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patterns_mpi.py
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patterns_mpi.py
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# coding: utf-8
import nest
import numpy as np
import operator
import json
import sys
from math import exp
from mpi4py import MPI
from sklearn.model_selection import train_test_split, StratifiedKFold
def set_spike_in_generators(data, spike_generators, start_time, end_time, h_time, start_h):
sp = []
for gen_num in data:
d_time = start_time
sp_tmp = {'spike_times': [],
'spike_weights': []}
while d_time < end_time:
sp_tmp['spike_times'] += map(lambda x: x + d_time + start_h, data[gen_num])
sp_tmp['spike_weights'] += np.ones_like(data[gen_num]).tolist()
d_time += h_time
# print gen_num, sp_tmp
sp.append(sp_tmp)
for gen_num, spp in zip(data, sp):
# print gen_num, spike_generators_1[gen_num - 1]
nest.SetStatus([spike_generators[gen_num - 1]], [spp])
def set_teacher_input(x, teacher, settings): # Network
ampl_times = []
ampl_values = []
h = settings['network']['h']
y = x + 2 * h + settings['learning']['reinforce_time'] # x + 0.2
ampl_times.append(x - h) # x - 1.1
ampl_times.append(y - h) # x - 1.1
ampl_values.append(settings['learning']['teacher_amplitude']) # 1 mA 1000000.0
ampl_values.append(0.0) # 0 pA
nest.SetStatus(teacher, {'amplitude_times': ampl_times,
'amplitude_values': ampl_values})
def count_acc(latency, data):
acc = 0
output_list = []
for i in range(len(data['input'])):
tmp_list = [latency[neuron_number][i]['latency'][:1] for neuron_number in latency]
min_index, min_value = min(enumerate(tmp_list),
key=operator.itemgetter(1))
if min_index == data['class'][i]:
acc += 1
output_list.append([tmp_list, data['class'][i], min_index])
acc = float(acc) / len(data['input'])
# print acc
return acc, output_list
def merge_raw_latency(raw_latency_list):
# raw_latency = json.load(open('latency_0.json', 'r'))
raw_latency = {
'spikes': [],
'senders': []
}
for tmp_latency in raw_latency_list:
raw_latency['spikes'].extend(tmp_latency['spikes'])
raw_latency['senders'].extend(tmp_latency['senders'])
raw_latency['spikes'] = np.array(raw_latency['spikes'])
raw_latency['senders'] = np.array(raw_latency['senders'])
return raw_latency
def save_latency_to_file(raw_latency, filename):
rank = nest.Rank()
with open((filename + str(rank) + '.json'), 'w') as latency_file:
json.dump(raw_latency, latency_file, indent=4)
def create_latency(input_latency, data, settings):
output_latency = []
d_time = settings['network']['start_delta']
for example, ex_class in zip(data['input'], data['class']):
mask = (input_latency['spikes'] > d_time) & \
(input_latency['spikes'] < d_time + settings['network']['h_time'])
spikes_tmp = input_latency['spikes'][mask]
senders_tmp = input_latency['senders'][mask]
tmp_dict = {'latency': spikes_tmp - d_time,
'senders': senders_tmp,
'class': ex_class}
d_time += settings['network']['h_time']
output_latency.append(tmp_dict)
return output_latency
def create_full_latency(latency, settings):
full_latency = {}
n_neurons = settings['topology']['n_layer_out']
neuron_out_ids = [i + 1 for i in range(settings['topology']['n_layer_out'])]
for i in range(n_neurons):
tmp_str = 'neuron_' + str(i)
full_latency[tmp_str] = []
for latencies in latency:
tmp_dicts = []
for _ in range(n_neurons):
tmp_dict = {'latency': [float('Inf')],
'class': latencies['class']}
tmp_dicts.append(tmp_dict)
for lat, sender in zip(latencies['latency'], latencies['senders']):
for num, neuron_id in enumerate(neuron_out_ids):
if sender == [neuron_id]:
tmp_dicts[num]['latency'] = [lat]
for latency_key, tmp_dict in zip(full_latency, tmp_dicts):
full_latency[latency_key].append(tmp_dict)
return full_latency
def fitness_func_time(latency, data):
fit_list = []
for i in range(len(data['input'])):
