This directory includes a demonstration of the fitness function
and optimization method described in
Weaver, CM and Wearne, SL. The role of action potential shape
and parameter constraints in optimization of compartment models.
Neurocomputing 69: 1053-1057, (2006).
I. To run this demo:
Either Auto-launch from ModelDB or
1) download and extract the archive.
2) Then under
unix/linux: type the following at the command line:
nrnivmodl model optmz
mswin: start nrngui (from the start button ->Programs -> NEURON 5.9
for example) then File -> working dir to first the model
directory and then File -> working dir to the optmz directory.
Then you can File -> load hoc and select mosinit.hoc.
mac OS X: running under mac is under development
Once the model is running you can press the "Testing Shapes" windows
buttons (e.g. "Matched to Target", etc.) to select alternate initial
A. Different Objective Functions
This demo evaluates the difference betweeen model and target data by
two different functions, specified under the Multiple Run Fitter
(1) RegionFitness, i.e. mean squared error between voltage traces
(2) APShpFRCVFitness: a linear combination of the errors in
time-aligned AP shape, mean FR, and irregularity measured by the
CV. (See Weaver and Wearne reference above). The weights of each
component can be changed by displaying the APShpFRCVFitness
generator, then choosing Select, followed by the appropriate
drop-down menu choice.
Click on one of the buttons to the left. This will initialize the
model, run it, and evaluate the error between that model and the
target data shown in the MRF windows.
Summary data are written to matlab files (.m extension) that print the
model and target voltage traces, plus a summary of the AP Shape / FR /
CV error. The name of this output file can be changed by bringing up
the appropriate MRF Generator and choosing Select -> Set output info.
B. Simulated annealing for parameter optimization
If you go to the MRF window and choose Parameters -> Select
Optimizer, there are two new options:
- Simulated Annealing
- Constrained Simulated Annealing with Recentering
The first, implemented by Andrew Davison, performs the
Simplex-based simulated annealing optimization algorithm found in
Numerical Recipes in C.
The second, implemented by Christina Weaver, performs a version of
this algorithm that incorporates constraints on the parameters to
be optimized. See Weaver and Wearne (2006) for details, and for
the original reference (Cardoso et al. 1996) which introduced this
algorithm. See the enclosed PDF help file for details of this
In addition to a new set of Optimizer menu items specific to these
optimization techniques, one change has been made to the general
MRF Optimize menu. In the past the output from a parameter search
was always output to the same filename, so that one would often
run the risk of overwriting previous searches. The name of the
output file can be changed by clicking on "Change output filename"
and entering a new string, e.g. "filename". Data will be written
to "filename".tmp during the search, and "filename".fit once the
search has finished.
II. Files in the model/ directory:
sample .m output files:
III. Files in the optmz/ directory
mulfit.hoc: goes just above mulfit/ directory
feature_weaver.mod: to incorporate new Vector functions
simanneal_seq_weaver_Feb07.hoc (Unconstrained SA)
simanneal_cardoso.hoc (Constrained SA + Recenter)
I think this is everything a user would need to reproduce my
functions. I removed a lot of comments & debugging stuff from the
e_apwinfrcv.hoc file - I hope I didn't break something in the
Other files in this directory:
weaver06_Optimization.pdf: The Weaver & Wearne reference cited above.
simanneal_unconst.html: HTML help file written by Andrew Davison
simannrctr_help.pdf: Constrained Simulated Annealing help file.
20131216 Model updated to work with NEURON version 7.3. A variable
"t" was changed to "tt" in the opmtx/feature_weaver.mod file.