def run_deap(model,
bounds,
labels_params,
summary,
obs_stats,
labels_sum_stats,
stats_std,
algo='ibea',
offspring_size=10,
max_ngen=10,
seed=None):
"""Runs genetic algorithm
Parameters
----------
model :
Model
bounds :
Bounds
labels_params : list of str
Labels of parameters
summary :
Function to compute summary statistics
obs_stats :
Observed summary statistics
labels_sum_stats :
Labels of summary statistics
stats_std : array
Standard deviations of summary statistics on pilot run
algo: str
Determines which genetic algorithm is run.
So far only ibea ('ibea') and deap default ('deap') are implemented
offspring_size : int
Offspring size
max_ngen : int
Maximum number of generations
seed : int or None
If set, randomness in sampling is disabled
"""
n_params = len(bounds[:, 0])
params = []
for i in range(n_params):
params.append(
Parameter(labels_params[i], bounds=[bounds[i, 0], bounds[i, 1]]))
# choose and run genetic algorithm
evaluator = hh_evaluator(model, summary, obs_stats, labels_sum_stats,
stats_std, params)
if algo == 'ibea':
opt = bpopt.deapext.optimisations.IBEADEAPOptimisation(
evaluator, offspring_size=offspring_size, seed=seed)
else:
opt = bpopt.deapext.optimisations.DEAPOptimisation(
evaluator, offspring_size=offspring_size, seed=seed)
final_pop, halloffame, log, hist = opt.run(max_ngen=max_ngen)
return final_pop, halloffame, log, hist
if feature_name in specific_filter_list:
#if 'Spikecount_3.0x' == tt.name or
if 'Spikecount_1.5x' == tt.name:
ft = NUFeatureAllenMultiSpike(tt,model,cnt,yes_list,yes_list,spike_obs)
objective = ephys.objectives.SingletonObjective(
feature_name,
ft)
objectives.append(objective)
score_calc = ephys.objectivescalculators.ObjectivesCalculator(objectives)
lop={}
for k,v in MODEL_PARAMS["ADEXP"].items():
p = Parameter(name=k,bounds=v,frozen=False)
lop[k] = p
simple_cell.params = lop
sweep_protocols = []
for protocol_name, amplitude in [('step1', 0.05)]:
protocol = ephys.protocols.SweepProtocol(protocol_name, [None], [None])
sweep_protocols.append(protocol)
twostep_protocol = ephys.protocols.SequenceProtocol('twostep', protocols=sweep_protocols)
