Federated learning enables big data for rare cancer boundary detection.
Journal: Nature communications
Volume: 13
Issue: 1
Year of Publication: 2022
Affiliated Institutions: Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA, USA. Intel Corporation, Santa Clara, CA, USA. Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany. Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ), Heidelberg, Germany. Division of Medical Image Computing, German Cancer Research Center, Heidelberg, Germany. Department of Radiology & Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA. Symbiosis Center for Medical Image Analysis, Symbiosis International University, Pune, Maharashtra, India. Department of Neuroimaging and Interventional Radiology, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India. Department of Radiology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA. Leeds Teaching Hospitals Trust, Department of Radiology, Leeds, UK. Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA. Catalan Institute of Oncology, Badalona, Spain. Consorci MAR Parc de Salut de Barcelona, Catalonia, Spain. Department of Radiology (IDI), Girona Biomedical Research Institute (IdIBGi), Josep Trueta University Hospital, Girona, Spain. Institute of Neuroradiology, Neuromed Campus (NMC), Kepler University Hospital Linz, Linz, Austria. Department of Neurooncology, Neuromed Campus (NMC), Kepler University Hospital Linz, Linz, Austria. Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. Department of Radiation Oncology, University of Maryland, Baltimore, MD, USA. Department of Radiation Oncology, The James Cancer Hospital and Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. Department of Radiology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA. Department of Radiation Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA. The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA. The Malone Center for Engineering in Healthcare, The Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA. Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA. The Chinese University of Hong Kong, Hong Kong, China. Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Department of Radiology and Nuclear Medicine, Faculty of Medicine, Masaryk University, Brno and University Hospital Brno, Brno, Czech Republic. Department of Neurosurgery, Faculty of Medicine, Masaryk University, Brno, and University Hospital and Czech Republic, Brno, Czech Republic. Department of Neuro Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. University of Alberta, Edmonton, AB, Canada. Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. University of Texas Southwestern Medical Center, Dallas, TX, USA. UCLA Brain Tumor Imaging Laboratory (BTIL), Center for Computer Vision and Imaging Biomarkers, Department of Radiological Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. UCLA Neuro-Oncology Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CaA, USA. Department of Radiological Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia. South Australia Medical Imaging, Flinders Medical Centre, Bedford Park, SA, Australia. Institute of Computing, University of Campinas, Campinas, São Paulo, Brazil. Federal Institute of São Paulo, Campinas, São Paulo, Brazil. Instituto de Neurologia de Curitiba, Curitiba, Paraná, Brazil. Department of Radiology, Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, Paraná, Brazil. Department of Informatics, Universidade Federal do Paraná, Curitiba, Paraná, Brazil. Department of Radiology, Washington University in St. Louis, St. Louis, MO, USA. Department of Diagnostic and Interventional Neuroradiology, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany. Department of Informatics, Technical University of Munich, Munich, Bavaria, Germany. Department of Radiology, NYU Grossman School of Medicine, New York, NY, USA. Support Center for Advanced Neuroimaging, University Institute of Diagnostic and Interventional Neuroradiology, University Hospital Bern, Inselspital, University of Bern, Bern, Switzerland. Department of Neurosurgery, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA. Department of Radiology, University Hospitals Cleveland, Cleveland, OH, USA. Department of Neurological Surgery, University Hospitals-Seidman Cancer Center, Cleveland, OH, USA. Department of Neurosurgery, Case Western Reserve University School of Medicine, Cleveland, OH, USA. National Cancer Institute, National Institute of Health, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA. Department of Radiology, Neuroradiology Division, University of Pittsburgh, Pittsburgh, PA, USA. University of Pittsburgh Medical Center, Pittsburgh, PA, USA. Department of Neuroradiology, University of Michigan, Ann Arbor, MI, USA. