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Federated learning enables big data for rare cancer boundary detection

Author

Listed:
  • Sarthak Pati

    (University of Pennsylvania
    University of Pennsylvania
    University of Pennsylvania
    Technical University of Munich)

  • Ujjwal Baid

    (University of Pennsylvania
    University of Pennsylvania
    University of Pennsylvania)

  • Brandon Edwards

    (Intel Corporation)

  • Micah Sheller

    (Intel Corporation)

  • Shih-Han Wang

    (Intel Corporation)

  • G. Anthony Reina

    (Intel Corporation)

  • Patrick Foley

    (Intel Corporation)

  • Alexey Gruzdev

    (Intel Corporation)

  • Deepthi Karkada

    (Intel Corporation)

  • Christos Davatzikos

    (University of Pennsylvania
    University of Pennsylvania)

  • Chiharu Sako

    (University of Pennsylvania
    University of Pennsylvania)

  • Satyam Ghodasara

    (University of Pennsylvania)

  • Michel Bilello

    (University of Pennsylvania
    University of Pennsylvania)

  • Suyash Mohan

    (University of Pennsylvania
    University of Pennsylvania)

  • Philipp Vollmuth

    (Heidelberg University Hospital)

  • Gianluca Brugnara

    (Heidelberg University Hospital)

  • Chandrakanth J. Preetha

    (Heidelberg University Hospital)

  • Felix Sahm

    (German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ)
    Heidelberg University Hospital)

  • Klaus Maier-Hein

    (German Cancer Research Center
    Heidelberg University Hospital)

  • Maximilian Zenk

    (German Cancer Research Center)

  • Martin Bendszus

    (Heidelberg University Hospital)

  • Wolfgang Wick

    (German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ)
    Neurology Clinic, Heidelberg University Hospital)

  • Evan Calabrese

    (University of California San Francisco)

  • Jeffrey Rudie

    (University of California San Francisco)

  • Javier Villanueva-Meyer

    (University of California San Francisco)

  • Soonmee Cha

    (University of California San Francisco)

  • Madhura Ingalhalikar

    (Symbiosis International University)

  • Manali Jadhav

    (Symbiosis International University)

  • Umang Pandey

    (Symbiosis International University)

  • Jitender Saini

    (National Institute of Mental Health and Neurosciences)

  • John Garrett

    (University of Wisconsin
    University of Wisconsin)

  • Matthew Larson

    (University of Wisconsin)

  • Robert Jeraj

    (University of Wisconsin
    University of Wisconsin)

  • Stuart Currie

    (Department of Radiology)

  • Russell Frood

    (Department of Radiology)

  • Kavi Fatania

    (Department of Radiology)

  • Raymond Y. Huang

    (Harvard Medical School)

  • Ken Chang

    (Massachusetts General Hospital)

  • Carmen Balaña

    (Catalan Institute of Oncology)

  • Jaume Capellades

    (Consorci MAR Parc de Salut de Barcelona)

  • Josep Puig

    (Josep Trueta University Hospital)

  • Johannes Trenkler

    (Kepler University Hospital Linz)

  • Josef Pichler

    (Kepler University Hospital Linz)

  • Georg Necker

    (Kepler University Hospital Linz)

  • Andreas Haunschmidt

    (Kepler University Hospital Linz)

  • Stephan Meckel

    (Kepler University Hospital Linz
    RKH Klinikum Ludwigsburg)

  • Gaurav Shukla

    (University of Pennsylvania
    Christiana Care Health System)

  • Spencer Liem

    (Thomas Jefferson University)

  • Gregory S. Alexander

    (University of Maryland)

  • Joseph Lombardo

    (Thomas Jefferson University
    Thomas Jefferson University)

  • Joshua D. Palmer

    (The Ohio State University Comprehensive Cancer Center)

  • Adam E. Flanders

    (Thomas Jefferson University)

  • Adam P. Dicker

    (Thomas Jefferson University)

