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Record W4310852955 · doi:10.1038/s41467-022-33407-5

Federated learning enables big data for rare cancer boundary detection

2022· article· en· W4310852955 on OpenAlexafffund
Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih‐Han Wang, G. Anthony Reina, Patrick Foley, А. Д. Груздев, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Kickingereder, Gianluca Brugnara, Chandrakanth Jayachandran Preetha, Felix Sahm, Klaus Maier‐Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey D. Rudie, Javier Villanueva‐Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John W. Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balañá, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph S. Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng‐Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim M. Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James Holcomb, Benjamin Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia C. Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh‐Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre X. Falcão, Samuel Botter Martins, Bernardo Corrêa de Almeida Teixeira, F Sprenger, David Menotti, Diego Rafael Lucio, Pamela LaMontagne, Daniel S. Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W. Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphaël Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John F. Thompson, D. Ryan Ormond, Chaitra Badve, Andrew E. Sloan, Vachan Vadmal, Kristin Waite, Rivka R. Colen, Linmin Pei, Murat Ak, Ashok Srinivasan, Jayapalli Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Yoshiaki Ota, Toshio Moritani, Sevcan Türk, Joonsang Lee, Snehal Prabhudesai, Fanny Morón, Jacob Mandel, Konstantinos Kamnitsas, Ben Glocker, Luke Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I. Zacharaki, Κωνσταντίνος Μουστάκας, Christina Kalogeropoulou, Dimitrios Kardamakis, Yoon Seong Choi, Seung‐Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R. van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten M.J. Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W. Schouten, Hendrikus J. Dubbink, Arnaud J.P.E. Vincent, Martin J. van den Bent, Pim J. French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P. Niclou, Olivier Keunen, Ann‐Christin Hau, Martin Vallières, David Fortin, Martin Lepage, Bennett A. Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B. Chambless, Akshitkumar M. Mistry, Reid C. Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C. Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael D. Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, S. Benson, Regina G. H. Beets‐Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, María Trujillo, William Escobar, Ana Lorena Abello, José Bernal, Jhon Gómez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan G. Allen, John M. Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiß, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F. Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik Mani, David Payne, Tahsin Kurç, Enrique Peláez, Heydy Franco-Maldonado, Francis R. Loayza, Sebastián Quevedo, Pamela Guevara, Esteban Torche, Cristóbal Mendoza, Franco Vera, Elvis Ríos, Eduardo López, Sergio A. Velastín, Godwin Ogbole, Mayowa Soneye, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu’aibu, Adeleye Dorcas, Farouk Dako, Amber L. Simpson, Mohammad Hamghalam, Jacob Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fábio Ynoe de Moraes, Michael A. Boss, James F. Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S. Barnholtz‐Sloan, Jason Martin, Spyridon Bakas

Bibliographic record

VenueNature Communications · 2022
Typearticle
Languageen
FieldMedicine
TopicGlioma Diagnosis and Treatment
Canadian institutionsQueen's UniversityCentre Hospitalier Universitaire de SherbrookeUniversité de SherbrookeUniversity of Alberta
FundersDOD Peer Reviewed Cancer Research ProgramCHIST-ERAFP7 People: Marie-Curie ActionsDavid Geffen School of Medicine, University of California, Los AngelesNational Center for Advancing Translational SciencesNational Institute of Biomedical Imaging and BioengineeringNational Institute of Mental HealthMedical Research CouncilAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalWhiting School of Engineering, Johns Hopkins UniversityAnschutz Medical Campus, University of ColoradoPerelman School of Medicine, University of PennsylvaniaMedical Center, University of PittsburghNational Institutes of HealthUniversitätsklinikum HeidelbergLékařská fakulta, Masarykova univerzitaMasarykova UniverzitaUniversidade Federal do ParanáDeutsche ForschungsgemeinschaftTechnische Universität MünchenNYU Grossman School of MedicineCase Comprehensive Cancer Center, Case Western Reserve UniversityDeutsches KrebsforschungszentrumFonds National de la Recherche LuxembourgEngineering and Physical Sciences Research CouncilEuropean CommissionFundação de Amparo à Pesquisa do Estado de São PauloFlinders UniversityMoffitt Cancer CenterNational Institute of Mental Health and NeurosciencesSchweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungUniversity of OxfordRadiological Society of North AmericaKepler UniversitätsklinikumUniversity of BernMinisterstvo Zdravotnictví Ceské RepublikyImperial College LondonUniversity of AlbertaNational Institute of Neurological Disorders and StrokeCanadian Institute for Advanced ResearchInselspital, Universitätsspital BernNational Cancer InstituteAlberta Machine Intelligence InstituteKWF KankerbestrijdingU.S. Department of DefenseCancer Research UKVarian Medical SystemsWellcome TrustAgenția Națională pentru Cercetare și DezvoltareThomas Jefferson UniversitySchool of Medicine, Case Western Reserve UniversityWashington University in St. LouisUniversity of PittsburghJohns Hopkins UniversityOhio State UniversityUniversity of Texas MD Anderson Cancer CenterCentre d'Imagerie BioMédicaleConselho Nacional de Desenvolvimento Científico e TecnológicoUK Research and InnovationDeutschen Konsortium für Translationale KrebsforschungOhio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research InstituteNational Science FoundationCase Western Reserve UniversityChinese University of Hong KongMassachusetts General HospitalUniversity of PennsylvaniaAmerican College of Radiology Imaging NetworkUniversity of California, Los AngelesIntel CorporationV Foundation for Cancer ResearchU.S. National Library of MedicineAgencia Nacional de Investigación y DesarrolloBrigham and Women's Hospital
KeywordsGeneralizability theoryComputer scienceGlioblastomaMachine learningData sharingScale (ratio)Sample (material)Task (project management)Data scienceArtificial intelligenceBig dataData miningMedicinePsychology

Abstract

fetched live from OpenAlex

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.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesScience and technology studies
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.852
Threshold uncertainty score0.999

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0020.000
Scholarly communication0.0000.000
Open science0.0000.001
Research integrity0.0000.001
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.075
GPT teacher head0.355
Teacher spread0.280 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one teacher head, not a consensus.

Study designNot applicable
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations340
Published2022
Admission routes2
Has abstractyes

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