PEtab-dev / PEtab-dev/petab_select

Doc unusual behavior of forward/backward methods

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Python
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Description

During their direct use (their use via FAMoS is not unusual), these methods keep trying to add parameters. i.e. if you start the forward method with the global subset model, and in the next iteration it's seen that all models with 1 greater parameter are worse, the usual forward method would terminate. However, in PEtab Select, then all models with 2 greater parameters are assessed, etc.

This is beneficial if a minimal number of parameters/processes/hypotheses are required in the model before a good fit to data is seen and thereby an improvement over the global subset model is found.

The usual forward method is the forward method used in the FAMoS method. We could add an option to choose between either the usual or unusual forward method during direct use.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Search the documentation and Python entry points for the direct forward and backward methods, then compare their behavior with the FAMoS use described in the issue. Document that direct use continues assessing models with additional parameters after the one-parameter step fails, explain why this can help, and distinguish it from the usual FAMoS method.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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