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Treffer: Guiding questions to avoid data leakage in biological machine learning applications.

Title:
Guiding questions to avoid data leakage in biological machine learning applications.
Authors:
Bernett J; TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Blumenthal DB; Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. david.b.blumenthal@fau.de., Grimm DG; TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany. dominik.grimm@tum.de.; Bioinformatics, Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany. dominik.grimm@tum.de.; TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany. dominik.grimm@tum.de., Haselbeck F; TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany.; Bioinformatics, Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany.; Smart Farming, Weihenstephan-Triesdorf University of Applied Sciences, Freising, Germany., Joeres R; Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.; Center for Bioinformatics, Saarland University, Saarbrücken, Germany., Kalinina OV; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany. olga.kalinina@helmholtz-hips.de.; Center for Bioinformatics, Saarland University, Saarbrücken, Germany. olga.kalinina@helmholtz-hips.de.; Medical Faculty, Saarland University, Homburg, Germany. olga.kalinina@helmholtz-hips.de., List M; TUM School of Life Sciences, Technical University of Munich, Freising, Germany. markus.list@tum.de.; Munich Data Science Institute (MDSI), Technical University of Munich, Garching, Germany. markus.list@tum.de.
Source:
Nature methods [Nat Methods] 2024 Aug; Vol. 21 (8), pp. 1444-1453. Date of Electronic Publication: 2024 Aug 09.
Publication Type:
Journal Article; Review
Language:
English
Journal Info:
Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE
Imprint Name(s):
Original Publication: New York, NY : Nature Pub. Group, c2004-
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Grant Information:
51618818 Deutsche Forschungsgemeinschaft (German Research Foundation); 51618818 Deutsche Forschungsgemeinschaft (German Research Foundation); 031L0309A Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research); 031L0305A Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research); 031L0305A Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
Entry Date(s):
Date Created: 20240809 Date Completed: 20240809 Latest Revision: 20240815
Update Code:
20250114
DOI:
10.1038/s41592-024-02362-y
PMID:
39122953
Database:
MEDLINE

Weitere Informationen

Machine learning methods for extracting patterns from high-dimensional data are very important in the biological sciences. However, in certain cases, real-world applications cannot confirm the reported prediction performance. One of the main reasons for this is data leakage, which can be seen as the illicit sharing of information between the training data and the test data, resulting in performance estimates that are far better than the performance observed in the intended application scenario. Data leakage can be difficult to detect in biological datasets due to their complex dependencies. With this in mind, we present seven questions that should be asked to prevent data leakage when constructing machine learning models in biological domains. We illustrate the usefulness of our questions by applying them to nontrivial examples. Our goal is to raise awareness of potential data leakage problems and to promote robust and reproducible machine learning-based research in biology.
(© 2024. Springer Nature America, Inc.)