The default models included with ampir are both SVMs with radial
kernel and have two tuning parameters, sigma and C (cost). Optimal
values for these tuning parameters were obtained by using model tuning
functions available in caret. Since this is computationally intensive
it was performed on an HPC system. The R script scripts/tune_model.R
provides a convenient wrapper for the required functions and allows it
to be run easily on an HPC system. See the scripts directory for
details of how this was run.
Inspecting the results for the mature peptide model reveals the variation of model performance with the tuning parameters.
Best tune:
## sigma C
## 57 0.06 1
And for the precursor model:
Best tune:
## sigma C
## 104 0.1 4