tmp_list = [latency[neuron_number][i]['latency'][:1][0] for neuron_number in latency]
latency_of_desired_neuron = tmp_list.pop(data['class'][i])
fit = -1 * latency_of_desired_neuron
fit_list.append(fit)
fitness = np.mean(fit_list)
if np.isnan(fitness):
fitness = 0
return fitness
def fitness_func_sigma(latency, data):
def sigmoid(x, alpha):
return 1 / (1 + np.exp(-2 * alpha * x))
fit_list = []
for i in range(len(data['input'])):
tmp_list = [latency[neuron_number][i]['latency'][:1][0] for neuron_number in latency]
latency_of_desired_neuron = tmp_list.pop(data['class'][i])
fit = 1
for lat in tmp_list:
fit *= sigmoid(lat - latency_of_desired_neuron, 0.1)
fit_list.append(fit)
fitness = np.mean(fit_list)
if np.isnan(fitness):
fitness = 0
return fitness
def fitness_func_exp(latency, data):
fit_list = []
for i in range(len(data['input'])):
tmp_list = [latency[neuron_number][i]['latency'][:1][0] for neuron_number in latency]
latency_of_desired_neuron = tmp_list.pop(data['class'][i])
fit = 1
for lat in tmp_list:
fit -= exp(latency_of_desired_neuron - lat)
fit_list.append(fit)
fitness = np.mean(fit_list)
if np.isnan(fitness):
fitness = 0
return fitness, fit_list
def save_weights_one_layer(input_layer, output_layer, settings):
weights = {'layer_out': {}}
for neuron_id in output_layer:
tmp_weight = []
for input_id in input_layer:
conn = nest.GetConnections([input_id], [neuron_id],
synapse_model=settings['model']['syn_dict_stdp']['model'])
weight_one = nest.GetStatus(conn, 'weight')
if len(weight_one) != 0:
tmp_weight.append(weight_one[0])
# else:
# tmp_weight.append([])
if len(tmp_weight) != 0:
weights['layer_out'][neuron_id] = tmp_weight
return weights
def save_weigths_two_layers(input_layer, hidden_layer, output_layer, settings):
weights = {'layer_out': {},
'layer_hid': {}}
for neuron_id in hidden_layer:
tmp_weight = []
for input_id in input_layer:
conn = nest.GetConnections([input_id], [neuron_id],
synapse_model=settings['model']['syn_dict_stdp_hid']['model'])
weight_one = nest.GetStatus(conn, 'weight')
if len(weight_one) != 0:
tmp_weight.append(weight_one[0])
# else:
# tmp_weight.append([])
if len(tmp_weight) != 0:
weights['layer_hid'][neuron_id] = tmp_weight
for neuron_id in output_layer:
tmp_weight = []
for input_id in hidden_layer:
conn = nest.GetConnections([input_id], [neuron_id],
synapse_model=settings['model']['syn_dict_stdp']['model'])
weight_one = nest.GetStatus(conn, 'weight')
if len(weight_one) != 0:
tmp_weight.append(weight_one[0])
# else:
# tmp_weight.append([])
if len(tmp_weight) != 0:
weights['layer_out'][neuron_id] = tmp_weight
return weights
def weight_norm(weights):
norm = []
for neuron in weights:
norm.append(np.linalg.norm(weights[neuron]))
return np.linalg.norm(norm)
def interconnect_layer(layer, syn_dict):
for neuron_1 in layer:
for neuron_2 in layer:
if neuron_1 != neuron_2:
nest.Connect([neuron_1], [neuron_2], syn_spec=syn_dict)
def prepare_data(data, train_index, test_index, settings):
data_train = {}
data_test = {}
data_out = {}
if settings['data']['use_valid']:
data_valid = {}
data_out = {'train': {},
'test': {},
'valid': {}}
input_train, input_valid, y_train, y_valid = train_test_split(data['input'][train_index],
data['class'][train_index],
test_size=settings['data']['valid_size'],
random_state=42)
data_train['input'] = input_train
data_train['class'] = y_train
data_valid['input'] = input_valid
data_valid['class'] = y_valid
data_test['input'] = data['input'][test_index]
data_test['class'] = data['class'][test_index]
data_out['test']['full'] = data_test
data_out['train']['full'] = data_train
data_out['valid']['full'] = data_valid
else:
data_out = {'train': {},
'test': {}}
data_train['input'] = data['input'][train_index]
data_train['class'] = data['class'][train_index]
data_test['input'] = data['input'][test_index]
