Federated learning for predicting clinical outcomes in patients with COVID-19.

Journal: Nature medicine
Published Date: Sep 15, 2021

Abstract

Federated learning (FL) is a method used for training artificial intelligence models with data from multiple sources while maintaining data anonymity, thus removing many barriers to data sharing. Here we used data from 20 institutes across the globe to train a FL model, called EXAM (electronic medical record (EMR) chest X-ray AI model), that predicts the future oxygen requirements of symptomatic patients with COVID-19 using inputs of vital signs, laboratory data and chest X-rays. EXAM achieved an average area under the curve (AUC) >0.92 for predicting outcomes at 24 and 72 h from the time of initial presentation to the emergency room, and it provided 16% improvement in average AUC measured across all participating sites and an average increase in generalizability of 38% when compared with models trained at a single site using that site's data. For prediction of mechanical ventilation treatment or death at 24 h at the largest independent test site, EXAM achieved a sensitivity of 0.950 and specificity of 0.882. In this study, FL facilitated rapid data science collaboration without data exchange and generated a model that generalized across heterogeneous, unharmonized datasets for prediction of clinical outcomes in patients with COVID-19, setting the stage for the broader use of FL in healthcare.

Authors

  • Ittai Dayan
  • Holger R Roth
  • Aoxiao Zhong
    Center for Clinical Data Science, Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
  • Ahmed Harouni
    Department of Medical Engineering, NVIDIA, Santa Clara, California, United States.
  • Amilcare Gentili
    San Diego VA Health Care System, San Diego, CA, USA.
  • Anas Z Abidin
    Department of Biomedical Engineering, University of Rochester Medical Center, Rochester, NY, USA. Electronic address: anas.abidin@rochester.edu.
  • Andrew Liu
    Massachusetts Institute of Technology, Cambridge, USA.
  • Anthony Beardsworth Costa
    Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Bradford J Wood
    Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
  • Chien-Sung Tsai
    Division of Cardiovascular Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center;
  • Chih-Hung Wang
    National Taiwan University Hospital, Department of Emergency Medicine, Taipei, Taiwan.
  • Chun-Nan Hsu
    University of California San Diego, La Jolla, CA.
  • C K Lee
    NVIDIA, Santa Clara, CA, USA.
  • Peiying Ruan
    NVIDIA, Santa Clara, CA, USA.
  • Daguang Xu
    NVIDIA, Santa Clara, CA, USA.
  • Dufan Wu
  • Eddie Huang
    NVIDIA, Santa Clara, CA, USA.
  • Felipe Campos Kitamura
    From the Department of Radiology, Stanford University, 300 Pasteur Dr, MC 5105, Stanford, CA 94305 (S.S.H.); Department of Radiology, The Ohio State University Wexner Medical Center, Columbus, Ohio (L.M.P.); Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Boston, Mass (J.K.C.); Massachusetts General Hospital & Brigham and Women's Hospital Center for Clinical Data Science, Boston, Mass (A.B.M., K.A.); Department of Radiology, University of Toronto, Toronto, Ontario, Canada (A.B.); Department of Radiology, St. Michael's Hospital, Toronto, Ontario, Canada (M.C.); Department of Diagnostic Imaging, Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI (I.P.); Universidade Federal de Goiás, Goiânia, Brazil (L.A.P., R.T.S.); Universidade Federal de São Paulo, São Paulo, Brazil (N.A., F.C.K.); Visiana, Hørsholm, Denmark (H.H.T.); MD.ai, New York, NY (L.C.); Department of Radiology, Weill Cornell Medicine, New York, NY (G.S.) Department of Radiology, University of California-San Francisco, San Francisco, Calif (M.D.K.); Department of Radiology, Mayo Clinic, Rochester, Minn (B.J.E.); and Department of Radiology, Thomas Jefferson University, Philadelphia, Pa (A.E.F.).
