Infrastructure for synthetic health data

Abstract

Machine learning (ML) methods are becoming ever more prevalent across all domains of lifesciences. However, a key component of effective ML is the availability of large datasets thatare diverse and representative. In the context of health systems, with significant heterogeneityof clinical phenotypes and diversity of healthcare systems, there exists a necessity to developand refine unbiased and fair ML models. Synthetic data are increasingly being used to protectthe patient’s right to privacy and overcome the paucity of annotated open-access medical data. Here, we present our proof of concept for the generation of synthetic health data and our proposed FAIR implementation of the generated synthetic datasets. The work was developed during and after the one-week-long BioHackathon Europe, by together 20 participants (10 new to the project), from different countries (NL, ES, LU, UK, GR, FL, DE, . . . ).

Authors 15

1. Núria Queralt-Rosiñach Aachen Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Human Genetics , Leiden University Medical Center , Leiden , Netherlands

   Human Genetics, Leiden University Medical Center, Leiden, Netherlands

2. Basel Alshaikhdeeb

   University of Luxembourg · Luxembourg Centre for Systems Biomedicine

   Affiliation as printed

   Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

   Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

3. Luca Bolzani

   University of Luxembourg · Luxembourg Centre for Systems Biomedicine

   Affiliation as printed

   Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

   Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

4. Muhammad Muneeb Shoaib

   University of Luxembourg · Luxembourg Centre for Systems Biomedicine

   Affiliation as printed

   Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

   Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

5. Marcos Casado Barbero

   European Bioinformatics Institute

   Affiliation as printed

   European Molecular Biology Laboratory -European Bioinformatics Institute (EMBL-EBI) , Hinxton CB10 1SD , UK

   European Molecular Biology Laboratory -European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK

6. Sergi Aguiló‐Castillo

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center , Barcelona , Spain

   Barcelona Supercomputing Center, Barcelona, Spain

7. Davide Cirillo

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center , Barcelona , Spain

   Barcelona Supercomputing Center, Barcelona, Spain

8. Leyla Jael Castro

   ZB MED - Information Centre for Life Sciences

   Affiliation as printed

   ZB MED Information Centre for Life Sciences , Cologne , Germany

   ZB MED Information Centre for Life Sciences, Cologne, Germany

9. Ginger Tsueng

   Scripps Research Institute

   Affiliation as printed

   Scripps Research Institute , La Jolla , CA 92037 , US

   Scripps Research Institute, La Jolla, CA 92037, US

10. Matúš Kalaš

    University of Bergen

    Affiliation as printed

    Department of Informatics , University of Bergen , Norway

    Department of Informatics, University of Bergen, Norway

11. Magnus Palmblad Aachen Center for Proteomics and Metabolomics

    Leiden University Medical Center

    Affiliation as printed

    BioHackathon Europe 2022 Paris , France

    Center for Proteomics and Metabolomics , Leiden University Medical Center , Leiden , Netherlands

    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands

12. Danielle Welter

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

    Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

13. Soumyabrata Ghosh

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

    Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

14. Venkata Satagopam

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Center for Systems Biomedicine , University of Luxembourg , Luxembourg

    Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg

15. Rahuman S. Malik‐Sheriff

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory -European Bioinformatics Institute (EMBL-EBI) , Hinxton CB10 1SD , UK

    European Molecular Biology Laboratory -European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK