Clarify interpretation of noise distributions #656
Merged
Conversation
This file contains hidden or 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
dweindl
reviewed
Jan 15, 2026
dweindl
reviewed
Jan 15, 2026
doc/v2/documentation_data_format.rst
Outdated
| :math:`y:=\text{observableFormula}` the simulated value | ||
| (the location parameter of the noise distribution), | ||
| (the median of the noise distribution), | ||
| and :math:`\sigma` the scale parameter of the noise distribution |
Member
There was a problem hiding this comment.
Same problem here, right? For the log-normal distribution, sigma wouldn't be the scale but its logarithm?
Contributor
Author
There was a problem hiding this comment.
Actually, for normal distributions it is the standard distribution (no log), while for Laplace it is the scale. I have made this clearer.
matthiaskoenig
approved these changes
Jan 15, 2026
Co-authored-by: Dilan Pathirana <[email protected]>
dilpath
approved these changes
Jan 18, 2026
Member
There was a problem hiding this comment.
Thanks, now just for consistency and to make the table narrower, I'll shorten the other descriptions too.
Removes the horizontal scrollbar on the table for me: https://petab--656.org.readthedocs.build/en/656/v2/documentation_data_format.html#noise-distributions
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
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Outdated suggestions cannot be applied.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.
When implementing support for
LogLaplacein PEtab.jl, I realized that the interpretation of the noise distributions in the spec is not entirely clear. In particular, for the supported distributions, the model output is not assumed to be the mean or location of the data distribution, but rather its median.For example, let ($m$ ) be the measured value, $y := \text{observableFormula}$ the simulated value, and $\sigma$ the noise. For the $\log(m) \sim \mathcal{N}(\log(y), \sigma)$ , which implies $m \sim \mathcal{LN}(\log(y), \sigma)$ . For this
LogNormaldistribution in PEtab we haveLogNormal, the median isy(expof first argument). A similar interpretation holds forLogLaplace. Overall, this PR aims to clarify this.