Advanced Features¶
Importing externallydefined cell models¶
NetPyNE provides support for internally defining cell properties of for example HodgkinHuxley type cells with one or multiple compartments, or Izhikevich type cells (eg. see NetPyNE Tutorial). However, it is also possible to import previously defined cells in external files eg. in hoc cell templates, or cell classes, using the importCellParams()
method. This method will convert all the cell information into the required NetPyNE format. This way it is possible to make use of cells which have been implemented separately.
The cellRule = netParams.importCellParams(label, conds, fileName, cellName, cellArgs={}, importSynMechs=False)
method takes as arguments the label of the new cell rule, the name of the file where the cell is defined (either .py or .hoc files), and the name of the cell template (hoc) or class (python). Optionally, a set of arguments can be passed to the cell template/class (eg. {'type': 'RS'}
). If you wish to import the synaptic mechanisms parameters, you can set the importSynMechs=True
. The method returns the new cell rule so that it can be further modified.
NetPyNE contains NO builtin information about any of the cell models being imported. Importing is based on temporarily instantiating the external cell model and reading all the required information (geometry, topology, distributed mechanisms, point processes, etc.).
Below we show example of importing 10 different cell models from external files. For each one we provide the required files as well as the NetPyNE code. Make sure you run nrnivmodl
to compile the mod files for each example. The list of example cell models is:
Additionally, we provide an example NetPyNE file (tut_import.py
) which imports all 10 cell models, creates a population of each type, provides background inputs, and randomly connects all cells. To run the example you also need to download all the files where cells models are defined and the mod files (see below). The resulting raster is shown below:
HodgkinHuxley model¶
Description: A 2compartment (soma and dendrite) cell with hh
and pas
mechanisms, and synaptic mechanisms. Defined as a Python class.
Required files:
HHCellFile.py
NetPyNE Code
netParams.importCellParams(
label='PYR_HH_rule',
conds={'cellType': 'PYR', 'cellModel': 'HH'},
fileName='HHCellFile.py',
cellName='HHCellClass',
importSynMechs=True)
HodgkinHuxley model with 3D geometry (from .hoc)¶
Description: A multicompartment cell. Defined as a HOC cell template. Only the cell geometry is included. Example of importing only geometry, and then adding biophysics (hh
and pas
channels) from NetPyNE.
Required files:
geom.hoc
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_HH3D_hoc',
conds={'cellType': 'PYR', 'cellModel': 'HH3D'},
fileName='geom.hoc',
cellName='E21',
importSynMechs=False)
cellRule['secs']['soma']['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': 70} # soma hh mechanism
for secName in cellRule['secs']:
cellRule['secs'][secName]['mechs']['pas'] = {'g': 0.0000357, 'e': 70}
cellRule['secs'][secName]['geom']['cm'] = 1
HodgkinHuxley model with 3D geometry (from .swc)¶
Description: A multicompartment cell, with imported morphology from an SWC file. Only the cell geometry is included. Example of importing only geometry, and then adding biophysics (hh
and pas
channels) from NetPyNE.
Importing a morphology into NetPyNE from an SWC file is simple, but NetPyNE does no testing or validation of morphologies, so you should ensure your morphology file is accurate and valid before using it in NetPyNE.
Required files:
BS0284.swc
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_HH3D_swc',
conds={'cellType': 'PYR', 'cellModel': 'HH3D'},
fileName='BS0284.swc',
cellName='swc_cell')
netParams.renameCellParamsSec('PYR_HH3D_swc_rule', 'soma_0', 'soma') # rename imported section 'soma_0' to 'soma'
for secName in cellRule['secs']:
cellRule['secs'][secName]['mechs']['pas'] = {'g': 0.0000357, 'e': 70}
cellRule['secs'][secName]['geom']['cm'] = 1
if secName.startswith('soma'):
cellRule['secs'][secName]['mechs']['hh'] = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': 70}
Traub model¶
Description: Traub cell model defined as hoc cell template. Requires multiple mechanisms defined in mod files. Downloaded from ModelDB and modified to remove calls to figure plotting and others. The km
mechanism was renamed km2
to avoid collision with a different km
mechanism required for the Traub cell model. Synapse added from NetPyNE.
