Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Decouple AmiciPredictor from AmiciObjective #1291

Open
dweindl opened this issue Jan 23, 2024 · 1 comment
Open

Decouple AmiciPredictor from AmiciObjective #1291

dweindl opened this issue Jan 23, 2024 · 1 comment
Labels
AMICI enhancement New feature or request ensembles Related to parameter ensembles

Comments

@dweindl
Copy link
Member

dweindl commented Jan 23, 2024

Currently, pypesto.predict.amici_predictor.AmiciPredictor.__init__ requires a pypesto.objective.amici.amici.AmiciObjective.
Constructing an AmiciPredictor from an AmiciObjective is admittedly convenient. However, requiring an AmiciObjective renders it unnecessarily complicated to make ensemble predictions for anything other than the original parameter estimation problem (e.g., prediction for unseen experimental conditions).

The only things that AmiciPredictor should require, are an amici model, a (potentially optional) list of amici.ExpData, an amici.Solver, and a parameter mapping. Therefore, I'd suggest to refactor AmiciPredictor to be constructable from only those inputs, while preserving the possibility to construct it from an AmiciObjective.

EDIT: Not so easy to decouple in the case of hierarchical optimization, since the inner parameters aren't included in the ensemble. However, it's questionable if the current state, i.e. recomputing the inner parameters is desirable. I'd say that mostly ones wants the optimal inner parameters computed from the training data and not from any unseen data.

@dweindl dweindl added enhancement New feature or request AMICI ensembles Related to parameter ensembles labels Jan 23, 2024
@PaulJonasJost
Copy link
Collaborator

so we could add a convenience static function from AmiciObjective? 🤔

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
AMICI enhancement New feature or request ensembles Related to parameter ensembles
Projects
None yet
Development

No branches or pull requests

2 participants