Predictions in biometric models

Palavras-chave: machine learning; genomic analysis; simulation; SNP.

Resumo

One of the domains of genetic enhancement that has extensively employed both simulation and authentic data is Biometrics. Selecting efficient models for the Genome-Wide Selection (GWS) process using molecular markers (SNPs) presents several challenges. Among these challenges is the effective identification of the optimal model for fitting a given dataset. To contribute to this endeavor, this paper's primary objective is to assess the predictive accuracy of nine (9) distinct models, each following different paradigms within the realm of Biometrics. The data employed in this study were generated through simulation, encompassing the primary issues encountered in this field of research, including high dimensionality, nonlinearity, and multicollinearity. As the primary findings, notable observations include the enhancement of predictive efficiency as data noise decreases, the predominance of the tree paradigm (for low noise levels, BOO), and the efficacy of the neural network paradigm (for high noise levels, RBF).

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Referências

Azodi, C. B., Bolger, E., McCarren, A., Roantree, M., De Los Campos, G., & Shiu, S.-H. (2019). Benchmarking oarametric and machine learning models for genomic prediction of complex traits. G3 Genes|Genomes|Genetics, 9(11), 3691-3702. DOI: https://doi.org/10.1534/g3.119.400498

Breiman, L. (1996). Bagging predictors. Machine Learning, 24(2), 123-140. DOI: https://doi.org/10.1007/BF00058655

Burman, P. (1989). A comparative study of ordinary cross-validation, v-fold cross-validation, and the repeated learning-testing methods. Biometrika, 76(3), 503-514. DOI: https://doi.org/10.2307/2336116

Costa, W. G., Celeri, M. O., Barbosa, I. P., Silva, G. N., Azevedo, C. F., Borém, A., ... Cruz, C. D. (2022). Genomic prediction through machine learning and neural networks for traits with epistasis. Computational and Structural Biotechnology Journal, 20, 5490-5499. DOI: https://doi.org/10.1016/j.csbj.2022.09.029

Cruz, C. D. (2005). Princípios de genética quantitativa. Viçosa, MG: UFV.

Cruz, C. D., Salgado, C. C., & Bhering, L. L. (2013). Genômica aplicada. Visconde do Rio Branco, MG: Suprema.

Cruz, C. D. (2016). Genes Software – extended and integrated with the R, Matlab and Selegen. Acta Scientiarum. Agronomy, 38(4), 547-552. DOI: https://doi.org/10.4025/actasciagron.v38i4.32629

Cruz, C. D., & Nascimento, M. (2018). Inteligência computacional aplicada ao melhoramento genético. Viçosa, MG: UFV.

Endelman, J. B. (2011). Ridge regression and other kernels for genomic selection with R Package rrBLUP. The Plant Genome, 4(3), 250-255. DOI: https://doi.org/10.3835/plantgenome2011.08.0024

Ghafouri-Kesbi, F., Rahimi-Mianji, G., Honarvar, M., & Nejati-Javaremi, A. (2017). Predictive ability of random forests, boosting, support vector machines and genomic best linear unbiased prediction in different scenarios of genomic evaluation. Animal Production Science, 57(2), 229-236. DOI: https://doi.org/10.1071/AN15538

Hastie, T., Tibshirani, R., & Friedman, J. H. (2009). The elements of statistical learning: Data mining, inference, and prediction (2nd ed). Berlin, GE: Springer.

Haykin, S. S. (2009). Neural networks and learning machines (3rd ed). New Jersey, NY: Prentice Hall.

Izbicki, R., & Santos, T. M. (2020). Aprendizado de máquina: Uma abordagem estatística. São Carlos, SP: Rafael Izbicki. Retrieved on Feb. 10, 2023 from http://www.rizbicki.ufscar.br/AME.pdf

James, G., Witten, D., Hastie, T., & Tibshirani, R. (2021). An introduction to statistical learning: With applications in R (2nd ed.). Berlin, GE: Springer. DOI: https://doi.org/10.1007/978-1-0716-1418-1

Kim, J.-H. (2009). Estimating classification error rate: Repeated cross-validation, repeated hold-out and bootstrap. Computational Statistics & Data Analysis, 53(11), 3735-3745. DOI: https://doi.org/10.1016/j.csda.2009.04.009

LeCun, Y., Bengio, Y., & Hinton, G. (2015). Deep learning. Nature, 521(7553), 436-444. DOI: https://doi.org/10.1038/nature14539

Li, B., Zhang, N., Wang, Y.-G., George, A. W., Reverter, A., & Li, Y. (2018). Genomic prediction of breeding values using a subset of snps identified by three machine learning methods. Frontiers in Genetics, 9(237), 1-20. DOI: https://doi.org/10.3389/fgene.2018.00237

Meuwissen, T. H., Hayes, B. J., & Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819-1829. DOI: https://doi.org/10.1093/genetics/157.4.1819

Montesinos López, O. A., Montesinos López, A., & Crossa, J. (2022). Multivariate statistical machine learning methods for genomic prediction. Berlin, GE: Springer International Publishing. DOI: https://doi.org/10.1007/978-3-030-89010-0

Park, J., & Sandberg, I. W. (1991). Universal approximation using radial-basis-function networks. Neural Computation, 3(2), 246-257. DOI: https://doi.org/10.1162/neco.1991.3.2.246

Prasad, A. M., Iverson, L. R., & Liaw, A. (2006). newer classification and regression tree techniques: bagging and random forests for ecological prediction. Ecosystems, 9(2), 181-199. DOI: https://doi.org/10.1007/s10021-005-0054-1

Publicado
2024-08-12
Como Citar
Guimaraes, P. W., Oliveira, A. de P., & Cruz, C. D. (2024). Predictions in biometric models . Acta Scientiarum. Agronomy, 46(1), e68599. https://doi.org/10.4025/actasciagron.v46i1.68599
Seção
Melhoramento Vegetal

Funding data

 

2.0
2019CiteScore
 
 
60th percentile
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2.0
2019CiteScore
 
 
60th percentile
Powered by  Scopus