University of Oulu

Mathew B, Hauptmann A, Léon J and Sillanpää MJ (2022) NeuralLasso: Neural Networks Meet Lasso in Genomic Prediction. Front. Plant Sci. 13:800161. doi: 10.3389/fpls.2022.800161

NeuralLasso : neural networks meet lasso in genomic prediction

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Author: Mathew, Boby1,2; Hauptmann, Andreas3,4; Léon, Jens2;
Organizations: 1Bayer CropScience, Monheim am Rhein, Germany
2Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
3Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
4Department of Computer Science, University College London, London, United Kingdom
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 0.4 MB)
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Language: English
Published: Frontiers Media, 2022
Publish Date: 2022-08-31


Prediction of complex traits based on genome-wide marker information is of central importance for both animal and plant breeding. Numerous models have been proposed for the prediction of complex traits and still considerable effort has been given to improve the prediction accuracy of these models, because various genetics factors like additive, dominance and epistasis effects can influence of the prediction accuracy of such models. Recently machine learning (ML) methods have been widely applied for prediction in both animal and plant breeding programs. In this study, we propose a new algorithm for genomic prediction which is based on neural networks, but incorporates classical elements of LASSO. Our new method is able to account for the local epistasis (higher order interaction between the neighboring markers) in the prediction. We compare the prediction accuracy of our new method with the most commonly used prediction methods, such as BayesA, BayesB, Bayesian Lasso (BL), genomic BLUP and Elastic Net (EN) using the heterogenous stock mouse and rice field data sets.

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Series: Frontiers in plant science
ISSN: 1664-462X
ISSN-E: 1664-462X
ISSN-L: 1664-462X
Volume: 13
Article number: 800161
DOI: 10.3389/fpls.2022.800161
Type of Publication: B1 Journal article
Field of Science: 112 Statistics and probability
1183 Plant biology, microbiology, virology
Funding: AH acknowledges funding from the Academy of Finland projects 338408 and 336796.
Academy of Finland Grant Number: 338408
Detailed Information: 338408 (Academy of Finland Funding decision)
336796 (Academy of Finland Funding decision)
Copyright information: © 2022 Mathew, Hauptmann, Léon and Sillanpää. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.