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machine-learning-for-genomic-selection-in-animals

Datasets Source

[1]Cleveland, M. A., J. M. Hickey, and S. Forni, 2012 A Common Dataset for Genomic Analysis of Livestock Populations. G3 Genes|Genomes|Genetics 2: 429-435.

[2]An, M., G. Zhou, Y. Li, T. Xiang and Y. Ma et al., 2022 Characterization of genetic fundamentals for piglet mortality at birth in Yorkshire, Landrace, and Duroc sows. Animal Genetics 53: 142-145.

[3]Yang, W., J. Wu, J. Yu, X. Zheng and H. Kang et al., 2021 A genome-wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs. Anim Genet 52: 749-753.

[4]Waldmann, P., Pfeiffer, C., & Mészáros, G. (2020). Sparse convolutional neural networks for genome-wide prediction. Frontiers in Genetics, 11, 25.

Genomic selection methods used on pig

Year Author ML based methods Traditional methods
2013 Tusell L et al. RKHS regression,RBFNN,BRNN GBLUP,BayesR,BayesLASSO
2018 Waldmann P et al. MLP GBLUP,BayesLASSO
2020 Waldmann P et al. CNN GBLUP,BayesLASSO
2022 Wang X et al. SVR,KRR,RF,Adaboost.R2 GBLUP,ssBLUP,BayesHE

Methods Implemented

GBLUP, LASSO, CNN, LSTM, LGBM, Transformer(+AE,+PCA,+ICA,+t-SNE)

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