  • Haris I. Sair

    (Johns Hopkins University School of Medicine
    Johns Hopkins University)

  • Craig K. Jones

    (Johns Hopkins University)

  • Archana Venkataraman

    (Johns Hopkins University)

  • Meirui Jiang

    (The Chinese University of Hong Kong)

  • Tiffany Y. So

    (The Chinese University of Hong Kong)

  • Cheng Chen

    (The Chinese University of Hong Kong)

  • Pheng Ann Heng

    (The Chinese University of Hong Kong)

  • Qi Dou

    (The Chinese University of Hong Kong)

  • Michal Kozubek

    (Faculty of Informatics, Masaryk University)

  • Filip Lux

    (Faculty of Informatics, Masaryk University)

  • Jan Michálek

    (Faculty of Informatics, Masaryk University)

  • Petr Matula

    (Faculty of Informatics, Masaryk University)

  • Miloš Keřkovský

    (Masaryk University, Brno and University Hospital Brno)

  • Tereza Kopřivová

    (Masaryk University, Brno and University Hospital Brno)

  • Marek Dostál

    (Masaryk University, Brno and University Hospital Brno
    Masaryk University)

  • Václav Vybíhal

    (Masaryk University, Brno, and University Hospital and Czech Republic)

  • Michael A. Vogelbaum

    (H. Lee Moffitt Cancer Center and Research Institute)

  • J. Ross Mitchell

    (University of Alberta
    Alberta Machine Intelligence Institute)

  • Joaquim Farinhas

    (H. Lee Moffitt Cancer Center and Research Institute)

  • Joseph A. Maldjian

    (University of Texas Southwestern Medical Center)

  • Chandan Ganesh Bangalore Yogananda

    (University of Texas Southwestern Medical Center)

  • Marco C. Pinho

    (University of Texas Southwestern Medical Center)

  • Divya Reddy

    (University of Texas Southwestern Medical Center)

  • James Holcomb

    (University of Texas Southwestern Medical Center)

  • Benjamin C. Wagner

    (University of Texas Southwestern Medical Center)

  • Benjamin M. Ellingson

    (University of California Los Angeles
    University of California Los Angeles)

  • Timothy F. Cloughesy

    (University of California Los Angeles)

  • Catalina Raymond

    (University of California Los Angeles)

  • Talia Oughourlian

    (University of California Los Angeles
    University of California Los Angeles)

  • Akifumi Hagiwara

    (University of California Los Angeles)

  • Chencai Wang

    (University of California Los Angeles)

  • Minh-Son To

    (Flinders University
    Flinders Medical Centre)

  • Sargam Bhardwaj

    (Flinders University)

  • Chee Chong

    (Flinders Medical Centre)

  • Marc Agzarian

    (Flinders Medical Centre
    Baylor College of Medicine)

  • Alexandre Xavier Falcão

    (University of Campinas)

  • Samuel B. Martins

    (Federal Institute of São Paulo)

  • Bernardo C. A. Teixeira

    (Instituto de Neurologia de Curitiba
    Hospital de Clínicas da Universidade Federal do Paraná, Curitiba)

  • Flávia Sprenger

    (Hospital de Clínicas da Universidade Federal do Paraná, Curitiba)

  • David Menotti

    (Universidade Federal do Paraná, Curitiba)

  • Diego R. Lucio

    (Universidade Federal do Paraná, Curitiba)

  • Pamela LaMontagne

    (Washington University in St. Louis)

  • Daniel Marcus

    (Washington University in St. Louis)

  • Benedikt Wiestler

    (Technical University of Munich
    Klinikum rechts der Isar)

  • Florian Kofler

    (Technical University of Munich
    Klinikum rechts der Isar
    Technical University of Munich)

  • Ivan Ezhov

    (Technical University of Munich
    Klinikum rechts der Isar
    Technical University of Munich)

