With bioinformatic predictions yielding little information (Fig. 2a, c), we set about the biochemical characterization of AcrIIA6.
A complementary continuity correction of 1 was added to each prediction count, yielding a sample error rate of 0.5 for values of k for which the training pool contains no predictions at all.
The QSAR model correctly classified 88.55% of compounds in this external prediction set, yielding a MCC of 0.77.
I am more in the parametric modeling camp, but appreciate the prediction perspective as yielding a simple and unified approach to problems in statistics the overarching objective being to predict the things you dont know, with appropriate measures of uncertainty.
Whether or not a given pair of proteins is truly orthologous is unknown (a latent class), but each of the methods under consideration makes a yes/no prediction as to orthology, yielding a pattern comprised of 1's and 0's representing the predictions from all methods.
Bady P, Sciuscio D, Diserens AC, Bloch J, van den Bent MJ, Marosi C, et al. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status.
In 10,000 replicates of this simulation, the proportion of replicates yielding a prediction rate exceeding that obtained in the actual data using the posterior expectations of the θi was only 0.0236.
Use of the CDS-ID score only represented a significant improvement over prediction using age only, yielding a c-statistic of 0.653 955% CI 0.617, 0.689, chi-square P=0.04).
This value is chosen in order to balance the contribution of molecular weight and thermodynamic penalty, yielding a prediction considering both costs (Additional file 1: Figure S1).
The weights assigned for the different signals were more relevant for the AP contribution compared to the HR in terms of syncope prediction, yielding 95% sensitivity and 93% specificity.
