In the calibration procedure, the subject was instructed to fixate the dot for more than 1000 ms, and we checked eye-tracking in the validation procedure in the same way as for the calibration procedure.
Importantly, we used the same bioinformatics pipeline in the original analysis and in the validation procedure: that is, the failure to validate most cases of putative superinfection did not arise from the (lack of) sensitivity of the original phylogenetics analysis, but due to erroneous entries (sequence or sample mix-up) in the original database.
In short, we did not succeed in getting GPs involved locally in the validation procedure.
In the post classification process, we applied a majority/minority analysis for generalisation of the classification image to minimise "salt and pepper effects", a term which describes the existence of dark pixels in bright regions and bright pixels in dark regions, usually causing noise in the validation procedure.
According to the experiment results, the parameter setting that achieves the lowest estimation error (12.7824) in the validation procedure is obtained as {a in = 1/8, a res = 1/2, f sparsity = 1/4, α = 1, β = 3, d S = 400}.
In the validation procedure Sulfachloropyradizine (SCL) was not eluded in any of the7 spiked samples.
Sequence alignments of both the original and the newly generated sequences of the 18 patients involved in the validation procedure and their control sequences are attached in Additional file 8. Finally, following the method of Cornelissen et al.[ 33] we also counted the number of degenerate base codes (DBC) in all available sequences.
Type-3-consistencies – based on weak evidence – and type-A-inconsistencies are not listed in this table, as they were not included in the validation procedure but needed further research for evidence (a list is provided as additional web-based material, TABLE W5).
Users can apply KJ3 to validate different types of KBSs without concerning the inference process involved in the validation procedure.
