OpenFreeEnergy / OpenFreeEnergy/openfe
Forward and reverse analysis: Subsample at each analysis fraction
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Currently, subsampling is done on the full amount of the data points to obtain the uncorrelated samples. That can lead to only very few uncorrelated samples at e.g. 10% of the simulation time.
This results in
- endless loops when doing the bootstrapping for the error and
- gigantic jumps in DG which prevents these plots from being useful for analysis.
We should think about subsampling the data to obtain the uncorrelated samples at every analysis point, meaning doing the subsampling at 10% of the data, 20%,...
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the forward and reverse analysis entry points and the subsampling and bootstrapping logic described in the issue. Trace how analysis fractions such as 10% and 20% currently obtain uncorrelated samples; done means each fraction is subsampled independently without endless bootstrapping loops or unusably large DG jumps.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100