  • Marie Metz

    (Technical University of Munich)

  • Rajan Jain

    (NYU Grossman School of Medicine
    NYU Grossman School of Medicine)

  • Matthew Lee

    (NYU Grossman School of Medicine)

  • Yvonne W. Lui

    (NYU Grossman School of Medicine)

  • Richard McKinley

    (University of Bern)

  • Johannes Slotboom

    (University of Bern)

  • Piotr Radojewski

    (University of Bern)

  • Raphael Meier

    (University of Bern)

  • Roland Wiest

    (University of Bern)

  • Derrick Murcia

    (Anschutz Medical Campus, University of Colorado)

  • Eric Fu

    (Anschutz Medical Campus, University of Colorado)

  • Rourke Haas

    (Anschutz Medical Campus, University of Colorado)

  • John Thompson

    (Anschutz Medical Campus, University of Colorado)

  • David Ryan Ormond

    (Anschutz Medical Campus, University of Colorado)

  • Chaitra Badve

    (University Hospitals Cleveland)

  • Andrew E. Sloan

    (University Hospitals-Seidman Cancer Center
    Case Comprehensive Cancer Center
    Case Western Reserve University School of Medicine)

  • Vachan Vadmal

    (Case Western Reserve University School of Medicine)

  • Kristin Waite

    (Division of Cancer Epidemiology and Genetics)

  • Rivka R. Colen

    (University of Pittsburgh
    University of Texas MD Anderson Cancer Center)

  • Linmin Pei

    (University of Pittsburgh Medical Center)

  • Murat Ak

    (University of Pittsburgh)

  • Ashok Srinivasan

    (University of Michigan)

  • J. Rajiv Bapuraj

    (University of Michigan)

  • Arvind Rao

    (University of Michigan)

  • Nicholas Wang

    (University of Michigan)

  • Ota Yoshiaki

    (University of Michigan)

  • Toshio Moritani

    (University of Michigan)

  • Sevcan Turk

    (University of Michigan)

  • Joonsang Lee

    (University of Michigan)

  • Snehal Prabhudesai

    (University of Michigan)

  • Fanny Morón

    (Baylor College of Medicine)

  • Jacob Mandel

    (Baylor College of Medicine)

  • Konstantinos Kamnitsas

    (Imperial College London
    University of Oxford)

  • Ben Glocker

    (Imperial College London)

  • Luke V. M. Dixon

    (Imperial College NHS Healthcare Trust)

  • Matthew Williams

    (Imperial College London)

  • Peter Zampakis

    (University of Patras)

  • Vasileios Panagiotopoulos

    (University of Patras)

  • Panagiotis Tsiganos

    (University of Patras)

  • Sotiris Alexiou

    (University of Patras)

  • Ilias Haliassos

    (University of Patras)

  • Evangelia I. Zacharaki

    (University of Patras)

  • Konstantinos Moustakas

    (University of Patras)

  • Christina Kalogeropoulou

    (University of Patras)

  • Dimitrios M. Kardamakis

    (University of Patras)

  • Yoon Seong Choi

    (Yonsei University College of Medicine)

  • Seung-Koo Lee

    (Yonsei University College of Medicine)

  • Jong Hee Chang

    (Yonsei University College of Medicine)

  • Sung Soo Ahn

    (Yonsei University College of Medicine)

  • Bing Luo

    (Henry Ford Health System)

  • Laila Poisson

    (Henry Ford Health System)

  • Ning Wen

    (Henry Ford Health System
    Shanghai Jiao Tong University School of Medicine)

  • Pallavi Tiwari

    (Case Western Reserve University)

  • Ruchika Verma

    (Alberta Machine Intelligence Institute
    Case Western Reserve University)

  • Rohan Bareja

    (Case Western Reserve University)

  • Ipsa Yadav

    (Case Western Reserve University)

  • Jonathan Chen

    (Case Western Reserve University)

