Dilan Pathirana

- A protocol for dynamic model calibration - https://doi.org/10.1093/bib/bbab387 - PEtab—Interoperable specification of parameter estimation problems in systems biology - https://doi.org/10.1371/journal.pcbi.1008646 - (mentioned, uncited) Mini-batch optimization enables training of ODE...

The messages appear far greater than `N` times, e.g. using the problem from #881 and the following script. ```python import pypesto.petab import pypesto.optimize petab_yaml = 'icg_sd.yaml' pypesto_importer = pypesto.petab.PetabImporter.from_yaml(petab_yaml) pypesto_problem...

> LGTM, but please wait for others' feedback. > > Why was the extra test model required? Would keep things simpler if we could use benchmark collection model that's already...

> Not sure whether the implementation here is correct. Might also explain why errors are high for petab test models. I agree with Daniel that we should ideally get this...

> a comment to the respective optimizers If it's made very clear to the user (e.g. a warning) then I agree, otherwise it could be an easy thing to overlook,...

Hi, could you please define the objective function that you'd like to use? If least squares is fine, you can simply set the following for all observables: `noiseDistribution=normal` and `noiseFormula=1`....

There's documentation on the objective function in the PEtab [1] and AMICI [2] docs. As for why the parameters are estimated to be at the lower bound, there could be...

> However, if we want to estimate more than those 4 parameters, the problem occurs again (all estimated parameters are estimated to their lower bound). Presumably, `objective_function(synthetic_parameters)` is the global...

Some of these errors shouldn't be ignored, e.g. > 2023-03-23 12:11:50.664 - amici.swig_wrappers - WARNING - [model1_data1][AMICI:NaN] AMICI encountered a NaN value for x0_rdata[0] (R) 2023-03-23 12:11:50.664 - amici.swig_wrappers -...

Thanks, are you able to share the scripts for optimization and then simulation? Since optimization for one start `"time"` in your log is just 19 seconds, I would suggest not...