian Lang, Robert A. Lee, Christina Loke, Thomas Lowe, Angus McKiernan, Keri Meyer, Johannes Jakob Montañez-Barrera, J.A. Moyard, Romain Niu, Zeyue O’Riordan, Lee James Oud, Steven Panigrahi, Ashish Park, Chae-Yeun Polatajko, Daniel Quesada, Nicolás Roberts, Chase Sá, Nahum Schoch, Isidor Shi, Borun Shu, Shuli Sim, Sukin Singh, Arshpreet Strandberg, Ingrid Soni, Jay Száva, Antal Thabet, Slimane Vargas-Hernández, Rodrigo A. Vincent, Trevor Vitucci, Nicola Weber, Maurice Wierichs, David Wiersema, Roeland Willmann, Moritz Wong, Vincent Zhang, Shaoming Killoran, Nathan Xanadu 777 Bay Street Toronto Canada Wallenberg Centre for Quantum Technology Department of Microtechnology and Nanoscience Chalmers University of Technology Gothenburg412 96 Sweden Indian Institute of Information Technology Kottayam India NASA Ames Research Center Moffett FieldCA94035 United States Mountain ViewCA94043 United States data cybernetics Martin-Kolmsperger-Str 26 Landsberg86899 Germany Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University PortlandOR97202 United States Dept. of Electrical and Computer Engineering The University of British Columbia VancouverBCV6T 1Z4 Canada Department of Physics Indian Institute of Technology Roorkee Uttarakhand Roorkee India qBraid 5235 South Harper Court ChicagoIL60615 United States Factal Analytics Level 2 Chimes Building Plot 61 Sector - 44 Haryana Gurgaon122003 India Centre for High Energy Physics Indian Institute of Science Karnataka Bengaluru560012 India ICFO - Institut de Ciencies Fotoniques The Barcelona Institute of Science and Technology Av. Carl Friedrich Gauss 3 Castelldefels Barcelona08860 Spain Chemical Physics Theory Group Department of Chemistry University of Toronto Canada DUG Technology 76 Kings Park Rd West PerthWA6005 Australia Rigetti Computing 2919 Seventh Street BerkeleyCA94710 United States Dahlem Center for Complex Quantum Systems Freie Universität Berlin Berlin14195 Germany Institute for Advanced Simulation Jülich Supercomputing Centre Forschungszentrum Jülich Jülich52425 Germany University of Amsterdam Netherlands School of Physical Sciences National Institute of Science Education and Research HBNI Odisha Jatni752 050 India Cervest United Kingdom Centro Brasileiro de Pesquisas Físicas Rua Dr. Xavier Sigaud 150 Rio de Janeiro22290-180 Brazil Zurich8092 Switzerland Neo4j UK Ltd United Kingdom Zapata Computing Inc. United States ITC Infotech Bangalore India Department of Microtechnology and Nanoscienc

PennyLane is a Python 3 software framework for differentiable programming of quantum computers. The library provides a unified architecture for near-term quantum computing devices, supporting both qubit and continuous-variable paradigms. PennyLane’s core feature is the ability to compute gradients of variational quantum circuits in a way that is compatible with classical techniques such as backpropagation. PennyLane thus extends the automatic differentiation algorithms common in optimization and machine learning to include quantum and hybrid computations. A plugin system makes the framework compatible with any gate-based quantum simulator or hardware. We provide plugins for hardware providers including the Xanadu Cloud, Amazon Braket, and IBM Quantum, allowing PennyLane optimizations to be run on publicly accessible quantum devices. On the classical front, PennyLane interfaces with accelerated machine learning libraries such as TensorFlow, PyTorch, JAX, and Autograd. PennyLane can be used for the optimization of variational quantum eigensolvers, quantum approximate optimization, quantum machine learning models, and many other applications. Copyright © 2018, The Authors. All rights reserved.

关键词： Machine learning

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Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

arXiv

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arXiv 2021年

作者： Sanders, Lauren M. Yang, Jason H. Scott, Ryan T. Qutub, Amina Ann Martin, Hector Garcia Berrios, Daniel C. Hastings, Jaden J.A. Rask, Jon Mackintosh, Graham Hoarfrost, Adrienne L. Chalk, Stuart Kalantari, John Khezeli, Kia Antonsen, Erik L. Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Delgado-Aparicio, Guillermo M. Glicksberg, Benjamin S. Greene, Casey S. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Mason, Christopher E. Matar, Mona Mias, George I. Miller, Jack Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Park, Seung-Min Parsons-Wingerter, Patricia Prabhu, R.K. Reynolds, Robert J. Saravia-Butler, Amanda Saria, Suchi Sawyer, Aenor Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik Theriot, Corey A. van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Zitnik, Marinka Costes, Sylvain V. Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Center for Emerging and Re-Emerging Pathogens Department of Microbiology Biochemistry and Molecular Genetics Rutgers New Jersey Medical School NewarkNJ07103 United States KBR Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States AI MATRIX Consortium Department of Biomedical Engineering University of Texas San Antonio and UT Health Sciences San AntonioTX78249 United States Biological Systems and Engineering Division Lawrence Berkeley National Lab. BerkeleyCA94608 United States DOE Agile BioFoundry EmeryvilleCA94608 United States Joint BioEnergy Institute EmeryvilleCA94608 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Office of the Center Director NASA Ames Research Center Moffett Field CA94035 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett Field CA94035 United States Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Center for Individualized Medicine Department of Surgery Department of Quantitative Health Sciences Mayo Clinic RochesterMN55905 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin - Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Data Science Analytics Georgia Institute of Technology Lima15024

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space. © 2021, CC BY.

关键词： Predictive analytics

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