Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction
The popularity of genomic selection as an efficient and cost-effective approach to estimate breeding values continues to increase, due in part to the significant saving in genotyping. Ridge regression is one ofthe most popular methods used for genomic prediction; however, its efficiency (in terms of...
| Autores principales: | , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/163378 |
| _version_ | 1855543128175411200 |
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| author | Montesinos-López, Abelardo Montesinos-Lopez, Osval A. Lecumberry, Federico Fariello, María I. Montesinos-Lopez, José C. Crossa, José |
| author_browse | Crossa, José Fariello, María I. Lecumberry, Federico Montesinos-Lopez, José C. Montesinos-Lopez, Osval A. Montesinos-López, Abelardo |
| author_facet | Montesinos-López, Abelardo Montesinos-Lopez, Osval A. Lecumberry, Federico Fariello, María I. Montesinos-Lopez, José C. Crossa, José |
| author_sort | Montesinos-López, Abelardo |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The popularity of genomic selection as an efficient and cost-effective approach to estimate breeding values continues to increase, due in part to the significant saving in genotyping. Ridge regression is one ofthe most popular methods used for genomic prediction; however, its efficiency (in terms of prediction performance) depends on the appropriate tunning of the penalization parameter. In this paper we propose a novel, more efficient method to select the optimal penalization parameter for Ridge regression. We compared the proposed method with the conventional method to select the penalization parameter in 14 real data sets and we found that in 13 of these, the proposed method outperformed the conventional method and across data sets the gains in prediction accuracy in terms of Pearson's correlation was of 56.15%, with not-gains observed in terms of normalized mean square error. Finally, our results show evidence of the potential of the proposed method, and we encourage its adoption to improve the selection of candidate lines in the context of plant breeding. |
| format | Journal Article |
| id | CGSpace163378 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1633782025-05-04T09:22:22Z Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction Montesinos-López, Abelardo Montesinos-Lopez, Osval A. Lecumberry, Federico Fariello, María I. Montesinos-Lopez, José C. Crossa, José genomics plant breeding breeding value marker-assisted selection best linear unbiased predictor statistical models The popularity of genomic selection as an efficient and cost-effective approach to estimate breeding values continues to increase, due in part to the significant saving in genotyping. Ridge regression is one ofthe most popular methods used for genomic prediction; however, its efficiency (in terms of prediction performance) depends on the appropriate tunning of the penalization parameter. In this paper we propose a novel, more efficient method to select the optimal penalization parameter for Ridge regression. We compared the proposed method with the conventional method to select the penalization parameter in 14 real data sets and we found that in 13 of these, the proposed method outperformed the conventional method and across data sets the gains in prediction accuracy in terms of Pearson's correlation was of 56.15%, with not-gains observed in terms of normalized mean square error. Finally, our results show evidence of the potential of the proposed method, and we encourage its adoption to improve the selection of candidate lines in the context of plant breeding. 2024 2024-12-11T17:43:50Z 2024-12-11T17:43:50Z Journal Article https://hdl.handle.net/10568/163378 en Open Access application/pdf Oxford University Press Montesinos-López, A., Montesinos-López, O. A., Lecumberry, F., Fariello, M. I., Montesinos-López, J. C., & Crossa, J. (2024). Refining penalized ridge regression: A novel method for optimizing the regularization parameter in genomic prediction. G3: Genes, Genomes, Genetics, jkae246. https://doi.org/10.1093/g3journal/jkae246 |
| spellingShingle | genomics plant breeding breeding value marker-assisted selection best linear unbiased predictor statistical models Montesinos-López, Abelardo Montesinos-Lopez, Osval A. Lecumberry, Federico Fariello, María I. Montesinos-Lopez, José C. Crossa, José Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title | Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title_full | Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title_fullStr | Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title_full_unstemmed | Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title_short | Refining penalized ridge regression: a novel method for optimizing the regularization parameter in genomic prediction |
| title_sort | refining penalized ridge regression a novel method for optimizing the regularization parameter in genomic prediction |
| topic | genomics plant breeding breeding value marker-assisted selection best linear unbiased predictor statistical models |
| url | https://hdl.handle.net/10568/163378 |
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