Making an iterative parameter scan


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26 days ago by
Dear reader,

I would like to make a series of simulations that change some of the parameters in the xml file depending on the result of previous simulation, e.g. general diffusion constant. This series would stop when the model solution value is close enough to the experimental value, e.g. distance of certain cells to other cells in a given region.

If I just run regular parameter scans, I can give a string of predefined values, but I would need that this value changes after each simulation run, according to e.g. Newton's method, towards the solution. Is this possible? This would come to my article's chapter called 'parameter estimation'.

Thank you once again for all possible help!

Best regards,
Pauli
Community: CompuCell3D

2 Answers


2
21 days ago by
I'm not sure if it is practical to modify and/or intervene in the parameter sweep scripts. I think a better approach would be to write a python script specifically for the optimization and fitting task.

I have a Particle Swarm script that wraps around a CC3D project that will attempt to locate an optimal set of parameters. For complex systems the swarm approach is more likely to find a global minimum than are gradient based methods. Swarms parallelize extremely well (unlike gradient methods) so if you have access to a cluster the process can be fast and efficient. If you are interested in this development code let me know and I'll tell you what is needed. If the project isn't too big, we can use our 64-cpu cluster for the optimization.
1
Hi,

I would be interested in this 'particle swarm' script, and would like to know what is needed. However, at the moment I do not have an access to cluster computing, but I do have a good computer, but possibly get an access to cluster quite soon.
written 19 days ago by Pauli Tikka  
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I am also interested in the particle swarm script.
written 18 days ago by Scott H  
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26 days ago by
I would like to know more also. This would help since I want to use the iteration number in naming the output files. How do I access the CurrentIteration value in the ParameterScan xml    from the .py steppables?
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