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Fix bounds and scales for some parameters in Isensee_JCB2018 #132
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Hi @dilpath
Why were these changes included? The original bounds and scales for the modified parameters in this pull request were originally set to be in linear scale with the given boundaries.
See https://github.com/Data2Dynamics/d2d/blob/master/arFramework3/Examples/Isensee_JCB2018/Setup.m
EDIT: Therefore, unless this was specifically requested for some reason, I think there is nothing to fix here.
The model doesn't appear to unscale the parameter, so estimating in |
I see what you mean. However, the parameter in the d2d implementation is set to |
If an error occurs in AMICI/pyPESTO, it could be fixed I think, since zero can still be used on log-scale with NumPy: >>> import numpy as np
>>> np.log(0.0)
-inf
>>> np.exp(np.log(0.0))
0.0 Inclusion of zero in the bounds would still be problematic. |
I believe this is an artifact from the d2d implementation where it seems like parameters can only be fixed on a linear scale (see for example reduced/regular version of Lucarelli) |
@FFroehlich would then fix the parameter value at zero + defining log10 scale work in the AMICI/pyPESTO import ? As far as I know, pyPESTO works with the parameters in the defined scale, therefore |
Ah, thats a good point. I did not check but I can definitely see this being problematic for other tools (e.g., d2d) , even if it works in AMICI/pyPESTO. So I wouldn't recommend changing this. |
I do however see the issue that this causes trouble when for example trying to run model selection where some parameters are fixed/unfixed. I would say the best way to address this is to add additional indicator variables (e.g., representing the matlab variables |
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