ModelDB link: http://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=20756
Required files:
pyr3_traub.hoc
,
ar.mod
,
cad.mod
,
cal.mod
,
cat.mod
,
k2.mod
,
ka.mod
,
kahp.mod
,
kc.mod
,
kdr.mod
,
km2.mod
,
naf.mod
,
nap.mod
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_Traub_rule',
conds= {'cellType': 'PYR', 'cellModel': 'Traub'},
fileName='pyr3_traub.hoc',
cellName='pyr3')
somaSec = cellRule['secLists']['Soma'][0]
cellRule['secs'][somaSec]['spikeGenLoc'] = 0.5
Mainen model¶
Description: Mainen cell model defined as python class. Requires multiple mechanisms defined in mod files. Adapted to python from hoc ModelDB version. Synapse added from NetPyNE.
ModelDB link: http://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=2488 (old hoc version)
Required files:
mainen.py
,
cadad.mod
,
kca.mod
,
km.mod
,
kv.mod
,
naz.mod
,
Nca.mod
NetPyNE Code:
netParams.importCellParams(
label='PYR_Mainen_rule',
conds={'cellType': 'PYR', 'cellModel': 'Mainen'},
fileName='mainen.py',
cellName='PYR2')
Friesen model¶
Required files: Friesen cell model defined as python class. Requires multiple mechanisms (including point processes) defined in mod files. Spike generation happens at the axon
section (not the soma
). This is indicated in NetPyNE adding the spikeGenLoc
item to the axon
section entry, and specifying the section location (eg. 0.5).
Required files:
friesen.py
,
A.mod
,
GABAa.mod
,
AMPA.mod
,
NMDA.mod
,
OFThpo.mod
,
OFThresh.mod
,
netcon.inc
,
ofc.inc
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_Friesen_rule',
conds={'cellType': 'PYR', 'cellModel': 'Friesen'},
fileName='friesen.py',
cellName='MakeRSFCELL')
cellRule['secs']['axon']['spikeGenLoc'] = 0.5 # spike generator location.
Izhikevich 2003a model (independent voltage variable)¶
Description: Izhikevich, 2003 cell model defined as python class. Requires point process defined in mod file. This version is added to a section but does not employ the section voltage or synaptic mechanisms. Instead it uses its own internal voltage variable and synaptic mechanism. This is indicated in NetPyNE adding the vref
item to the point process entry, and specifying the name of the internal voltage variable (V
).
Modeldb link: https://senselab.med.yale.edu/modeldb/showModel.cshtml?model=39948
Required files:
izhi2003Wrapper.py
,
izhi2003a.mod
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_Izhi03a_rule',
conds={'cellType': 'PYR', 'cellModel':'Izhi2003a'},
fileName='izhi2003Wrapper.py',
cellName='IzhiCell',
cellArgs={'type':'tonic spiking', 'host':'dummy'})
cellRule['secs']['soma']['pointps']['Izhi2003a_0']['vref'] = 'V' # specify that uses its own voltage V
Izhikevich 2003b model (uses section voltage)¶
Description: Izhikevich, 2003 cell model defined as python class. Requires point process defined in mod file. This version is added to a section and shares the section voltage and synaptic mechanisms. A synaptic mechanism is added from NetPyNE during the connection phase.
Modeldb link: https://senselab.med.yale.edu/modeldb/showModel.cshtml?model=39948
Required files:
izhi2003Wrapper.py
,
izhi2003b.mod
NetPyNE Code:
netParams.importCellParams(
label='PYR_Izhi03b_rule',
conds={'cellType': 'PYR', 'cellModel':'Izhi2003b'},
fileName='izhi2003Wrapper.py',
cellName='IzhiCell',
cellArgs={'type':'tonic spiking'})
Izhikevich 2007a model (independent voltage variable)¶
Description: Izhikevich, 2007 cell model defined as python clas. Requires point process defined in mod file. This version is added to a section but does not employ the section voltage or synaptic mechanisms. Instead it uses its own internal voltage variable and synaptic mechanism. This is indicated in NetPyNE adding the vref
item to the point process entry, and specifying the name of the internal voltage variable (V
). The cell model includes several internal synaptic mechanisms, which can be specified as a list in NetPyNE by adding the synList
item to the point process entry.
