Pypesto Optimization ignores bounds

I recently found that the parameter estimation of the ICG PEtab model resulted in parameters that violate the bounds given in the PEtab parameter table.

The PEtab problem I used is: icg_sd.omex.zip

And I used the following code that produced the error:

import pypesto import pypesto.petab import pypesto.optimize as optimize import pypesto.store as store

pypesto_importer = pypesto.petab.PetabImporter.from_yaml(yaml_file) pypesto_problem = pypesto_importer.create_problem()

optimizer = optimize.ScipyDifferentialEvolutionOptimizer(options = {'strategy':'best1bin', 'maxiter':8000 ,'mutation':(0.2, 1), 'recombination':0.7, 'popsize':70, 'init':'latinhypercube', 'polish':True, 'workers' : 8})

n_starts = 10 result = optimize.minimize(pypesto_problem, optimizer=optimizer, n_starts=n_starts)

store.save_to_hdf5.write_result(result, os.path.join(Path , M + '_Pypesto_Parameters.hdf5'), overwrite= True)

[shoepfl]

Okay thanks for the help - maybe that needs more clairification in the PEtab documentation as the description for the bounds state there: “Must be provided in linear space, independent of parameterScale.”

from this at least it is confusing when I have to give the bounds in linear scale explicitly but indeed the log of them are taken as boundaries. But thats probably a topic for the PEtab implementation so I will shift the discussion to there.

Thanks for your help!

[yannikschaelte]

Closing here as this concerns the petab documentation