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Nature . 2021 May 26

Swarm Learning for decentralized and confidential clinical machine learning

Stefanie Warnat-Herresthal, Hartmut Schultze, Krishnaprasad Lingadahalli Shastry, Sathyanarayanan Manamohan, Saikat Mukherjee, Vishesh Garg, Ravi Sarveswara, Kristian Händler, Peter Pickkers, N Ahmad Aziz, Sofia Ktena, Florian Tran, Michael Bitzer, Stephan Ossowski, Nicolas Casadei, Christian Herr, Daniel Petersheim, Uta Behrends, Fabian Kern, Tobias Fehlmann, Philipp Schommers, Clara Lehmann, Max Augustin, Jan Rybniker, Janine Altmüller, Neha Mishra, Joana P Bernardes, Benjamin Krämer, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Elena De Domenico, Christian Siever, Michael Kraut, Milind Desai, Bruno Monnet, Maria Saridaki, Charles Martin Siegel, Anna Drews, Melanie Nuesch-Germano, Heidi Theis, Jan Heyckendorf, Stefan Schreiber, Sarah Kim-Hellmuth, COVID-19 Aachen Study (COVAS), Jacob Nattermann, Dirk Skowasch, Ingo Kurth, Andreas Keller, Robert Bals, Peter Nürnberg, Olaf Rieß, Philip Rosenstiel, Mihai G Netea, Fabian Theis, Sach Mukherjee, Michael Backes, Anna C Aschenbrenner, Thomas Ulas, Deutsche COVID-19 Omics Initiative (DeCOI), Monique M B Breteler, Evangelos J Giamarellos-Bourboulis, Matthijs Kox, Matthias Becker, Sorin Cheran, Michael S Woodacre, Eng Lim Goh, Joachim L Schultze

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. 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.

PMID: 34040261