Modeldb link: https://senselab.med.yale.edu/modeldb/showModel.cshtml?model=39948
Required files:
izhi2007Wrapper.py
,
izhi2007a.mod
NetPyNE Code:
cellRule = netParams.importCellParams(
label='PYR_Izhi07a_rule',
conds={'cellType': 'PYR', 'cellModel':'Izhi2007a'},
fileName='izhi2007Wrapper.py',
cellName='IzhiCell',
cellArgs={'type':'RS', 'host':'dummy'})
cellRule['secs']['soma']['pointps']['Izhi2007a_0']['vref'] = 'V' # specify that uses its own voltage V
cellRule['secs']['soma']['pointps']['Izhi2007a_0']['synList'] = ['AMPA', 'NMDA', 'GABAA', 'GABAB'] # specify its own synapses
Izhikevich 2007b model (uses section voltage)¶
Description: Izhikevich, 2007 cell model defined as python class. Requires point process defined in mod file. This version is added to a section and shares the section voltage and synaptic mechanisms.
Modeldb link: https://senselab.med.yale.edu/modeldb/showModel.cshtml?model=39948
Required files:
izhi2007Wrapper.py
,
izhi2007b.mod
NetPyNE Code:
netParams.importCellParams(
label='PYR_Izhi07b_rule',
conds={'cellType': 'PYR', 'cellModel':'Izhi2007b'},
fileName='izhi2007Wrapper.py',
cellName='IzhiCell',
cellArgs={'type':'RS'})
The full code to import all cell models above and create a network with them is available here: tut_import.py
.
Parameter Optimization of a Simple Neural Network Using An Evolutionary Algorithm¶
This tutorial provides an example of how to use inspyred, an evolutionary algorithm toolkit, to optimize parameters in our prior tut2.py** neural network–modified to remove any code relating to initiating network simulation and output display–, such that it achieves a target average firing rate around (~) 17 Hz.
**Some modification is required near the end of the tut2.py code, to
remove any code relating to initiating network simulation and output
display, all of which has now been handled in the new top level code
(tut_optimization.py
):
# Create network and run simulation
# sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig) # line commented out
# import pylab; pylab.show() # if figures appear empty # line commented out
excerpt from tut2.py
Additional Background Reading¶
A description of the algorithm methodology that will be used to optimize the simple neural network in this example.
Introduction¶
Using the inspyred python package to find neural network parameters so that some property of the network (e.g. firing rate) matches a desired target can be broken down into 3 steps. First, 1) defining a desired target model (in this case, some measurable value) and fitness function–fitness defined here as a calculable value that represents how close a neural network with a given parameters matches the target. Subsequently, it is necessary to 2) determine the appropriate neural network parameters to modify to achieve that model/value. Finally, 3) appropriate parameters for the evolutionary algorithm are defined. Ultimately, If the inputs to the evolutionary algorithm are appropriate, then over successive iterations, the parameters determined by the evolutionary algorithm should generate models closer to the target.
Particularizing these 3 steps to our example we get:
Defining a desired target model and fitness function.
Defining a desired target model is largely arbitrary, some constraints being that there must be a way to adjust parameters such that the results are closer to the target model than before (or that fitness is improved), and that there must be a way to evaluate the fitness of a model with given parameters. In this case, our target model is a neural network that achieves an average firing rate of 17 Hz. The fitness for such a model can be defined as the difference between the average firing rate of a certain model and the target firing rate of 17 Hz.
Selecting the model parameters to be optimized.