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. Department of Radiology, Baylor College of Medicine, Houston, TX, USA. Department of Neurology, Baylor College of Medicine, Houston, TX, USA. Department of Computing, Imperial College London, London, UK. Department of Radiology, Imperial College NHS Healthcare Trust, London, UK. Computational Oncology Group, Institute for Global Health Innovation, Imperial College London, London, UK. Department of NeuroRadiology, University of Patras, Patras, Greece. Department of Neurosurgery, University of Patras, Patras, Greece. Clinical Radiology Laboratory, Department of Medicine, University of Patras, Patras, Greece. Department of Electrical and Computer Engineering, University of Patras, Patras, Greece. Department of Neuro-Oncology, University of Patras, Patras, Greece. Department of Radiation Oncology, University of Patras, Patras, Greece. Yonsei University College of Medicine, Seoul, Korea. Department of Radiation Oncology, Henry Ford Health System, Detroit, MI, USA. Public Health Sciences, Henry Ford Health System, Detroit, MI, USA. Case Western Reserve University, Cleveland, OH, USA. Alberta Machine Intelligence Institute, Edmonton, AB, Canada. Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Centre Rotterdam, Rotterdam, Netherlands. Department of Neurology, Brain Tumor Center, Erasmus MC Cancer Institute, Rotterdam, Netherlands. Department of Neurosurgery, Brain Tumor Center, Erasmus MC University Medical Centre Rotterdam, Rotterdam, Netherlands. Department of Pathology, Brain Tumor Center, Erasmus MC Cancer Institute, Rotterdam, Netherlands. Biomedical Imaging Group Rotterdam, Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Centre Rotterdam, Rotterdam, Netherlands. Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg. Translation Radiomics, Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, Luxembourg. Department of Computer Science, Université de Sherbrooke, Sherbrooke, QC, Canada. Centre de Recherche du Centre Hospitalière Universitaire de Sherbrooke, Sherbrooke, QC, Canada. Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA. Department of Computer Science, Vanderbilt University, Nashville, TN, USA. Department of Neurosurgery, Vanderbilt University Medical Center, Nashville, TN, USA. Innovation Center for Biomedical Informatics (ICBI), Georgetown University, Washington, DC, USA. Division of Neuroradiology & Neurointerventional Radiology, Department of Radiology, MedStar Georgetown University Hospital, Washington, DC, USA. School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK. Stoke Mandeville Hospital, Mandeville Road, Aylesbury, UK. Neosoma Inc., Groton, MA, USA. University of Cairo School of Medicine, Giza, Egypt. University of Bern, Bern, Switzerland. Department of Radiology, Asan Medical Center, Seoul, South Korea. The Clatterbridge Cancer Centre NHS Foundation Trust Pembroke Place, Liverpool, UK. Department of Radiology, University of Washington, Seattle, WA, USA. Netherlands Cancer Institute, Amsterdam, Netherlands. Department of Radiology, Netherlands Cancer Institute, Amsterdam, Netherlands. Clínica Imbanaco Grupo Quirón Salud, Cali, Colombia. Universidad del Valle, Cali, Colombia. Department of Industrial and Systems Engineering, University of Iowa, Iowa, USA. Department of Industrial and Systems Engineering, Department of Radiation Oncology, University of Iowa, Iowa City, IA, USA. Department of Radiation Oncology, University of Iowa, Iowa City, IA, USA. MD Anderson Cancer Center, University of Texas, Houston, TX, USA. Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland. Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland. Department of Neuroradiology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland. University of Alabama in Birmingham, Birmingham, AL, USA. Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA. Department of Radiology, Stony Brook University, Stony Brook, NY, USA. Escuela Superior Politecnica del Litoral, Guayaquil, Guayas, Ecuador. Sociedad de Lucha Contral el Cancer - SOLCA, Guayaquil Ecuador, Guayaquil, Ecuador. Universidad Católica de Cuenca, Cuenca, Ecuador. Universidad de Concepción, Concepción, Biobío, Chile. School of Electronic Engineering and Computer Science, Queen Mary University of London, London, UK. Department of Radiology, University College Hospital Ibadan, Oyo, Nigeria. Clinix Healthcare, Lagos, Lagos, Nigeria. Department of Radiology, Muhammad Abdullahi Wase Teaching Hospital, Kano, Nigeria. Department of Radiology, Obafemi Awolowo University Ile-Ife, Ile-Ife, Osun, Nigeria. Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada. School of Computing, Queen's University, Kingston, ON, Canada. The Faculty of Arts & Sciences, Queen's University, Kingston, ON, Canada. Department of Oncology, Queen's University, Kingston, ON, Canada. Center for Research and Innovation, American College of Radiology, Philadelphia, PA, USA. Data Science Institute, American College of Radiology, Reston, VA, USA. Center for Biomedical Image Computing and Analytics (CBICA), University of Pennsylvania, Philadelphia, PA, USA. sbakas@upenn.edu.
