Swarm Learning for decentralized and confidential clinical machine learning.

Journal: Nature
PMID: 34040261

Abstract

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning-a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.

Authors

  • Stefanie Warnat-Herresthal
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Hartmut Schultze
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Krishnaprasad Lingadahalli Shastry
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Sathyanarayanan Manamohan
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Saikat Mukherjee
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Vishesh Garg
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Ravi Sarveswara
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Kristian Händler
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Peter Pickkers
    Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.
  • N Ahmad Aziz
    Population Health Sciences, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Sofia Ktena
    4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece.
  • Florian Tran
    Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.
  • Michael Bitzer
    Department of Internal Medicine I, University Hospital, University of Tübingen, Tübingen, Germany.
  • Stephan Ossowski
    Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
  • Nicolas Casadei
    Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
  • Christian Herr
    Department of Internal Medicine V, Saarland University Hospital, Homburg, Germany.
  • Daniel Petersheim
    Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany.
  • Uta Behrends
    Children's Hospital, Medical Faculty, Technical University Munich, Munich, Germany.
  • Fabian Kern
    Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
  • Tobias Fehlmann
    Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
  • Philipp Schommers
    Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
  • Clara Lehmann
    Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
  • Max Augustin
    Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
  • Jan Rybniker
    Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.
  • Janine Altmüller
    Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany.
  • Neha Mishra
    Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.
  • Joana P Bernardes
    Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.
  • Benjamin Krämer
    Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
  • Lorenzo Bonaguro
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Jonas Schulte-Schrepping
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Elena De Domenico
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Christian Siever
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Michael Kraut
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Milind Desai
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Bruno Monnet
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Maria Saridaki
    4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece.
  • Charles Martin Siegel
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Anna Drews
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Melanie Nuesch-Germano
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Heidi Theis
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Jan Heyckendorf
    Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.
  • Stefan Schreiber
    Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany.
  • Sarah Kim-Hellmuth
    Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany.
  • Jacob Nattermann
    Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany.
  • Dirk Skowasch
    Department of Internal Medicine II - Cardiology/Pneumology, University of Bonn, Bonn, Germany.
  • Ingo Kurth
    Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
  • Andreas Keller
    Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany. Electronic address: andreas.keller@ccb.uni-saarland.de.
  • Robert Bals
    From the Department of Internal Medicine V-Pneumology, Allergology and Intensive Care Medicine, University Hospital of Saarland, Homburg, Germany.
  • Peter Nürnberg
    Cologne Center for Genomics, West German Genome Center, University of Cologne, Cologne, Germany.
  • Olaf Rieß
    Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
  • Philip Rosenstiel
    Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, 24105, Germany.
  • Mihai G Netea
    Department of Internal Medicine Radboud University Medical Center Nijmegen The Netherlands.
  • Fabian Theis
    Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany.
  • Sach Mukherjee
    Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Michael Backes
    CISPA Helmholtz Center for Information Security, Saarbrücken, Germany.
  • Anna C Aschenbrenner
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Thomas Ulas
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.
  • Monique M B Breteler
    Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
  • Evangelos J Giamarellos-Bourboulis
    4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece.
  • Matthijs Kox
    Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.
  • Matthias Becker
    Department of Medical Informatics, University of Applied Sciences and Arts, Dortmund, Germany.
  • Sorin Cheran
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Michael S Woodacre
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Eng Lim Goh
    Hewlett Packard Enterprise, Houston, TX, USA.
  • Joachim L Schultze
    Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany. joachim.schultze@dzne.de.

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