If a parameter can in some way alter the fitness of the final model, it may be an appropriate candidate for optimization, depending on what the model is seeking to achieve. As well as a host of other parameters, altering the probability, weight or delay of the synaptic connections in the neural network can affect the average firing rate. In this example, we will optimize the values of the probability, weight and delay of connections from the sensory to the motor population.
Selecting appropriate parameters for the evolutionary algorithm.
inspyred allows customization of the various components of the evolutionary algorithm, including:
a selector that determines which sets of parameter values become parents and thus which parameter values will be used to form the next generation in the evolutionary iteration,
a variator that determines how each current iteration of parameter sets is formed from the previous iteration,
a replacer which determines whether previous sets of parameter values are brought into the next iteration,
a terminator which defines when to end evolutionary iterations,
an observer which allows for tracking of parameter values through each evolutionary iteration.
Using inspyred¶
The evolutionary algorithm is implemented the ec module from the inspyred package:
from inspyred import ec # import evolutionary computation from inspyred
excerpt from tut_optimization.py
ec includes a class for the evolutionary computation algorithm: ec.EvolutionaryComputation(), which allows entering parameters to customize the algorithm. The evolutionary algorithm involves random processes (e.g. randomly mutating genes) and so requires random number generator. In this case we will use python’s Random() method, which we initialize using a specific seed value so that we can reproduce the results in the future:
# create random seed for evolutionary computation algorithm
rand = Random()
rand.seed(1)
# instantiate evolutionary computation algorithm
my_ec = ec.EvolutionaryComputation(rand)
excerpt from tut_optimization.py
Parameters for the evolutionary algorithm are then established for our ec evolutionary computation instance by assigning various variator, replacer, terminator and observer elements–essentially toggling specific components of the algorithm– to ec.selectors, ec.variators, ec.replacers, ec.terminators, ec.observers:
#toggle variators
my_ec.variator = [ec.variators.uniform_crossover, # implement uniform crossover & gaussian replacement
ec.variators.gaussian_mutation]
my_ec.replacer = ec.replacers.generational_replacement # implement generational replacement
my_ec.terminator = ec.terminators.evaluation_termination # termination dictated by no. evaluations
#toggle observers
my_ec.observer = [ec.observers.stats_observer, # print evolutionary computation statistics
ec.observers.plot_observer, # plot output of the evolutionary computation as graph
ec.observers.best_observer] # print the best individual in the population to screen
excerpt from ex_optimization.py
where:
ec.variators.uniform_crossover 
variator where coin flip to determine whether ‘mom’ or ‘dad’ element is inherited by offspring 
ec.variators.gaussian_mutation 
variator implements gaussian mutation which makes use of bounder function as specified in: my_ec.evolve(…,bounder=ec.Bou nder(minParamValues, maxParamValues) ,…) 
ec.replacers.generational_replacement 
replacer implements generational replacement with elitism (as specified in my_ec.evolve(…,num_elites=1,…) , where the existing generation is replaced by offspring, and <num_elites> existing individuals will survive if they have better fitness than the offspring 
ec.terminators.evaluation_termination 
terminator runs based on the number of evaluations that have occurred 
ec.observers.stats_observer 
indicates how many of the generated individuals (parameter sets) will be selected for the next evolutionary iteration. 
ec.observers.plot_observer 
indicates the rate of mutation, or the rate at which values for each parameter (probability, weight and delay) taken from a prior generation are altered in the next generation 
ec.observers.best_observer 
sets the number of parameters that will be optimized to 3, corresponding to the length of [probability, weight, delay]. 
These predefined selector, variator, replacer, terminator and observer elements as well as other options can be found in the inspyred documentation.
