Transformers for genomic prediction : working with Yeast and Wheat traits
Resumen:
AI is becoming state-of-the-art across scientific fields, giving novel solutions to age-old problems. In genomic prediction, Machine Learning methods could not outperform linear regressions in a general way yet, but are becoming closer. An important feature when working with genomic data, which is non other than a long sequence of information, is to account for the linkage disequilibrium, i.e. dependencies between genome variations that do not need to be close in the genome, and variate with respect to the reference genome. To explode this feature, we evaluate Transformers, known for their great performance with long sequences. We worked with two databases: the first one composed of Yeast SNPs seeking to predict the growth of each individual in two different environments and the second one composed of Wheat SNPs seeking to predict four phenotypes. We compare the results with different linear models (BRR, BayesA, BayesB, BayesC and BayesL) typically used for genomic prediction and also with XGBoost, commonly known to have well performance in the area. We conclude that Transformers have shown to be a competitive model for genomic prediction, even tho it does not achieve the state-of-the-art yet.
| 2025 | |
| ANII IA_1_2022_1_173411. | |
|
Genomic prediction Deep Learning Transformers |
|
| Inglés | |
| Universidad de la República | |
| COLIBRI | |
| https://hdl.handle.net/20.500.12008/51574 | |
| Acceso abierto | |
| Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| _version_ | 1875693218197143552 |
|---|---|
| author | Castro, Graciana |
| author2 | Hoffman, Romina Musitelli, Mateo Fariello, María Inés Lecumberry, Federico |
| author2_role | author author author author |
| author_facet | Castro, Graciana Hoffman, Romina Musitelli, Mateo Fariello, María Inés Lecumberry, Federico |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | Castro Graciana, Universidad de la República (Uruguay). Facultad de Ingeniería. Hoffman Romina, Universidad de la República (Uruguay). Facultad de Ingeniería. Musitelli Mateo, Universidad de la República (Uruguay). Facultad de Ingeniería. Fariello María Inés, Universidad de la República (Uruguay). Facultad de Ingeniería. Lecumberry Federico, Universidad de la República (Uruguay). Facultad de Ingeniería. |
| dc.creator.none.fl_str_mv | Castro, Graciana Hoffman, Romina Musitelli, Mateo Fariello, María Inés Lecumberry, Federico |
| dc.date.accessioned.none.fl_str_mv | 2025-09-11T12:12:02Z |
| dc.date.available.none.fl_str_mv | 2025-09-11T12:12:02Z |
| dc.date.issued.none.fl_str_mv | 2025 |
| dc.description.abstract.none.fl_txt_mv | AI is becoming state-of-the-art across scientific fields, giving novel solutions to age-old problems. In genomic prediction, Machine Learning methods could not outperform linear regressions in a general way yet, but are becoming closer. An important feature when working with genomic data, which is non other than a long sequence of information, is to account for the linkage disequilibrium, i.e. dependencies between genome variations that do not need to be close in the genome, and variate with respect to the reference genome. To explode this feature, we evaluate Transformers, known for their great performance with long sequences. We worked with two databases: the first one composed of Yeast SNPs seeking to predict the growth of each individual in two different environments and the second one composed of Wheat SNPs seeking to predict four phenotypes. We compare the results with different linear models (BRR, BayesA, BayesB, BayesC and BayesL) typically used for genomic prediction and also with XGBoost, commonly known to have well performance in the area. We conclude that Transformers have shown to be a competitive model for genomic prediction, even tho it does not achieve the state-of-the-art yet. |
| dc.description.sponsorship.none.fl_txt_mv | ANII IA_1_2022_1_173411. |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | Castro, G., Hoffman, R., Musitelli, M. y otros. Transformers for genomic prediction : working with Yeast and Wheat traits [en línea] Póster, 2025. |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/51574 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.relation.none.fl_str_mv | Póster presentado en la Conferencia : KHIPU 2025, Santiago, Chile. |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución - No Comercial - Sin Derivadas (CC - By-NC-ND 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 | Genomic prediction Deep Learning Transformers |
| dc.title.none.fl_str_mv | Transformers for genomic prediction : working with Yeast and Wheat traits |
