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A multivariate Poisson deep learning model for genomic prediction of count data

Creator: Montesinos-Lopez, O.A.
Creator: Montesinos-Lopez, J.C.
Creator: Singh, P.K.
Creator: Lozano-Ramirez, N.
Creator: Barrón-López, A.
Creator: Montesinos-Lopez, A.
Creator: Crossa, J.
Year: 2020
Language: English
Publisher: Genetics Society of America
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: Bethesda, MD (USA)
Pages: 4177-4190
Issue: 11
Volume: 10
DOI: 10.1534/g3.120.401631
Keywords: Genomic Selection
Keywords: Genomic Prediction
Keywords: Count Data of Wheat Lines
Keywords: GenPred
Keywords: Shared Data Resources
Description: The paradigm called genomic selection (GS) is a revolutionary way of developing new plants and animals. This is a predictive methodology, since it uses learning methods to perform its task. Unfortunately, there is no universal model that can be used for all types of predictions; for this reason, specific methodologies are required for each type of output (response variables). Since there is a lack of efficient methodologies for multivariate count data outcomes, in this paper, a multivariate Poisson deep neural network (MPDN) model is proposed for the genomic prediction of various count outcomes simultaneously. The MPDN model uses the minus log-likelihood of a Poisson distribution as a loss function, in hidden layers for capturing nonlinear patterns using the rectified linear unit (RELU) activation function and, in the output layer, the exponential activation function was used for producing outputs on the same scale of counts. The proposed MPDN model was compared to conventional generalized Poisson regression models and univariate Poisson deep learning models in two experimental data sets of count data. We found that the proposed MPDL outperformed univariate Poisson deep neural network models, but did not outperform, in terms of prediction, the univariate generalized Poisson regression models. All deep learning models were implemented in Tensorflow as back-end and Keras as front-end, which allows implementing these models on moderate and large data sets, which is a significant advantage over previous GS models for multivariate count data.
Agrovoc: DATA
Agrovoc: MODELS
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ISSN: 2160-1836
Journal: G3: Genes, Genomes, Genetics

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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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