  • Griffin Lacey
    NVIDIA, Santa Clara, CA, USA.
  • Gustavo César de Antônio Corradi
    DasaInova, Diagnósticos da América SA, Barueri, Brazil.
  • Gustavo Nino
  • Hao-Hsin Shin
    Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Hirofumi Obinata
    Self-Defense Forces Central Hospital, Tokyo, Japan.
  • Hui Ren
  • Jason C Crane
    Center for Intelligent Imaging, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA.
  • Jesse Tetreault
    NVIDIA Corporation, Bethesda, Maryland, USA.
  • Jiahui Guan
    Nvidia, Boston, United States.
  • John W Garrett
    From the Departments of Medical Physics (R.Z., X.T., C.Z., D.G., J.W.G., K.L., S.B.R., G.H.C.) and Radiology (M.L.S., J.W.G., K.L., S.B.R., G.H.C.), University of Wisconsin-Madison School of Medicine and Public Health, 1111 Highland Ave, Madison, WI 53705; and Department of Radiology, Henry Ford Health System, Detroit, Mich (Z.Q., N.B.B., T.K.S., J.D.N,).
  • Joshua D Kaggie
    Department of Radiology, University of Cambridge, Cambridge, United Kingdom. Electronic address: jk636@cam.ac.uk.
  • Jung Gil Park
  • Keith Dreyer
    Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts.
  • Krishna Juluru
    From the Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 29, New York, NY 10065.
  • Kristopher Kersten
    NVIDIA, Santa Clara, CA, USA.
  • Marcio Aloisio Bezerra Cavalcanti Rockenbach
    Center for Clinical Data Science, Massachusetts General Brigham, Boston, MA, USA.
  • Marius George Linguraru
    Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Medical Center, Washington, DC 20010, USA; Departments of Radiology and Pediatrics, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA.
  • Masoom A Haider
    Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
  • Meena AbdelMaseeh
    Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.
  • Nicola Rieke
    NVIDIA, Santa Clara, CA, USA.
  • Pablo F Damasceno
    Department of Radiology and Biomedical Imaging, School of Medicine, University of California, San Francisco, San Francisco, CA, United States.
  • Pedro Mario Cruz E Silva
    NVIDIA, Santa Clara, CA, USA.
  • Pochuan Wang
    MeDA Lab Institute of Applied Mathematical Sciences, National Taiwan University, Taipei, Taiwan.
  • Sheng Xu
    School of Physics and Information Engineering, Jiangsu Second Normal University, Nanjing, 211200, China.
  • Shuichi Kawano
    Self-Defense Forces Central Hospital, Tokyo, Japan.
  • Sira Sriswasdi
    Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  • Soo Young Park
  • Thomas M Grist
    Departments of Radiology, Medical Physics, and Biomedical Engineering, The University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
  • Varun Buch
    Cera Care, London, UK.
  • Watsamon Jantarabenjakul
    Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  • Weichung Wang
    Graduate Program of Data Science, National Taiwan University and Academia Sinica, Taipei, Taiwan.
  • Won Young Tak
  • Xiang Li
    Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.
  • Xihong Lin
    Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
  • Young Joon Kwon
    Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Abood Quraini
    NVIDIA, Santa Clara, CA, USA.
  • Andrew Feng
    NVIDIA, Santa Clara, CA, USA.
  • Andrew N Priest
    Department of Radiology, NIHR Cambridge Biomedical Resource Centre, Cambridge University Hospital, Cambridge, UK.
  • Baris Turkbey
    Molecular Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
  • Benjamin Glicksberg
    Hasso Plattner Institute of Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York.
  • Bernardo Bizzo
  • Byung Seok Kim
    Department of Internal Medicine, Catholic University of Daegu School of Medicine, Daegu, South Korea.
  • Carlos Tor-Díez
    IMT Atlantique, LaTIM U1101 INSERM, UBL, Brest, France. Electronic address: carlos.tordiez@imt-atlantique.fr.
  • Chia-Cheng Lee