| dc.type.es.fl_str_mv | Póster |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/conferenceObject |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | AI is becoming state-of-the-art across scientific fields, giving novel solutions to age-old problems. In genomic prediction, Machine Learning methods could not outperform linear regressions in a general way yet, but are becoming closer. An important feature when working with genomic data, which is non other than a long sequence of information, is to account for the linkage disequilibrium, i.e. dependencies between genome variations that do not need to be close in the genome, and variate with respect to the reference genome. To explode this feature, we evaluate Transformers, known for their great performance with long sequences. We worked with two databases: the first one composed of Yeast SNPs seeking to predict the growth of each individual in two different environments and the second one composed of Wheat SNPs seeking to predict four phenotypes. We compare the results with different linear models (BRR, BayesA, BayesB, BayesC and BayesL) typically used for genomic prediction and also with XGBoost, commonly known to have well performance in the area. We conclude that Transformers have shown to be a competitive model for genomic prediction, even tho it does not achieve the state-of-the-art yet. |
| eu_rights_str_mv | openAccess |
| format | conferenceObject |
| id | COLIBRI_eedb235cbd092f129b84ff6ecdc636e2 |
| identifier_str_mv | Castro, G., Hoffman, R., Musitelli, M. y otros. Transformers for genomic prediction : working with Yeast and Wheat traits [en línea] Póster, 2025. |
| 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:20.500.12008/51574 |
| publishDate | 2025 |
| 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 - No Comercial - Sin Derivadas (CC - By-NC-ND 4.0) |
| spelling | Castro Graciana, Universidad de la República (Uruguay). Facultad de Ingeniería.Hoffman Romina, Universidad de la República (Uruguay). Facultad de Ingeniería.Musitelli Mateo, Universidad de la República (Uruguay). Facultad de Ingeniería.Fariello María Inés, Universidad de la República (Uruguay). Facultad de Ingeniería.Lecumberry Federico, Universidad de la República (Uruguay). Facultad de Ingeniería.2025-09-11T12:12:02Z2025-09-11T12:12:02Z2025Castro, G., Hoffman, R., Musitelli, M. y otros. Transformers for genomic prediction : working with Yeast and Wheat traits [en línea] Póster, 2025.https://hdl.handle.net/20.500.12008/51574AI is becoming state-of-the-art across scientific fields, giving novel solutions to age-old problems. In genomic prediction, Machine Learning methods could not outperform linear regressions in a general way yet, but are becoming closer. An important feature when working with genomic data, which is non other than a long sequence of information, is to account for the linkage disequilibrium, i.e. dependencies between genome variations that do not need to be close in the genome, and variate with respect to the reference genome. To explode this feature, we evaluate Transformers, known for their great performance with long sequences. We worked with two databases: the first one composed of Yeast SNPs seeking to predict the growth of each individual in two different environments and the second one composed of Wheat SNPs seeking to predict four phenotypes. We compare the results with different linear models (BRR, BayesA, BayesB, BayesC and BayesL) typically used for genomic prediction and also with XGBoost, commonly known to have well performance in the area. We conclude that Transformers have shown to be a competitive model for genomic prediction, even tho it does not achieve the state-of-the-art yet.Submitted by Machado Jimena (jmachado@fing.edu.uy) on 2025-09-10T16:24:41Z No. of bitstreams: 2 license_rdf: 26539 bytes, checksum: 3b50ae24bd8bd076d49a70878a8a2d2c (MD5) CHMLF25.pdf: 975249 bytes, checksum: b24885e887f4c7a98683bb5f89f8cad2 (MD5)Approved for entry into archive by Machado Jimena (jmachado@fing.edu.uy) on 2025-09-10T18:32:32Z (GMT) No. of bitstreams: 2 license_rdf: 26539 bytes, checksum: 3b50ae24bd8bd076d49a70878a8a2d2c (MD5) CHMLF25.pdf: 975249 bytes, checksum: b24885e887f4c7a98683bb5f89f8cad2 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2025-09-11T12:12:02Z (GMT). No. of bitstreams: 2 license_rdf: 26539 bytes, checksum: 3b50ae24bd8bd076d49a70878a8a2d2c (MD5) CHMLF25.pdf: 975249 bytes, checksum: b24885e887f4c7a98683bb5f89f8cad2 (MD5) Previous issue date: 2025ANII IA_1_2022_1_173411.application/pdfenengPóster presentado en la Conferencia : KHIPU 2025, Santiago, Chile.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. 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- Universidad de la Repúblicafalse |
| spellingShingle | Transformers for genomic prediction : working with Yeast and Wheat traits Castro, Graciana Genomic prediction Deep Learning Transformers |
| status_str | publishedVersion |
| title | Transformers for genomic prediction : working with Yeast and Wheat traits |
| title_full | Transformers for genomic prediction : working with Yeast and Wheat traits |
| title_fullStr | Transformers for genomic prediction : working with Yeast and Wheat traits |
| title_full_unstemmed | Transformers for genomic prediction : working with Yeast and Wheat traits |
| title_short | Transformers for genomic prediction : working with Yeast and Wheat traits |
| title_sort | Transformers for genomic prediction : working with Yeast and Wheat traits |
| topic | Genomic prediction Deep Learning Transformers |
| url | https://hdl.handle.net/20.500.12008/51574 |