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These measures are either based on the RMSD (root mean squared deviation: average squared distance between homologous alpha carbons) or the dRMSD (distance RMSD: average square difference of distances between equivalent pairs of amino acids) like the DALI score (Holm and Sander, 1995), APDB (O'Sullivan et al., 2003) or the iRMSD (Armougom et al., 2006a).
Correlation-Based Methods: Cross-Correlation (CC), ML, PHAT, Average Square Difference Function (ASDF).
In an overall view, the time delay estimation methods are as follows [17 20, 31 39]: Correlation-Based Methods: Cross-Correlation (CC), ML, PHAT, Average Square Difference Function (ASDF) Adaptive Filter-Based Methods: Sync Filter, LMS.
Average square difference (ASD) was calculated as described previously.
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Second, the estimates are regularized, i.e. shrunk towards a common value that minimizes the average squared difference between the initial estimates and the shrinkage estimates.
Diversity for NEX and ENDEX genes in the respective tissues was calculated as the average squared difference in expression between the two biological replicates.
The effect MSE is then defined as the average squared difference between parameters in target and estimate, normalized by the variance of the target; i.e., Effect MSE = T p × Var.
Using egg production records from White Leghorn crosses, Amuzu-Aweh et al. [ 1] showed that heterosis can be predicted using the genome-wide average squared difference in allele frequency (SDAF) between the two parental lines, with an accuracy of ~0.5.
In total, twelve of the 51 haplotypes are shared between North Africans and Iberians, but Iberians show a lower diversity (average squared difference [ASD] = 2.85) than North Africans (ASD = 9.13).
We calculate the appearance score as the average squared difference between normalized cell images (between 0 and 1) and minimize this score by rotating the images relative to each other.
The Brier score (BS) [ 25] (the average squared difference between the predicted probability and the true occurrence of a binary outcome), and the Brier score scaled (BSS) (a version of the BS that will give a more robust comparability of the accuracy of a model because it is not depending on population differences of the outcome), were also calculated.
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