Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction.
Resumen:
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 phenotyping. Ridge regression is one of the 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 | |
| Bill & Melinda Gates Foundation | |
|
Ridge regression Genomic prediction GenPred Shared Data Resource Plant breeding Breeding values Penalized regression |
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| Inglés | |
| Universidad de la República | |
| COLIBRI | |
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https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae246/7888815
https://hdl.handle.net/20.500.12008/46936 |
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| Acceso abierto | |
| Licencia Creative Commons Atribución (CC - By 4.0) |
| _version_ | 1875692332489113600 |
|---|---|
| author | Montesinos-López, Abelardo |
| author2 | Montesinos-López, Osval A. Lecumberry, Federico Fariello, Maria Ines Montesinos-López, José C. Crossa, José |
| author2_role | author author author author author |
| author_facet | Montesinos-López, Abelardo Montesinos-López, Osval A. Lecumberry, Federico Fariello, Maria Ines Montesinos-López, José C. Crossa, José |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | Montesinos-López Abelardo, Universidad de Guadalajara, Jalisco, México Montesinos-López Osval A., Universidad de Colima, Colima, México Lecumberry Federico, Universidad de la República (Uruguay). Facultad de Ingeniería. Fariello Maria Ines, Universidad de la República (Uruguay). Facultad de Ingeniería. Montesinos-López José C., University of California Davis, CA, USA Crossa José, Louisiana State University, LA, USA |
| dc.creator.none.fl_str_mv | Montesinos-López, Abelardo Montesinos-López, Osval A. Lecumberry, Federico Fariello, Maria Ines Montesinos-López, José C. Crossa, José |
| dc.date.accessioned.none.fl_str_mv | 2024-11-12T16:12:35Z |
| dc.date.available.none.fl_str_mv | 2024-11-12T16:12:35Z |
| dc.date.issued.none.fl_str_mv | 2024 |
| dc.description.abstract.none.fl_txt_mv | 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 phenotyping. Ridge regression is one of the 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. |
| dc.description.sponsorship.none.fl_txt_mv | Bill & Melinda Gates Foundation |
| dc.format.extent.es.fl_str_mv | 15 p. |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | Montesinos-López, A., Montesinos-López, O., Lecumberry, F. y otros. "Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction". G3 : Genes, Genomes, Genetics. [en línea]. 2024, pp. 1-15. DOI: 10.1093/g3journal/jkae246. |
| dc.identifier.doi.none.fl_str_mv | 10.1093/g3journal/jkae246 |
| dc.identifier.eissn.none.fl_str_mv | 2160-1836 |
| dc.identifier.uri.none.fl_str_mv | https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae246/7888815 https://hdl.handle.net/20.500.12008/46936 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.publisher.es.fl_str_mv | Genetics Society of America, Oxford University Press. |
| dc.relation.none.fl_str_mv | G3 : Genes, Genomes, Genetics, nov. 2024, pp. 1-15. |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.es.fl_str_mv | Ridge regression Genomic prediction GenPred Shared Data Resource Plant breeding Breeding values Penalized regression |
| dc.title.none.fl_str_mv | Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction. |
| dc.type.es.fl_str_mv | Artículo |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| 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 phenotyping. Ridge regression is one of the 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. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | COLIBRI_07feddf09c3ddcfb2a6c0c8dee3d27c8 |
| identifier_str_mv | Montesinos-López, A., Montesinos-López, O., Lecumberry, F. y otros. "Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction". G3 : Genes, Genomes, Genetics. [en línea]. 2024, pp. 1-15. DOI: 10.1093/g3journal/jkae246. 10.1093/g3journal/jkae246 2160-1836 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | COLIBRI |
| network_name_str | COLIBRI |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/46936 |
| publishDate | 2024 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | karina.camps@seciu.edu.uy |
| repository.name.fl_str_mv | COLIBRI - Universidad de la República |
| repository_id_str | 4771 |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| spelling | Montesinos-López Abelardo, Universidad de Guadalajara, Jalisco, MéxicoMontesinos-López Osval A., Universidad de Colima, Colima, MéxicoLecumberry Federico, Universidad de la República (Uruguay). Facultad de Ingeniería.Fariello Maria Ines, Universidad de la República (Uruguay). Facultad de Ingeniería.Montesinos-López José C., University of California Davis, CA, USACrossa José, Louisiana State University, LA, USA2024-11-12T16:12:35Z2024-11-12T16:12:35Z2024Montesinos-López, A., Montesinos-López, O., Lecumberry, F. y otros. "Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction". G3 : Genes, Genomes, Genetics. [en línea]. 2024, pp. 1-15. DOI: 10.1093/g3journal/jkae246.https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae246/7888815https://hdl.handle.net/20.500.12008/4693610.1093/g3journal/jkae2462160-1836The 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 phenotyping. Ridge regression is one of the 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.Submitted by Ribeiro Jorge (jribeiro@fing.edu.uy) on 2024-11-11T18:12:46Z No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) MMLFMC24.pdf: 1749663 bytes, checksum: 26925fd1fd41c1942262ed1f98512dd7 (MD5)Approved for entry into archive by Machado Jimena (jmachado@fing.edu.uy) on 2024-11-12T15:31:08Z (GMT) No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) MMLFMC24.pdf: 1749663 bytes, checksum: 26925fd1fd41c1942262ed1f98512dd7 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2024-11-12T16:12:35Z (GMT). No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) MMLFMC24.pdf: 1749663 bytes, checksum: 26925fd1fd41c1942262ed1f98512dd7 (MD5) Previous issue date: 2024Bill & Melinda Gates Foundation15 p.application/pdfenengGenetics Society of America, Oxford University Press.G3 : Genes, Genomes, Genetics, nov. 2024, pp. 1-15.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)Ridge regressionGenomic predictionGenPredShared Data ResourcePlant breedingBreeding valuesPenalized regressionRefining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction.Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaMontesinos-López, AbelardoMontesinos-López, Osval A.Lecumberry, FedericoFariello, Maria InesMontesinos-López, José C.Crossa, JoséProcesamiento de SeñalesTratamiento de ImagenesLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/46936/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; 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- Universidad de la Repúblicafalse |
| spellingShingle | Refining penalized ridge regression : A novel method for optimizing the regularization parameter in genomic prediction. Montesinos-López, Abelardo Ridge regression Genomic prediction GenPred Shared Data Resource Plant breeding Breeding values Penalized regression |
| status_str | publishedVersion |
| 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 | Ridge regression Genomic prediction GenPred Shared Data Resource Plant breeding Breeding values Penalized regression |
| url | https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae246/7888815 https://hdl.handle.net/20.500.12008/46936 |