Abstract summary
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.Authors & Co-authors: Pati Sarthak S Baid Ujjwal U Edwards Brandon B Sheller Micah M Wang Shih-Han SH Reina G Anthony GA Foley Patrick P Gruzdev Alexey A Karkada Deepthi D Davatzikos Christos C Sako Chiharu C Ghodasara Satyam S Bilello Michel M Mohan Suyash S Vollmuth Philipp P Brugnara Gianluca G Preetha Chandrakanth J CJ Sahm Felix F Maier-Hein Klaus K Zenk Maximilian M Bendszus Martin M Wick Wolfgang W Calabrese Evan E Rudie Jeffrey J Villanueva-Meyer Javier J Cha Soonmee S Ingalhalikar Madhura M Jadhav Manali M Pandey Umang U Saini Jitender J Garrett John J Larson Matthew M Jeraj Robert R Currie Stuart S Frood Russell R Fatania Kavi K Huang Raymond Y RY Chang Ken K Balaña Carmen C Capellades Jaume J Puig Josep J Trenkler Johannes J Pichler Josef J Necker Georg G Haunschmidt Andreas A Meckel Stephan S Shukla Gaurav G Liem Spencer S Alexander Gregory S GS Lombardo Joseph J Palmer Joshua D JD Flanders Adam E AE Dicker Adam P AP Sair Haris I HI Jones Craig K CK Venkataraman Archana A Jiang Meirui M So Tiffany Y TY Chen Cheng C Heng Pheng Ann PA Dou Qi Q Kozubek Michal M Lux Filip F Michálek Jan J Matula Petr P Keřkovský Miloš M Kopřivová Tereza T Dostál Marek M Vybíhal Václav V Vogelbaum Michael A MA Mitchell J Ross JR Farinhas Joaquim J Maldjian Joseph A JA Yogananda Chandan Ganesh Bangalore CGB Pinho Marco C MC Reddy Divya D Holcomb James J Wagner Benjamin C BC Ellingson Benjamin M BM Cloughesy Timothy F TF Raymond Catalina C Oughourlian Talia T Hagiwara Akifumi A Wang Chencai C To Minh-Son MS Bhardwaj Sargam S Chong Chee C Agzarian Marc M Falcão Alexandre Xavier AX Martins Samuel B SB Teixeira Bernardo C A BCA Sprenger Flávia F Menotti David D Lucio Diego R DR LaMontagne Pamela P Marcus Daniel D Wiestler Benedikt B Kofler Florian F Ezhov Ivan I Metz Marie M Jain Rajan R Lee Matthew M Lui Yvonne W YW McKinley Richard R Slotboom Johannes J Radojewski Piotr P Meier Raphael R Wiest Roland R Murcia Derrick D Fu Eric E Haas Rourke R Thompson John J Ormond David Ryan DR Badve Chaitra C Sloan Andrew E AE Vadmal Vachan V Waite Kristin K Colen Rivka R RR Pei Linmin L Ak Murat M Srinivasan Ashok A Bapuraj J Rajiv JR Rao Arvind A Wang Nicholas N Yoshiaki Ota O Moritani Toshio T Turk Sevcan S Lee Joonsang J Prabhudesai Snehal S Morón Fanny F Mandel Jacob J Kamnitsas Konstantinos K Glocker Ben B Dixon Luke V M LVM Williams Matthew M Zampakis Peter P Panagiotopoulos Vasileios V Tsiganos Panagiotis P Alexiou Sotiris S Haliassos Ilias I Zacharaki Evangelia I EI Moustakas Konstantinos K Kalogeropoulou Christina C Kardamakis Dimitrios