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Biblioteca(s): |
Embrapa Florestas. |
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Data corrente: |
17/11/2011 |
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Data da última atualização: |
11/10/2017 |
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Tipo da produção científica: |
Nota Técnica/Nota Científica |
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Autoria: |
SILVA, F. F.; VARONA, L.; RESENDE, M. D. V. de; BUENO FILHO, J. S. S.; ROSA, G. J. M.; VIANA, J. M. S. |
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Afiliação: |
Fabyano Fonseca Silva, UFV; Luis Varona, Universidad de Zaragoza; MARCOS DEON VILELA DE RESENDE, CNPF; Júlio Sílvio S. Bueno Filho, UFLA; Guilherme J. M. Rosa, University of Wisconsin; José Marcelo Soriano Viana, UFV. |
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Título: |
A note on accuracy of Bayesian LASSO regression in GWS. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
Livestock Science, v. 142, p. 310-314, 2011. |
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DOI: |
10.1016/j.livsci.2011.09.010 |
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Idioma: |
Inglês |
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Notas: |
Short communication. |
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Conteúdo: |
Several genome wide selection (GWS) statistical methods have been proposed in the last years, and among these stands out the Bayesian LASSO (BL), which is a penalized regression method based on the regularization parameter (?) estimates. In general, the posterior mean values for ? are those that minimize the residual sum of squares (RSS) while controlling the L1 norm (absolute values) of the regression coefficients. However, another option is to use fixed values of ?, which is independent of this minimization process. Nevertheless, the most important aim of GWS is to make predictions about genomic breeding values (GBV=u) for individuals that have not been measured directly for the trait, and for this reason the parameter to maximize should be the accuracy (ru; ?u ). Thus, a question can arise as to whether such estimated ? values that minimize RSS are the same as that which maximize ru; ?u . In order to answer this question, this paper aims to provide methodological and computational resources in order to evaluate the influence of BL regularization parameter estimates on the correlation between true and estimated GBV (accuracy) depending on genetic structure of the target trait (few or many QTLs and low or medium heritability). In general, it is possible to report, on average, that GBV prediction is robust in relation to the ? estimation, since the different values for ? lead to similar accuracy values. Moreover, the fixed ? values grid request high computational costs, implying that the random ? method is more attractive, since it is much faster to use just one Gibbs sampler run, while the grid must to use one run for each fixed ? value. MenosSeveral genome wide selection (GWS) statistical methods have been proposed in the last years, and among these stands out the Bayesian LASSO (BL), which is a penalized regression method based on the regularization parameter (?) estimates. In general, the posterior mean values for ? are those that minimize the residual sum of squares (RSS) while controlling the L1 norm (absolute values) of the regression coefficients. However, another option is to use fixed values of ?, which is independent of this minimization process. Nevertheless, the most important aim of GWS is to make predictions about genomic breeding values (GBV=u) for individuals that have not been measured directly for the trait, and for this reason the parameter to maximize should be the accuracy (ru; ?u ). Thus, a question can arise as to whether such estimated ? values that minimize RSS are the same as that which maximize ru; ?u . In order to answer this question, this paper aims to provide methodological and computational resources in order to evaluate the influence of BL regularization parameter estimates on the correlation between true and estimated GBV (accuracy) depending on genetic structure of the target trait (few or many QTLs and low or medium heritability). In general, it is possible to report, on average, that GBV prediction is robust in relation to the ? estimation, since the different values for ? lead to similar accuracy values. Moreover, the fixed ? values grid request high computational costs, impl... Mostrar Tudo |
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Palavras-Chave: |
Genome wide selection; Penalized regression; SNP markers. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02366naa a2200241 a 4500
001 1906248
005 2017-10-11
008 2011 bl uuuu u00u1 u #d
024 7 $a10.1016/j.livsci.2011.09.010$2DOI
100 1 $aSILVA, F. F.
245 $aA note on accuracy of Bayesian LASSO regression in GWS.$h[electronic resource]
260 $c2011
500 $aShort communication.