  • Neeraj Kumar

    (University of Alberta
    Alberta Machine Intelligence Institute)

  • Marion Smits

    (Erasmus MC University Medical Centre Rotterdam)

  • Sebastian R. Voort

    (Erasmus MC University Medical Centre Rotterdam)

  • Ahmed Alafandi

    (Erasmus MC University Medical Centre Rotterdam)

  • Fatih Incekara

    (Erasmus MC University Medical Centre Rotterdam
    Erasmus MC University Medical Centre Rotterdam)

  • Maarten M. J. Wijnenga

    (Brain Tumor Center, Erasmus MC Cancer Institute)

  • Georgios Kapsas

    (Erasmus MC University Medical Centre Rotterdam)

  • Renske Gahrmann

    (Erasmus MC University Medical Centre Rotterdam)

  • Joost W. Schouten

    (Erasmus MC University Medical Centre Rotterdam)

  • Hendrikus J. Dubbink

    (Brain Tumor Center, Erasmus MC Cancer Institute)

  • Arnaud J. P. E. Vincent

    (Erasmus MC University Medical Centre Rotterdam)

  • Martin J. Bent

    (Brain Tumor Center, Erasmus MC Cancer Institute)

  • Pim J. French

    (Brain Tumor Center, Erasmus MC Cancer Institute)

  • Stefan Klein

    (Erasmus MC University Medical Centre Rotterdam)

  • Yading Yuan

    (Icahn School of Medicine at Mount Sinai)

  • Sonam Sharma

    (Icahn School of Medicine at Mount Sinai)

  • Tzu-Chi Tseng

    (Icahn School of Medicine at Mount Sinai)

  • Saba Adabi

    (Icahn School of Medicine at Mount Sinai)

  • Simone P. Niclou

    (Luxembourg Institute of Health)

  • Olivier Keunen

    (Luxembourg Institute of Health)

  • Ann-Christin Hau

    (Luxembourg Institute of Health
    Laboratoire National De Santé)

  • Martin Vallières

    (Université de Sherbrooke
    Centre de Recherche du Centre Hospitalière Universitaire de Sherbrooke)

  • David Fortin

    (Centre de Recherche du Centre Hospitalière Universitaire de Sherbrooke
    Université de Sherbrooke)

  • Martin Lepage

    (Centre de Recherche du Centre Hospitalière Universitaire de Sherbrooke
    Sherbrooke Molecular Imaging Centre, Université de Sherbrooke)

  • Bennett Landman

    (Vanderbilt University)

  • Karthik Ramadass

    (Vanderbilt University)

  • Kaiwen Xu

    (Vanderbilt University)

  • Silky Chotai

    (Vanderbilt University Medical Center)

  • Lola B. Chambless

    (Vanderbilt University Medical Center)

  • Akshitkumar Mistry

    (Vanderbilt University Medical Center)

  • Reid C. Thompson

    (Vanderbilt University Medical Center)

  • Yuriy Gusev

    (Georgetown University)

  • Krithika Bhuvaneshwar

    (Georgetown University)

  • Anousheh Sayah

    (MedStar Georgetown University Hospital)

  • Camelia Bencheqroun

    (Georgetown University)

  • Anas Belouali

    (Georgetown University)

  • Subha Madhavan

    (Georgetown University)

  • Thomas C. Booth

    (King’s College London
    Ruskin Wing, King’s College Hospital NHS Foundation Trust)

  • Alysha Chelliah

    (King’s College London)

  • Marc Modat

    (King’s College London)

  • Haris Shuaib

    (Stoke Mandeville Hospital
    Queen’s University)

  • Carmen Dragos

    (Stoke Mandeville Hospital)

  • Aly Abayazeed

    (Neosoma Inc.)

  • Kenneth Kolodziej

    (Neosoma Inc.)

  • Michael Hill

    (Neosoma Inc.)

