Model tuning

The most basic command to tune your model looks like the following; it looks for the file that was generated in the training step:

# Running GenoML supervised tuning after munging and training on discrete data

genoml discrete supervised tune \

--prefix outputs/test_discrete_geno

If you are interested in changing the number of iterations the tuning process goes through by modifying --max_tune (default is 50), or the number of cross-validations by modifying --n_cv (default is 5), this is what the command would look like:

# Running GenoML supervised tuning after munging and training on discrete data, modifying the number of iterations and cross-validations

genoml discrete supervised tune \

--prefix outputs/test_discrete_geno \

--max_tune 10 --n_cv 3

If you are interested in tuning on another metric other than AUC (default is AUC), you can modify --metric_tune (options are AUC or Balanced_Accuracy) by doing the following:

# Running GenoML supervised tuning after munging and training on discrete data, modifying the metric to tune by

genoml discrete supervised tune \

--prefix outputs/test_discrete_geno \

--metric_tune Balanced_Accuracy