PEtab import: Fix potentially incorrect sensitivities with state-depe… #2562
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ndent sigmas Due to PEtab not allowing and observables in noiseFormula and AMICI not allowing state variables in sigma expressions, we are trying to replace any state variables by matching observables during PEtab import. However, if there were multiple observables with the same observableFormula, or one observableFormula was contained in another one, the substition of observableFormula for observableId could - depending on the ordering - result in noiseFormulas depending on other observables, which could lead to incorrect sensivities due to AMICI-dev#2561. This change ensures that we are only using the observableId from the same row of the observable table as the noiseFormula. --------- Co-authored-by: Dilan Pathirana <[email protected]>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #2562 +/- ##
===========================================
- Coverage 77.76% 77.75% -0.01%
===========================================
Files 325 325
Lines 21858 21857 -1
Branches 1473 1473
===========================================
- Hits 16997 16996 -1
Misses 4834 4834
Partials 27 27
Flags with carried forward coverage won't be shown. Click here to find out more.
|
FFroehlich
approved these changes
Oct 24, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
…ndent sigmas
Due to PEtab not allowing and observables in noiseFormula and AMICI not allowing state variables in sigma expressions, we are trying to replace any state variables by matching observables during PEtab import.
However, if there were multiple observables with the same observableFormula, or one observableFormula was contained in another one, the substition of observableFormula for observableId could - depending on the ordering - result in noiseFormulas depending on other observables, which could lead to incorrect sensitivities due to #2561.
This change ensures that we are only using the observableId from the same row of the observable table as the noiseFormula.