    Planning and Management Office, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.
  • Chia-Jung Hsu
    Planning and Management Office, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.
  • Chin Lin
    School of Public Health, National Defense Medical Center, Taipei, Taiwan.
  • Chiu-Ling Lai
    Medical Review and Pharmaceutical Benefits Division, National Health Insurance Administration, Taipei, Taiwan.
  • Christopher P Hess
    Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
  • Colin Compas
    NVIDIA, Santa Clara, CA, USA.
  • Deepeksha Bhatia
    NVIDIA, Santa Clara, CA, USA.
  • Eric K Oermann
    Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Evan Leibovitz
    Center for Clinical Data Science, Massachusetts General Brigham, Boston, MA, USA.
  • Hisashi Sasaki
    Self-Defense Forces Central Hospital, Tokyo, Japan.
  • Hitoshi Mori
    Self-Defense Forces Central Hospital, Tokyo, Japan.
  • Isaac Yang
    NVIDIA, Santa Clara, CA, USA.
  • Jae Ho Sohn
    Radiology & Biomedical Imaging, UCSF Medical Center, 505 Parnassus Ave, San Francisco, CA, 94158, USA. sohn87@gmail.com.
  • Krishna Nand Keshava Murthy
    Memorial Sloan Kettering Cancer Center, New York, NY, USA.
  • Li-Chen Fu
  • Matheus Ribeiro Furtado de Mendonça
    DasaInova, Diagnósticos da América SA, Barueri, Brazil.
  • Mike Fralick
    Li Ka Shing Centre for Healthcare Analytics Research and Training, Toronto, ON, Canada mike.fralick@mail.utoronto.ca.
  • Min Kyu Kang
  • Mohammad Adil
    NVIDIA, Santa Clara, CA, USA.
  • Natalie Gangai
    From the Department of Radiology (R.K.G.D., P.I.C.A., M.T., N.G., K.J., H.H.), Human Pathology and Pathogenesis Program, Center for Molecular Oncology (A.L.), Department of Strategy and Innovation (H.N., P.R., L.G., K.N.), and Biostatistics Service, Department of Epidemiology and Biostatistics (C.J.F., N.S., V.S.), Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; and School of Computing, Queens University, Kingston, Canada (K.L., K.B., F.Z., A.S.).
  • Peerapon Vateekul
    Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand.
  • Pierre Elnajjar
    From the Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 29, New York, NY 10065.
  • Sarah Hickman
    Department of Radiology, NIHR Cambridge Biomedical Resource Centre, University of Cambridge, Cambridge, UK.
  • Sharmila Majumdar
    Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, Byers Hall, Suite 203, Room 203D, San Francisco, CA 94158, USA.
  • Shelley L McLeod
    Schwartz/Reisman Emergency Medicine Institute, Sinai Health, Toronto, Ontario, Canada.
  • Sheridan Reed
    Radiology & Imaging Sciences/Clinical Center, National Institutes of Health, Bethesda, MD, USA.
  • Stefan Gräf
    Department of Medicine and NIHR BioResource for Translational Research, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK.
  • Stephanie Harmon
  • Tatsuya Kodama
    Self-Defense Forces Central Hospital, Tokyo, Japan.
  • Thanyawee Puthanakit
    Department of Pediatrics and Center of Excellence in Pediatric Infectious Diseases and Vaccine Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  • Tony Mazzulli
    5 Department of Microbiology, Mount Sinai Hospital/University Health Network, Ontario, Canada.
  • Vitor Lima de Lavor
    DasaInova, Diagnósticos da América SA, Barueri, Brazil.
  • Yothin Rakvongthai
    Chulalongkorn University Biomedical Imaging Group and Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
  • Yu Rim Lee
  • Yuhong Wen
    NVIDIA, Santa Clara, CA, USA.
  • Fiona J Gilbert
    Department of Radiology, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom; NIHR Cambridge Biomedical Research Center, Cambridge, United Kingdom.
  • Mona G Flores
    NVIDIA Corporation, Bethesda, Maryland, USA.
  • Quanzheng Li
    Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.

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