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Simbiology Previous Initial Parameters

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grace
grace ongeveer 20 uur ago
Commented: grace ongeveer 19 uur ago
Hi! So I saved a run when I was doing fitting for my data, and put the results in a folder on the Simbiology model analzyer dashboard. I wanted to replicate that saved data but I can't seem to find where the initial parameters for that run are stored? If anyone could help or if there's any way I can further clarify please let me know!

Answers (1)

Arthur Goldsipe
Arthur Goldsipe ongeveer 20 uur ago
The results of a fit only contain the outputs of the fit itself (for example, parameter estimates). If you want to reproduce those results, you would need to save a copy of the program and make sure you don't change the program's configuration or anything else the program depends on (like your model). The easiest way to do that is probably to make a backup copy of your SimBiology project (sbproj file), so that you can rerun the same program.
That said, you might need to take extra steps to ensure the project contains everything you need to reproduce the results. For example, if you are using a global optimization method that has a stochastic/random element to it (like scattersearch), you would need to ensure that the random number generator is in the same state every time you run the program. The easiest way to ensure that is to configure your program to set the random number generator's seed.
Even then, don't assume that you will get exactly the same results if you use a different computer or a different version of MATLAB. Remember that you are calculating approximate solutions subject to the limitations of floating point arithmetic. Hardware and software differences can lead to changes in the approximations. For simple arithmetic operations, such changes are typicall quite small. When simulating a complex SimBiology model, the differences can compound. And then when you add optimization on top of that, you might see even more differences. You can often reduce those differences by using tight solver tolerances for your SimBiology simulations, and tight convergence criteria for your optimizations.
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Arthur Goldsipe
Arthur Goldsipe ongeveer 19 uur ago
That's mostly correctly. There's no documented way to get the initial parameters.
However, I just took a closer look at the internal implementation details of fit results and I may have found an undocumented way to recover that information. If you would like to try, can you message me directly via my profile? If you are willing to share your project, I can see if I can extract the initial parameter values. If you can't share your project, I will see if I can sharing the undocumented approach with you.
grace
grace ongeveer 19 uur ago
Yes, I will message you

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