Jonas Arruda comments

Results 12 comments of


                                            Jonas Arruda

Adding a small tutorial how to use SBML models with BayesFlow

I just rerun the notebook and pushed it again. At least I can view it with the GitHub renderer

Calling prior in sampling with fixed parameters does not work

I reverted the inital fix since I found a better solution. If you now call `problem.x_priors` it behaves exactly as `problem.objective`, which is the behaviour I would expect (wrt fixed...

Calling prior in sampling with fixed parameters does not work

After discussion, @PaulJonasJost and I removed the deepcopy of the `NegLogParameterPriors` class. Otherwise, copying the prior does not work. This happens in the parallel tempering sampler, when the prior is...

Adaptive Stopping and Continuation of Sampling

Actually, the dynesty sampler already allows to do both

Update `test_thermodynamic_integration`

True, this is not neceassary as a test. It was included to check convergence of the evidence estimation. Okay for me to remove it to speed up testing time.

Missing Dependency

I agree, same here! #6 seems related

Make spline parameters available for user for non-linear semi-quantitative data

Is the spline mapping saved somewhere? In other words, if I load a result and create the same petab problem, will I get the same results? I noticed that for...

Aggregated Objective does not return expected outputs using `return_dict`

maybe @dweindl can help here?

Aggregated Objective does not return expected outputs using `return_dict`

> I would rather handle `AggregatedObjective` separately in the visualization code instead of adding `amici_model` to `AggregatedObjective`, since there will probably be multiple models. Okay, I thought that `AggregatedObjective` is...

Aggregated Objective does not return expected outputs using `return_dict`

> @arrjon can this be closed with the merge of #1411? Regarding visualisation the bug is fixed. However, `pypesto_problem.objective(x, return_dict=True)` does still return empty `rdatas` when using an aggregated objective,...