M DM Choi Yoon Seong YS Lee Seung-Koo SK Chang Jong Hee JH Ahn Sung Soo SS Luo Bing B Poisson Laila L Wen Ning N Tiwari Pallavi P Verma Ruchika R Bareja Rohan R Yadav Ipsa I Chen Jonathan J Kumar Neeraj N Smits Marion M van der Voort Sebastian R SR Alafandi Ahmed A Incekara Fatih F Wijnenga Maarten M J MMJ Kapsas Georgios G Gahrmann Renske R Schouten Joost W JW Dubbink Hendrikus J HJ Vincent Arnaud J P E AJPE van den Bent Martin J MJ French Pim J PJ Klein Stefan S Yuan Yading Y Sharma Sonam S Tseng Tzu-Chi TC Adabi Saba S Niclou Simone P SP Keunen Olivier O Hau Ann-Christin AC Vallières Martin M Fortin David D Lepage Martin M Landman Bennett B Ramadass Karthik K Xu Kaiwen K Chotai Silky S Chambless Lola B LB Mistry Akshitkumar A Thompson Reid C RC Gusev Yuriy Y Bhuvaneshwar Krithika K Sayah Anousheh A Bencheqroun Camelia C Belouali Anas A Madhavan Subha S Booth Thomas C TC Chelliah Alysha A Modat Marc M Shuaib Haris H Dragos Carmen C Abayazeed Aly A Kolodziej Kenneth K Hill Michael M Abbassy Ahmed A Gamal Shady S Mekhaimar Mahmoud M Qayati Mohamed M Reyes Mauricio M Park Ji Eun JE Yun Jihye J Kim Ho Sung HS Mahajan Abhishek A Muzi Mark M Benson Sean S Beets-Tan Regina G H RGH Teuwen Jonas J Herrera-Trujillo Alejandro A Trujillo Maria M Escobar William W Abello Ana A Bernal Jose J Gómez Jhon J Choi Joseph J Baek Stephen S Kim Yusung Y Ismael Heba H Allen Bryan B Buatti John M JM Kotrotsou Aikaterini A Li Hongwei H Weiss Tobias T Weller Michael M Bink Andrea A Pouymayou Bertrand B Shaykh Hassan F HF Saltz Joel J Prasanna Prateek P Shrestha Sampurna S Mani Kartik M KM Payne David D Kurc Tahsin T Pelaez Enrique E Franco-Maldonado Heydy H Loayza Francis F Quevedo Sebastian S Guevara Pamela P Torche Esteban E Mendoza Cristobal C Vera Franco F Ríos Elvis E López Eduardo E Velastin Sergio A SA Ogbole Godwin G Soneye Mayowa M Oyekunle Dotun D Odafe-Oyibotha Olubunmi O Osobu Babatunde B Shu'aibu Mustapha M Dorcas Adeleye A Dako Farouk F Simpson Amber L AL Hamghalam Mohammad M Peoples Jacob J JJ Hu Ricky R Tran Anh A Cutler Danielle D Moraes Fabio Y FY Boss Michael A MA Gimpel James J Veettil Deepak Kattil DK Schmidt Kendall K Bialecki Brian B Marella Sailaja S Price Cynthia C Cimino Lisa L Apgar Charles C Shah Prashant P Menze Bjoern B Barnholtz-Sloan Jill S JS Martin Jason J Bakas Spyridon S
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Citations : Mårtensson G, et al. The reliability of a deep learning model in clinical out-of-distribution MRI data: a multicohort study. Med. Image Anal. 2020;66:101714.Authors : 279
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Doi : 7346SSN : 2041-1723