FInally, the evolutionary computation algorithm instance includes a method: my_ec.evolve() , which will move through successive evolutionary iterations evaluating different parameter sets until the terminating condition is achieved. This function comes with multiple arguments, with two significant arguments being the generator and evaluator functions. A function call for my_ec.evolve() will look similar to the following:
# call evolution iterator
final_pop = my_ec.evolve(generator=generate_netparams, # assign model parameter generator to iterator generator
evaluator=evaluate_netparams, # assign fitness function to iterator evaluator
pop_size=10,
maximize=False,
bounder=ec.Bounder(minParamValues, maxParamValues),
max_evaluations=50,
num_selected=10,
mutation_rate=0.2,
num_inputs=3,
num_elites=1)
excerpt from tut_optimization.py
where:
pop_size=10 
means that each generation of parameter sets will consist of 10 individuals 
maximize=False 
means that we are taking higher fitness to correspond to minimal values in terms of difference between model firing frequency and 17 Hz 

defines boundaries for each of the parameters. The format to describe the minimum and maximum values for the parameters we are seeking to optimize: minParamValues is an array of minimum of values corresponding to [probability, weight, delay], and maxParamValues is the array of maximum values. 
max_evaluations=50 
indicates how many parameter sets are evaluated prior termination of the evolutionary iterations 
num_selected=10 
indicates how many of the generated individuals (parameter sets) will be selected for the next evolutionary iteration. 
mutation_rate=0.2 
indicates the rate of mutation, or the rate at which values for each parameter (probability, weight and delay) taken from a prior generation are altered in the next generation 
num_inputs=3 
sets the number of parameters that will be optimized to 3, corresponding to the length of [probability, weight, delay]. 
num_elites=1 
sets the number of elites to 1. That is, one individual from the existing generation may be retained (as opposed to a complete generational replacement) if it has better fitness than an individual selected from the offspring. 
The generator and evaluator arguments expect user defined functions as inputs, with generator used to define a population of initial parameter value sets for the very first iteration, and evaluator being the fitness function that will be used to evaluate each model for how close it is to the target. In this example, the generator is a fairly straightforward function which creates an initial set of parameter values (i.e. [probability, weight, delay] ) by drawing from a parameterized uniform distribution:
# return a set of initialParams which contains a [probability, weight, delay]
def generate_netparams(random, args):
size = args.get('num_inputs')
initialParams = [random.uniform(minParamValues[i], maxParamValues[i]) for i in range(size)]
return initialParams
excerpt from tut_optimization.py
The fitness function involves taking a list of sets of parameter values, i.e. : [ [ a0, b0, c0], [a1, b1, c1], [a2, b2, c2], … , [an, bn, cn ] ] where a, b, c represent the parameter values and 1 through n representing the individual number within the population, and calculating a fitness score for each element of the list, which is then returned as a list of fitness values (i.e. : [ f0, f1, f2, … , fn ] ) corresponding to the initial sets of parameter values. It follows the general template:
def evaluate_fitness(candidates, args):
fitness = []
for candidate in candidates:
fit = some_fitness_function(candidate)
fitness.append(fit)
return fitness
excerpt from tut_optimization.py
The actual code that is used to serve as some_fitness_function(candidate) is described below:
Overview of the Fitness Function¶
The fitness function in this case involves 1) creating a neural network with the given parameters, 2) simulating it to find the average firing rate, then 3) comparing this firing rate to a target firing rate.
Creating a neural network with the parameters to evaluate
We will employ the NetPyNE defined network in tut2.py, and modify the [probability, weight, delay] parameters. This involves redefining specific values found in tut2.py found within the connectivity rule between the S and M populations: netParams.connParams[‘S>M’]
## Cell connectivity rules
netParams.connParams['S>M'] = { # S > M label
'preConds': {'popLabel': 'S'}, # conditions of presyn cells
'postConds': {'popLabel': 'M'}, # conditions of postsyn cells
'probability': 0.5, # probability of connection < to be optimized by evolutionary algorithm
'weight': 0.01, # synaptic weight < to be optimized by evolutionary algorithm
'delay': 5, # transmission delay (ms) < to be optimized by evolutionary algorithm
'synMech': 'exc'} # synaptic mechanism
excerpt from tut2.py
these values are replaced in the fitness function with the parameter values generated by the evolutionary algorithm. As the fitness function resides within a for loop iterating through the list of candidates ( for icand,cand in enumerate(candidates): ), the individual parameters can be accessed as cand[0], cand[1], and cand[2]. Reassigning values to the parameters in tut_optimization.py can be done via the following line:
tut2.netParams.connParams['S>M']['<parameter>'] = <value>
Simulating the created neural network and finding the average firing rate
Once the network parameters have been modified we can call the sim.createSimulate() NetPyNE function to run the simulation. We will pass as arguments the tut2 netParams and simConfig objects that we just modified. Once the simulation has ran we will have access to the simulation output via sim.simData.
