[HTML][HTML] Deep kernel and deep learning for genome-based prediction of single traits in multienvironment breeding trials

J Crossa, JWR Martini, D Gianola… - Frontiers in …, 2019 - frontiersin.org
Deep learning (DL) is a promising method for genomic-enabled prediction. However, the
implementation of DL is difficult because many hyperparameters (number of hidden layers …

Multi-environment genomic prediction of plant traits using deep learners with dense architecture

A Montesinos-López… - G3: Genes …, 2018 - academic.oup.com
Genomic selection is revolutionizing plant breeding and therefore methods that improve
prediction accuracy are useful. For this reason, active research is being conducted to build …

Multi-trait, multi-environment deep learning modeling for genomic-enabled prediction of plant traits

OA Montesinos-López… - G3: Genes, genomes …, 2018 - academic.oup.com
Multi-trait and multi-environment data are common in animal and plant breeding programs.
However, what is lacking are more powerful statistical models that can exploit the correlation …

Deep kernel for genomic and near infrared predictions in multi-environment breeding trials

J Cuevas, O Montesinos-López… - G3: Genes …, 2019 - academic.oup.com
Kernel methods are flexible and easy to interpret and have been successfully used in
genomic-enabled prediction of various plant species. Kernel methods used in genomic …

New deep learning genomic-based prediction model for multiple traits with binary, ordinal, and continuous phenotypes

OA Montesinos-López, J Martín-Vallejo… - G3: Genes, genomes …, 2019 - academic.oup.com
Multiple-trait experiments with mixed phenotypes (binary, ordinal and continuous) are not
rare in animal and plant breeding programs. However, there is a lack of statistical models …

[HTML][HTML] Nonlinear kernels, dominance, and envirotyping data increase the accuracy of genome-based prediction in multi-environment trials

G Costa-Neto, R Fritsche-Neto, J Crossa - Heredity, 2021 - nature.com
Modern whole-genome prediction (WGP) frameworks that focus on multi-environment trials
(MET) integrate large-scale genomics, phenomics, and envirotyping data. However, the …

[HTML][HTML] A stacking ensemble learning framework for genomic prediction

M Liang, T Chang, B An, X Duan, L Du, X Wang… - Frontiers in …, 2021 - frontiersin.org
Machine learning (ML) is perhaps the most useful tool for the interpretation of large genomic
datasets. However, the performance of a single machine learning method in genomic …

[HTML][HTML] Multi-trait, multi-environment genomic prediction of durum wheat with genomic best linear unbiased predictor and deep learning methods

OA Montesinos-López, A Montesinos-López… - Frontiers in Plant …, 2019 - frontiersin.org
Although durum wheat (Triticum turgidum var. durum Desf.) is a minor cereal crop
representing just 5–7% of the world's total wheat crop, it is a staple food in Mediterranean …

[HTML][HTML] A guide on deep learning for complex trait genomic prediction

M Pérez-Enciso, LM Zingaretti - Genes, 2019 - mdpi.com
Deep learning (DL) has emerged as a powerful tool to make accurate predictions from
complex data such as image, text, or video. However, its ability to predict phenotypic values …

[HTML][HTML] Deep learning for predicting complex traits in spring wheat breeding program

KS Sandhu, DN Lozada, Z Zhang… - Frontiers in Plant …, 2021 - frontiersin.org
Genomic selection (GS) is transforming the field of plant breeding and implementing models
that improve prediction accuracy for complex traits is needed. Analytical methods for …