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Willem, T. ; Shitov, V.A. ; Luecken, M. ; Kilbertus, N. ; Bauer, S. ; Piraud, M. ; Buyx, A.* ; Theis, F.J.

Biases in machine-learning models of human single-cell data.

Nat. Cell Biol. 27, 384–392 (2025)
Postprint DOI PMC
Open Access Green
Recent machine-learning (ML)-based advances in single-cell data science have enabled the stratification of human tissue donors at single-cell resolution, promising to provide valuable diagnostic and prognostic insights. However, such insights are susceptible to biases. Here we discuss various biases that emerge along the pipeline of ML-based single-cell analysis, ranging from societal biases affecting whose samples are collected, to clinical and cohort biases that influence the generalizability of single-cell datasets, biases stemming from single-cell sequencing, ML biases specific to (weakly supervised or unsupervised) ML models trained on human single-cell samples and biases during the interpretation of results from ML models. We end by providing methods for single-cell data scientists to assess and mitigate biases, and call for efforts to address the root causes of biases.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Review
Schlagwörter Genomics; Racism; Race
Sprache englisch
Veröffentlichungsjahr 2025
HGF-Berichtsjahr 2025
ISSN (print) / ISBN 1465-7392
e-ISSN 1476-4679
Zeitschrift Nature Cell Biology
Quellenangaben Band: 27, Heft: , Seiten: 384–392 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort Heidelberger Platz 3, Berlin, 14197, Germany
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Institute of Lung Health and Immunity (LHI)
POF Topic(s) 30205 - Bioengineering and Digital Health
80000 - German Center for Lung Research
Forschungsfeld(er) Enabling and Novel Technologies
Lung Research
PSP-Element(e) G-503800-001
G-530001-001
G-530003-001
G-501800-833
Förderungen Helmholtz Association under the joint research school 'Munich School for Data Science'
DOI 10.1038/s41556-025-01619-8
WOS ID 001425309900001
Scopus ID 85219564022
PubMed ID 39972066
Erfassungsdatum 2025-04-14
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