520 $aSeveral genome wide selection (GWS) statistical methods have been proposed in the last years, and among these stands out the Bayesian LASSO (BL), which is a penalized regression method based on the regularization parameter (?) estimates. In general, the posterior mean values for ? are those that minimize the residual sum of squares (RSS) while controlling the L1 norm (absolute values) of the regression coefficients. However, another option is to use fixed values of ?, which is independent of this minimization process. Nevertheless, the most important aim of GWS is to make predictions about genomic breeding values (GBV=u) for individuals that have not been measured directly for the trait, and for this reason the parameter to maximize should be the accuracy (ru; ?u ). Thus, a question can arise as to whether such estimated ? values that minimize RSS are the same as that which maximize ru; ?u . In order to answer this question, this paper aims to provide methodological and computational resources in order to evaluate the influence of BL regularization parameter estimates on the correlation between true and estimated GBV (accuracy) depending on genetic structure of the target trait (few or many QTLs and low or medium heritability). In general, it is possible to report, on average, that GBV prediction is robust in relation to the ? estimation, since the different values for ? lead to similar accuracy values. Moreover, the fixed ? values grid request high computational costs, implying that the random ? method is more attractive, since it is much faster to use just one Gibbs sampler run, while the grid must to use one run for each fixed ? value.
653 $aGenome wide selection
653 $aPenalized regression
653 $aSNP markers
700 1 $aVARONA, L.
700 1 $aRESENDE, M. D. V. de
700 1 $aBUENO FILHO, J. S. S.
700 1 $aROSA, G. J. M.
700 1 $aVIANA, J. M. S.
773 $tLivestock Science$gv. 142, p. 310-314, 2011.
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Embrapa Florestas (CNPF) |
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| Registros recuperados : 131 | |
| 9. |  | CAMPOS, A. D.; PORTO, F. G. da S. Direitos de propriedade e os laboratórios de pesquisa. In: ENCONTRO NACIONAL SOBRE METODOLOGIAS E GESTÃO DE LABORATÓRIOS DA EMBRAPA, 15.; SIMPÓSIO SOBRE METODOLOGIAS DE LABORATÓRIO DE PESQUISA AGROPECUÁRIA, 2., Pelotas, 2010. A Pesquisa Agropecuária como instrumento para a competividade e o desenvolvimento sustentável: resumos... Pelotas: Embrapa Clima Temperado, 2010. Editado por Denilson Gouvea Anthonisen, Rosa Lia Barbieri, Glaucia de Figueiredo Nachtigal. 1 CD-ROM.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 13. | | PORTO, F. G. da S.; CAMPOS, A. D. Gestão de laboratórios de pesquisas visando propriedade intelectual. In: ENCONTRO NACIONAL SOBRE METODOLOGIAS E GESTÃO DE LABORATÓRIOS DA EMBRAPA, 15.; SIMPÓSIO SOBRE METODOLOGIAS DE LABORATÓRIO DE PESQUISA AGROPECUÁRIA, 2., Pelotas, 2010. A Pesquisa Agropecuária como instrumento para a competividade e o desenvolvimento sustentável: resumos... Pelotas: Embrapa Clima Temperado, 2010. Editado por Denilson Gouvea Anthonisen, Rosa Lia Barbieri, Glaucia de Figueiredo Nachtigal. 1 CD-ROM.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 18. | | SANTOS, A. V.; GOMES, C. B.; UNO, B.; RODRIGUES, A. C.; CAMPOS, A. D. Avaliação do aditivante biológico PSB na supressão de uma população mista de Meloidogyne incognita e M. arenaria em tomateiro. In: CONGRESSO BRASILEIRO DE NEMATOLOGIA, 27., 2007, Goiânia. Anais: programação, palestras, resumos. Goiânia: UFG, 2007. p. 71| Tipo: Resumo em Anais de Congresso | Circulação/Nível: -- - -- |
| Biblioteca(s): Embrapa Clima Temperado. |
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| 19. | | CAMPOS, A. D.; SONÊGO, O. R.; GOMES, C. B.; GARRIDO, L.; RODRIGUES, A. C. Alterações no metabolismo de açúcares das gemas vegetativas de videiras parasitadas por filoxera radícola ou apresentando sintomas de escurecimento da casca. In: CONGRESSO BRASILEIRO DE FRUTICULTURA, 20.; ANNUAL MEETING OF THE INTERAMERICAN SOCIETY FOR TROPICAL HORTICULTURE, 54., 2008, Vitória. Anais... Frutas para todos: estratégias, tecnologias e visão sustentável. Vitória: Sociedade Brasileira de Fruticultura, 2008. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Clima Temperado. |
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| Registros recuperados : 131 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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