However, the resulting false positives in Fig 2D show that the information within these shape metrics is insufficient to distinguish the grinder with high specificity.

In other words, we aim to minimize false negatives while tolerating a moderate number of false positives .

Therefore, we optimize the SVM parameters via the minimization of an adjusted error rate that penalizes false negatives more than false positives (Fig 3B).

along with the selection of the most likely candidate in images with multiple positive classification results is used to eliminate these false positives .

The precision plot shows, given a value of Ml°, the number of true positives with MI>M|0 identified with deep sequencing divided by the number of true and false positives with MI>M|0 versus the percentage of all pairs with MI>M|°.

As additional evidence that we observe meaningful correlations derived from the deep sequencing using our bounding procedure to constrain the bivariate probabilities, we note that many of the apparent false positive pairs of mutations in protease identified in our analysis may be biologically important because these pairs contain at least one variant associated with PI-eXposure.

Moreover, in the top 5% of pairs with highest MI from deep sequencing, 34 of the 58 pairs identified as putative false positives involve at least one known resistance mutation.