Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany
Malte D. Luecken, Daniel C. Strobl, Luke Zappia, Giovanni Palla, Michaela F. Mueller, Artur Szałata, Yuge Ji & Fabian J. Theis
Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
Malte D. Luecken & Michaela F. Mueller
Immunai, New York, USA
Scott Gigante & Drausin Wulsin
NVIDIA, Santa Clara, CA, USA
Daniel B. Burkhardt
Data Intuitive, Lebbeke, Belgium
Robrecht Cannoodt, Luke Zappia, Kai Waldrant & Sai Nirmayi Yasa
Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium
Robrecht Cannoodt, Louise Deconinck & Yvan Saeys
Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
Robrecht Cannoodt, Louise Deconinck & Yvan Saeys
Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
Daniel C. Strobl
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
Daniel C. Strobl, Giovanni Palla & Michaela F. Mueller
Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
Nikolay S. Markov
Department of Mathematics, School of Computing, Information and Technology, Technical University of Munich, Munich, Germany
Luke Zappia, Artur Szałata & Fabian J. Theis
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
Wesley Lewis & Smita Krishnaswamy
Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
Daniel Dimitrov & Julio Saez-Rodriguez
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
Michael E. Vinyard
Broad Institute of MIT and Harvard, Cambridge, MA, USA
Michael E. Vinyard, Qian Qin & Zhijian Li
Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
Michael E. Vinyard, Zhijian Li & Luca Pinello
Department of Computer Science, Yale University, New Haven, CT, USA
D. S. Magruder, Alexander Tong & Smita Krishnaswamy
Genentech Inc, South San Francisco, CA, USA
Alma Andersson & Romain Lopez
Gene Technology, Royal Institute of Technology (KTH), Stockholm, Sweden
Alma Andersson
Science for Life Laboratory (SciLifeLab), Solna, Sweden
Alma Andersson
Wellcome Sanger Institute, Cambridge, UK
Emma Dann & Vitalii Kleshchevnikov
Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
Dominik J. Otto
Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
Dominik J. Otto
Translational Data Science IRC, Fred Hutchinson Cancer Center, Seattle, WA, USA
Dominik J. Otto
Apple, Paris, France
Michal Klein
Data Sciences Platform, Chan Zuckerberg Biohub, San Francisco, CA, USA
Olga Borisovna Botvinnik, Ann T. Chen & Angela Oliveira Pisco
Bridge Bio Pharma, Palo Alto, CA, USA
Olga Borisovna Botvinnik
Cellarity, Inc, Somerville, MA, USA
Andrew Benz & Benjamin DeMeo
Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
Jonathan M. Bloom
Insitro, South San Francisco, USA
Angela Oliveira Pisco
VIB Center for AI & Computational Biology (VIB.AI), Ghent, Belgium
Yvan Saeys
Cellular Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
Fabian J. Theis
Department of Genetics, Yale University, New Haven, CT, USA
Smita Krishnaswamy
Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany
Bastian Rieck
Department of Informatics, University of Fribourg, Fribourg, Switzerland
Bastian Rieck
Genome Biology Unit, EMBL, Heidelberg, Germany
Constantin Ahlmann-Eltze
Mohamed bin Zayed University of Artificial Intelligence (MBZUAI), Abu Dhabi, United Arab Emirates
Eduardo da Veiga Beltrame
VIB Center for Brain & Disease Research, Leuven, Belgium
Carmen Bravo González-Blas & Swann Floc’hlay
Orion Medicines, Foster City, CA, USA
Ann T. Chen
Department of Biomedical Informatics, Harvard University, Cambridge, MA, USA
Benjamin DeMeo
Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
Can Ergen, Adam Gayoso, Galen Xing & Chenling Xu
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
Stephanie Hicks
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
Stephanie Hicks
Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
Stephanie Hicks
Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Gioele La Manno
Chan Zuckerberg Initiative, Redwood City, CA, USA
Maximilian G. Lombardo
Department of Genetics, Stanford University, Stanford, CA, USA
Romain Lopez
Department of Statistical Sciences, University of Padua, Padua, Italy
Dario Righelli
Department of Computer Science, Princeton University, Princeton, NJ, USA
Hirak Sarkar
Princeton Ludwig Institute, Princeton University, Princeton, NJ, USA
Hirak Sarkar
Altos Labs, San Diego, CA, USA
Valentine Svensson
Mila–Quebec AI Institute, Montreal, Quebec, Canada
Alexander Tong
Université de Montréal, Montréal, Quebec, Canada
Alexander Tong
Gladstone–UCSF Institute of Genomic Immunology, San Francisco, CA, USA
Galen Xing
M.D.L., S.G., and D.B.B. conceived the idea. M.D.L., S.G., D.B.B., R.C., and O.B.B. developed the infrastructure. M.D.L., S.G., D.B.B., R.C., D.C.S., N.S.M., L.Z., G.P., W.L., D.D., M.E.V., M.F.M., A.A., E.D., Q.Q., A.S., A.B., and Z.L. formalized a benchmarking task. M.D.L., S.G., D.B.B., R.C., D.C.S., N.S.M., L.Z., G.P., W.L., D.D., M.E.V., D.S.M., M.F.M., A.A., E.D., Q.Q., D.J.O., M.K., O.B.B., K.W., S.N.Y., A.S., A.B., Z.L., C.A-E., E.d.V.B., A.T.C., B.D., C.E., V.K., H.S., V.S. and A.T. contributed to the codebase. M.D.L., S.G., R.C., D.C.S., N.S.M., L.Z., G.P., W.L., D.D., L.D. and K.W. analyzed the results. M.D.L., S.G., D.B.B., J.M.B., A.O.P., J.S.-R., D.W., L.P., Y.S., F.J.T. and S.K. provided resources and supervised the work. M.D.L., S.G., D.B.B., R.C., D.C.S., N.S.M., L.Z., G.P., W.L. and D.D. coordinated the research. M.D.L., S.G., D.B.B., F.J.T. and S.K. acquired funding for the work. M.D.L., S.G., D.B.B., R.C., D.C.S., N.S.M., L.Z., G.P., W.L., D.D., M.E.V., M.F.M., A.A., E.D., Q.Q., D.J.O., M.K., O.B.B., A.S., A.B., Z.L., B.R., J.M.B., A.O.P., C.A-E., E.d.V.B., A.B., C.B.G-B., A.T.C., B.D., C.E., S.F., A.G., S.H., Y.J., V.K., G.L.M., M.G.L., R.L., D.R., H.S., V.S., A.T., G.X. and C.X. contributed to benchmarking task definition. M.D.L., S.G., D.B.B., R.C., D.C.S., N.S.M., L.Z., G.P., W.L., D.D., M.E.V. and D.S.M. prepared the manuscript. D.C.S., N.S.M., L.Z., G.P., W.L., D.D., M.E.V., D.S.M. and M.F.M. contributed equally as second authors. All authors reviewed the manuscript.