  • Ahmed Abbassy

    (University of Cairo School of Medicine)

  • Shady Gamal

    (University of Cairo School of Medicine)

  • Mahmoud Mekhaimar

    (University of Cairo School of Medicine)

  • Mohamed Qayati

    (University of Cairo School of Medicine)

  • Mauricio Reyes

    (University of Bern)

  • Ji Eun Park

    (Asan Medical Center)

  • Jihye Yun

    (Asan Medical Center)

  • Ho Sung Kim

    (Asan Medical Center)

  • Abhishek Mahajan

    (The Clatterbridge Cancer Centre NHS Foundation Trust Pembroke Place)

  • Mark Muzi

    (University of Washington)

  • Sean Benson

    (Netherlands Cancer Institute)

  • Regina G. H. Beets-Tan

    (Netherlands Cancer Institute
    GROW School of Oncology and Developmental Biology)

  • Jonas Teuwen

    (Netherlands Cancer Institute)

  • Alejandro Herrera-Trujillo

    (Clínica Imbanaco Grupo Quirón Salud
    Universidad del Valle)

  • Maria Trujillo

    (Universidad del Valle)

  • William Escobar

    (Clínica Imbanaco Grupo Quirón Salud
    Universidad del Valle)

  • Ana Abello

    (Universidad del Valle)

  • Jose Bernal

    (Universidad del Valle
    The University of Edinburgh)

  • Jhon Gómez

    (Universidad del Valle)

  • Joseph Choi

    (University of Iowa)

  • Stephen Baek

    (University of Iowa)

  • Yusung Kim

    (University of Iowa)

  • Heba Ismael

    (University of Iowa)

  • Bryan Allen

    (University of Iowa)

  • John M. Buatti

    (University of Iowa)

  • Aikaterini Kotrotsou

    (University of Texas)

  • Hongwei Li

    (University of Zurich)

  • Tobias Weiss

    (University Hospital Zurich and University of Zurich)

  • Michael Weller

    (University Hospital Zurich and University of Zurich)

  • Andrea Bink

    (University Hospital Zurich and University of Zurich)

  • Bertrand Pouymayou

    (University Hospital Zurich and University of Zurich)

  • Hassan F. Shaykh

    (University of Alabama in Birmingham)

  • Joel Saltz

    (Stony Brook University, Stony Brook)

  • Prateek Prasanna

    (Stony Brook University, Stony Brook)

  • Sampurna Shrestha

    (Stony Brook University, Stony Brook)

  • Kartik M. Mani

    (Stony Brook University, Stony Brook
    Stony Brook University)

  • David Payne

    (Stony Brook University)

  • Tahsin Kurc

    (Stony Brook University, Stony Brook
    Oak Ridge National Laboratory)

  • Enrique Pelaez

    (Escuela Superior Politecnica del Litoral)

  • Heydy Franco-Maldonado

    (Sociedad de Lucha Contral el Cancer - SOLCA, Guayaquil Ecuador)

  • Francis Loayza

    (Escuela Superior Politecnica del Litoral)

  • Sebastian Quevedo

    (Universidad Católica de Cuenca)

  • Pamela Guevara

    (Universidad de Concepción)

  • Esteban Torche

    (Universidad de Concepción)

  • Cristobal Mendoza

    (Universidad de Concepción)

  • Franco Vera

    (Universidad de Concepción)

  • Elvis Ríos

    (Universidad de Concepción)

  • Eduardo López

    (Universidad de Concepción)

  • Sergio A. Velastin

    (Queen Mary University of London)

  • Godwin Ogbole

    (University College Hospital Ibadan)

  • Mayowa Soneye

    (University College Hospital Ibadan)

  • Dotun Oyekunle

    (University College Hospital Ibadan)

  • Olubunmi Odafe-Oyibotha

    (Clinix Healthcare, Lagos)

  • Babatunde Osobu

    (University College Hospital Ibadan)

  • Mustapha Shu’aibu

    (Muhammad Abdullahi Wase Teaching Hospital)

  • Adeleye Dorcas

    (Obafemi Awolowo University Ile-Ife)

  • Farouk Dako

    (University of Pennsylvania
    University of Pennsylvania)

  • Amber L. Simpson

    (Queen’s University
    Queen’s University)

  • Mohammad Hamghalam

    (Queen’s University
    Islamic Azad University)

  • Jacob J. Peoples

    (Queen’s University)

  • Ricky Hu

    (Queen’s University)

  • Anh Tran

    (Queen’s University)

  • Danielle Cutler

    (Queen’s University)

  • Fabio Y. Moraes

    (Queen’s University)

  • Michael A. Boss

    (American College of Radiology)

  • James Gimpel

    (American College of Radiology)

  • Deepak Kattil Veettil

    (American College of Radiology)

  • Kendall Schmidt

    (American College of Radiology)

  • Brian Bialecki

    (American College of Radiology)

  • Sailaja Marella

    (American College of Radiology)

  • Cynthia Price

    (American College of Radiology)

  • Lisa Cimino

    (American College of Radiology)

  • Charles Apgar

    (American College of Radiology)

  • Prashant Shah

    (Intel Corporation)

  • Bjoern Menze

    (Technical University of Munich
    University of Zurich)

  • Jill S. Barnholtz-Sloan

    (Division of Cancer Epidemiology and Genetics
    National Institute of Health)

  • Jason Martin

    (Intel Corporation)

  • Spyridon Bakas

    (University of Pennsylvania
    University of Pennsylvania
    University of Pennsylvania)

Abstract

Although machine learning (ML) has shown promise across disciplines, out-of-sample generalizability is concerning. This is currently addressed by sharing multi-site data, but such centralization is challenging/infeasible to scale due to various limitations. Federated ML (FL) provides an alternative paradigm for accurate and generalizable ML, by only sharing numerical model updates. Here we present the largest FL study to-date, involving data from 71 sites across 6 continents, to generate an automatic tumor boundary detector for the rare disease of glioblastoma, reporting the largest such dataset in the literature (n = 6, 314). We demonstrate a 33% delineation improvement for the surgically targetable tumor, and 23% for the complete tumor extent, over a publicly trained model. We anticipate our study to: 1) enable more healthcare studies informed by large diverse data, ensuring meaningful results for rare diseases and underrepresented populations, 2) facilitate further analyses for glioblastoma by releasing our consensus model, and 3) demonstrate the FL effectiveness at such scale and task-complexity as a paradigm shift for multi-site collaborations, alleviating the need for data-sharing.

Suggested Citation

  • Sarthak Pati & Ujjwal Baid & Brandon Edwards & Micah Sheller & Shih-Han Wang & G. Anthony Reina & Patrick Foley & Alexey Gruzdev & Deepthi Karkada & Christos Davatzikos & Chiharu Sako & Satyam Ghodasa, 2022. "Federated learning enables big data for rare cancer boundary detection," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33407-5
    DOI: 10.1038/s41467-022-33407-5
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    Cited by:

    1. Qi Chang & Zhennan Yan & Mu Zhou & Hui Qu & Xiaoxiao He & Han Zhang & Lohendran Baskaran & Subhi Al’Aref & Hongsheng Li & Shaoting Zhang & Dimitris N. Metaxas, 2023. "Mining multi-center heterogeneous medical data with distributed synthetic learning," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Shengyu Tao & Haizhou Liu & Chongbo Sun & Haocheng Ji & Guanjun Ji & Zhiyuan Han & Runhua Gao & Jun Ma & Ruifei Ma & Yuou Chen & Shiyi Fu & Yu Wang & Yaojie Sun & Yu Rong & Xuan Zhang & Guangmin Zhou , 2023. "Collaborative and privacy-preserving retired battery sorting for profitable direct recycling via federated machine learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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