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Table 2 Total prediction accuracy (TPA), true positive rate (TPR) and true negative rate (TNR) with kNN, Lasso, SVML and SVMR in Brown Swiss and Fleckvieh cattle

From: Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations

 

Method

TPA

TPR

TNR

Brown

KNN

0.837 (±0.047)

0.862 (±0.062)

0.798 (±0.088)

 

Lasso

0.988 (±0.010)

1.000 (±0.000)

0.968 (±0.029)

 

SVML

0.991 (±0.010)

0.998 (±0.005)

0.976 (±0.025)

 

SVMR

0.978 (±0.016)

0.989 (±0.015)

0.961 (±0.034)

 

MAG

0.983 (±0.015)

0.992 (±0.011)

0.984 (±0.016)

Fleckvieh

KNN

0.970 (±0.007)

0.288 (±0.087)

0.998 (±0.002)

 

Lasso

0.998 (±0.002)

0.957 (±0.037)

0.999 (±0.001)

 

SVML

0.996 (±0.002)

0.924 (±0.047)

0.999 (±0.001)

 

SVMR

0.991 (±0.003)

0.775 (±0.073)

0.999 (±0.001)

 

MAG

0.994 (±0.003)

0.991 (±0.003)

0.998 (±0.002)

  1. KNN k-nearest neighbors, Lasso â„“1-penalized logistic regression, SVML suport vector machine with linear kernel, SVMR support vector machine with radial kernel MAG multi-allelic gene prediction