# create network
sim.createSimulate(netParams=tut2.netParams, simConfig=tut2.simConfig)
excerpt from tut_optimization.py
Comparing the average firing rate to a target average firing rate
To calculate the average firing rate (in spikes/sec = Hz) of the network, we divide the spikes that have occurred during the simulation, by the number of neurons and the duration. A list of spike times and a list of neurons can be accessed via the NetPyNE sim module: sim.simData[‘spkt’] and sim.net.cells . These are populated after running sim.createSimulate() . From these lists, getting the number of spike times and neurons is done by using python’s len() function. The duration of the simulation can be accessed in the tut_optimization.py code via tut2.simConfig.duration . The calculation for average firing rate is thus as follows:
# calculate firing rate
numSpikes = float(len(sim.simData['spkt']))
numCells = float(len(sim.net.cells))
duration = tut2.simConfig.duration/1000.0
netFiring = numSpikes/numCells/duration
excerpt from tut_optimization.py
Finally, the average firing rate of the model is compared to the target firing rate as follows:
# calculate fitness for this candidate
fitness = abs(targetFiring  netFiring) # minimize absolute difference in firing rate
excerpt from tut_optimization.py
Displaying Findings¶
The results of the evolutionary algorithm are displayed on the standard output (terminal) as well as plotted using the matplotlib package. The following lines are relevant to showing results of the various candidates within the iterator:
for icand,cand in enumerate(candidates):
...
print '\n CHILD/CANDIDATE %d: Network with prob:%.2f, weight:%.2f, delay:%.1f \n firing rate: %.1f, FITNESS = %.2f \n'\
%(icand, cand[0], cand[1], cand[2], netFiring, fitness)
excerpt from tut_optimization.py
The first line: for icand,cand in enumerate(candidates): is analogous to the the iterator for candidate in candidates: used in the pseudocode example above, except that the enumerate() function will also return an index–starting from 0– for each element in the list, and is used in the subsequent print statement.
This example also displays the generated candidate with average frequency closest to 17 Hz. This candidate will exist in the final generation, and possess the best fitness score (corresponding to a minimum difference). Since num_elites=1 there is no risk that a prior generation will have a candidate with a better fitness.
After the evolution finishes, to access the candidate with the best fitness score, the final generation of candidates, which is returned by the my_ec.evolve() function is then sorted in reverse (least to greatest), placing the candidate that achieves an average firing rate closest to 17 Hz (and therefore has the minimum difference) at the start of the list (or at position 0). We will use NetPyNE to visualize the output of this network, by setting the optimized parameters, simulating the network and plotting a raster plot. The code that performs this task is isolated below:
final_pop = my_ec.evolve(...)
...
# plot raster of top solutions
final_pop.sort(reverse=True) # sort final population so best fitness (minimum difference) is first in list
bestCand = final_pop[0].candidate # bestCand < candidate in first position of list
tut2.simConfig.analysis['plotRaster'] = True # plotting
tut2.netParams.connParams['S>M']['probability'] = bestCand[0] # set tut2 values to corresponding
tut2.netParams.connParams['S>M']['weight'] = bestCand[1] # best candidate values
tut2.netParams.connParams['S>M']['delay'] = bestCand[2]
sim.createSimulateAnalyze(netParams=tut2.netParams, simConfig=tut2.simConfig) # run simulation
excerpt from tut_optimization.py
The code for neural network optimization through evolutionary algorithm used in this tutorial can be found here: tut_optimization.py
.