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--quick-validation flag has bad hyperparameter selection
https://github.com/percolator/percolator/commit/6b325c23665d6ff64b0ff1ce28371424dcc88d17 seems to have introduced a bug in the --quick-validation
flag.
Previously, the best cpos
and cfrac
were found using a grid search in the first cross validation set. These optimal values were then reused in the remaining folds. After the commit, cpos=1
and cfrac=1
were hard coded for all folds. This can lead to suboptimal results.
This behavior affects v3.05 and beyond.