Dilan Pathirana
Dilan Pathirana
Now handled on the PEtab Select side
I have been using hdfdict [1] with pydantic objects, no issues so far in my basic use cases (including numpy arrays), which has lazy loading on by default. Hopefully the...
Yes, fine for me :+1:
Agreed, I haven't looked into it, but it would be great to be able to apply ArviZ methods to pyPESTO sampling results. For now, since you mentioned the emcee output...
@Doresic you can use https://github.com/PEtab-dev/petab_select/pull/86 for nicer model hashes, when saving histories
Mostly re-iterating what @PaulJonasJost said. re: PEtab Timecourse, you can use PEtab Timecourse to specify your problem as, e.g. "simulate with condition H for 100 time units, then use the...
You can achieve this with yaml2sbml, there's an example of a piecewise [1]. In your case, the yaml2sbml expression for `k = k_H if H_flag == 1 else k_P` could...
Yes, the objective function (here, written as the negative log likelihood) will be constructed from the measurements table, so will look like J_healthy_1 + J_patient_1 + J_healthy_2 + J_patient_2 +...
The conditions and measurements table are what I meant :+1: The error when linting occurs because the parameters `*_H` and `*_P` are now the estimated parameters, so remove e.g. `p38`...
Sorry for the mistake, I spoke with @dweindl , it seems that this setup is currently not supported by AMICI, because gradients for parameter estimation will only be returned for...