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Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.

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Názov: Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.
Autori: Quelin A; UMR 7206 Eco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris Cité, Paris, France. arnaud.quelin@mnhn.fr.; UMR 9015 - Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CNRS, INRIA, Université Paris-Saclay, Orsay, France. arnaud.quelin@mnhn.fr., Austerlitz F; UMR 7206 Eco-Anthropologie (EA), CNRS, Muséum National d'Histoire Naturelle, Université Paris Cité, Paris, France., Jay F; UMR 9015 - Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CNRS, INRIA, Université Paris-Saclay, Orsay, France.
Zdroj: Heredity [Heredity (Edinb)] 2025 Jul; Vol. 134 (7), pp. 417-426. Date of Electronic Publication: 2025 Jun 06.
Spôsob vydávania: Journal Article
Jazyk: English
Informácie o časopise: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0373007 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-2540 (Electronic) Linking ISSN: 0018067X NLM ISO Abbreviation: Heredity (Edinb) Subsets: MEDLINE
Imprint Name(s): Publication: <2003->: London : Nature Publishing Group
Original Publication: London, Oliver and Boyd.
Výrazy zo slovníka MeSH: Supervised Machine Learning* , Computer Simulation* , Genetics, Population*/methods , Genomics*/methods , Machine Learning*, Models, Genetic ; Bayes Theorem ; Humans ; Algorithms ; Neural Networks, Computer
Abstrakt: The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Several demographic inference methods have been developed to take advantage of these massive genomic data. Simulation-based approaches, such as approximate Bayesian computation (ABC), have proved particularly efficient for complex demographic models. However, taking full advantage of the comprehensive information contained in massive genomic data remains a challenge for demographic inference methods, which generally rely on partial information from these data. Using advanced computational methods, such as machine learning, is valuable for efficiently integrating more comprehensive information. Here, we showed how simulation-based supervised machine learning methods applied to an extensive range of summary statistics are effective in inferring demographic parameters for connected populations. We compared three machine learning (ML) methods: a neural network, the multilayer perceptron (MLP), and two ensemble methods, random forest (RF) and the gradient boosting system XGBoost (XGB), to infer demographic parameters from genomic data under a standard isolation with migration model and a secondary contact model with varying population sizes. We showed that MLP outperformed the other two methods and that, on the basis of permutation feature importance, its predictions involved a larger combination of summary statistics. Moreover, they outperformed all three tested ABC algorithms. Finally, we demonstrated how a method called SHAP, from the field of explainable artificial intelligence, can be used to shed light on the contribution of summary statistics within the ML models.
(© 2025. The Author(s).)
Competing Interests: Competing interests: The authors declare no competing interests.
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Grant Information: ANR-20-CE45-0010-01 RoDAPoG Agence Nationale de la Recherche (French National Research Agency)
Entry Date(s): Date Created: 20250605 Date Completed: 20250702 Latest Revision: 20250704
Update Code: 20250704
PubMed Central ID: PMC12216105
DOI: 10.1038/s41437-025-00773-x
PMID: 40473775
Databáza: MEDLINE
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  Data: The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Several demographic inference methods have been developed to take advantage of these massive genomic data. Simulation-based approaches, such as approximate Bayesian computation (ABC), have proved particularly efficient for complex demographic models. However, taking full advantage of the comprehensive information contained in massive genomic data remains a challenge for demographic inference methods, which generally rely on partial information from these data. Using advanced computational methods, such as machine learning, is valuable for efficiently integrating more comprehensive information. Here, we showed how simulation-based supervised machine learning methods applied to an extensive range of summary statistics are effective in inferring demographic parameters for connected populations. We compared three machine learning (ML) methods: a neural network, the multilayer perceptron (MLP), and two ensemble methods, random forest (RF) and the gradient boosting system XGBoost (XGB), to infer demographic parameters from genomic data under a standard isolation with migration model and a secondary contact model with varying population sizes. We showed that MLP outperformed the other two methods and that, on the basis of permutation feature importance, its predictions involved a larger combination of summary statistics. Moreover, they outperformed all three tested ABC algorithms. Finally, we demonstrated how a method called SHAP, from the field of explainable artificial intelligence, can be used to shed light on the contribution of summary statistics within the ML models.&lt;br /&gt; (&#169; 2025. The Author(s).)
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        Value: 10.1038/s41437-025-00773-x
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      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        StartPage: 417
    Subjects:
      – SubjectFull: Models, Genetic
        Type: general
      – SubjectFull: Bayes Theorem
        Type: general
      – SubjectFull: Humans
        Type: general
      – SubjectFull: Algorithms
        Type: general
      – SubjectFull: Neural Networks, Computer
        Type: general
      – SubjectFull: Supervised Machine Learning
        Type: general
      – SubjectFull: Computer Simulation
        Type: general
      – SubjectFull: Genetics, Population methods
        Type: general
      – SubjectFull: Genomics methods
        Type: general
      – SubjectFull: Machine Learning
        Type: general
    Titles:
      – TitleFull: Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data.
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              M: 07
              Text: 2025 Jul
              Type: published
              Y: 2025
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              Value: 1365-2540
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              Value: 134
            – Type: issue
              Value: 7
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            – TitleFull: Heredity
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