How it works¶

Model fitting script requires three components:
• A Fitter of choice: object that will perform the optimization
• A metric: to compare results and decide which one is the best
• An optimization algorithm: to decide which parameter combinations to try

All of which need to be initialized for fitting application. Each optimization works with a following scheme:

opt = Optimizer()
metric = Metric()

fitter = Fitter(...)
result, error = fitter.fit(metric=metric, optimizer=opt, ...)


The proposed solution is developed using a modular approach, where both the optimization method and metric to be optimized can be easily swapped out by a custom implementation.

Fitter objects require ‘model’ defined as an Equations object or as a string, that has parameters that will be optimized specified as constants in the following way:

model = '''
...
g_na : siemens (constant)
g_kd : siemens (constant)
gl   : siemens (constant)
'''

Initialization of Fitter requires:
• dt - time step
• input - set of input traces (list or array)
• output - set of goal output (traces/spike trains) (list or array)
• input_var - name of the input trace variable (string)
• output_var - name of the output trace variable (string)
• n_samples - number of samples to draw in each round (limited by method)
• reset, and threshold in case of spiking neurons (can take refractory as well)

Additionally, upon call of fit(), object requires:

• n_rounds - number of rounds to optimize over
• parameters with ranges to be optimized over

…as well as an optimizer and a metric

Each free parameter of the model that shall be fitted is defined by two values:

param_name = [min, max]


Alongside three optimization classes:
and metrics:

Example of TraceFitter with all of the necessary arguments:

fitter = TraceFitter(model=model,
input=inp_traces,
output=out_traces,
input_var='I',
output_var='v',
dt=0.1*ms,
n_samples=5)

result, error = fitter.fit(optimizer=optimizer,
metric=metric,
n_rounds=1,
gl=[1e-8*siemens*cm**-2 * area, 1e-3*siemens*cm**-2 * area],)


Remarks¶

• After performing first fitting, user can continue the optimization with another fit() run.
• Number of samples can not be changed between rounds or fit() calls, due to parallelization of the simulations.

Warning

User is not allowed to change the optimizer or metric between fit() calls.