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To classify an unknown tuple, X, each tree returns its class prediction counting as one vote.
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Only one of these (CID 659940) actually has a pIC50 value above 5.5 but the toxic prediction counts it as true active.
We also note that many of the predictions counted as FP nonetheless have biologically relevant connections between the predicted family and the compound, so the quoted MCC may underestimate the true number of biologically meaningful predictions.
Another truism is that novel predictions count more.
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.
Prediction counts indicate the number of deleterious predictions (Del count) and conservation predictions (Con count) by six and three programs, respectively.
Although there is such a large difference in prediction count, the final results are about the same, indicating that a lot of the predictions are redundant.
The TNL and CNL prediction counts are summarised in Table 2 and compared to the initial analysis from the PGSC [ 22].
This leads to the prediction that counting rate with mouse perturbation will decrease, as participants are able to allocate less attention to that task.
Most methods have a single vote, while PSIPRED for secondary structure prediction and Phobius for signal peptide prediction are counted as two votes due to their documented high accuracy [ 60, 65].
Conflicting predictions of a signal peptide and a transmembrane region in the same sequence were resolved as follows: i) if the prediction was within 15 codons from the 5' end then the prediction was counted as a signal peptide; ii) if the signal peptide was predicted anywhere else, Phobius [ 57] was used to confirm either prediction.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com