data_test['class'] = data['class'][test_index]
data_out['test']['full'] = data_test
data_out['train']['full'] = data_train
return data_out
def train(settings, data):
np.random.seed()
rank = nest.Rank()
rng = np.random.randint(500)
num_v_procs = settings['network']['num_threads'] \
* settings['network']['num_procs']
nest.ResetKernel()
nest.SetKernelStatus({
'local_num_threads': settings['network']['num_threads'],
'total_num_virtual_procs': num_v_procs,
'resolution': settings['network']['h'],
'rng_seeds': range(rng, rng + num_v_procs)
})
layer_out = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_out'])
if settings['topology']['two_layers']:
layer_hid = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_hid'])
teacher_1 = nest.Create('step_current_generator',
settings['topology']['n_layer_out'])
spike_generators_1 = nest.Create('spike_generator',
settings['topology']['n_input'])
poisson_layer = nest.Create('poisson_generator',
settings['topology']['n_input'])
parrot_layer = nest.Create('parrot_neuron',
settings['topology']['n_input'])
spike_detector_1 = nest.Create('spike_detector')
spike_detector_2 = nest.Create('spike_detector')
spike_detector_3 = nest.Create('spike_detector')
voltmeter = nest.Create(
'voltmeter',
1,
{
'withgid': True,
'withtime': True
}
)
if not settings['network']['noise_after_pattern']:
nest.SetStatus(poisson_layer,
{'rate': settings['network']['noise_freq'],
'origin': 0.0})
nest.Connect(spike_generators_1, parrot_layer, 'one_to_one',
syn_spec='static_synapse')
nest.Connect(poisson_layer, parrot_layer, 'one_to_one',
syn_spec='static_synapse')
if settings['learning']['use_teacher']:
nest.Connect(teacher_1, layer_out, 'one_to_one',
syn_spec='static_synapse')
nest.Connect(layer_out, spike_detector_1, 'all_to_all')
nest.Connect(parrot_layer, spike_detector_2, 'all_to_all')
nest.Connect(voltmeter, layer_out)
nest.SetStatus(layer_out, settings['model']['neuron_out'])
if settings['topology']['two_layers']:
if settings['learning']['use_inhibition']:
interconnect_layer(layer_hid, settings['model']['syn_dict_inh'])
# nest.Connect(layer_out, layer_hid,
# 'all_to_all', syn_spec=settings['syn_dict_inh'])
nest.Connect(parrot_layer, spike_detector_3, 'all_to_all')
nest.Connect(parrot_layer, layer_hid, 'all_to_all',
syn_spec=settings['model']['syn_dict_stdp_hid'])
nest.Connect(layer_hid, layer_out, 'all_to_all',
syn_spec=settings['model']['syn_dict_stdp'])
if settings['topology']['use_reciprocal']:
nest.Connect(layer_out, layer_hid, 'all_to_all',
syn_spec=settings['model']['syn_dict_rec'])
nest.Connect(layer_hid, spike_detector_3, 'all_to_all')
nest.SetStatus(layer_hid, settings['model']['neuron_hid'])
else:
nest.Connect(parrot_layer, layer_out, 'all_to_all',
syn_spec=settings['model']['syn_dict_stdp'])
if settings['topology']['use_inhibition']:
interconnect_layer(layer_out, settings['model']['syn_dict_inh'])
np.random.seed(500)
i = 0
hi = 1
last_norms = []
norm_history = []
output_latency = []
weights_history = []
early_stop = False
d_time = settings['network']['start_delta']
full_time = settings['learning']['epochs'] \
* len(data['input']) \
* settings['network']['h_time'] \
+ settings['network']['start_delta']
# if settings['two_layers']:
# initial_weights = save_weigths_two_layers(parrot_layer, layer_hid, layer_out, settings)
# else:
# initial_weights = save_weights_one_layer(parrot_layer, layer_out, settings)
nest.Simulate(settings['network']['start_delta'])
while not early_stop:
set_spike_in_generators(
data['input'][i],
spike_generators_1,
d_time,
d_time + settings['network']['h_time'],
settings['network']['h_time'],
settings['network']['h']
)
# if True:
# set_spike_in_generators(data['input'][i], spike_generators_1,
# d_time + 1.5, d_time + settings['h_time'] + 1.5,
# settings['h_time'], settings['h'])
# set_spike_in_generators(data['input'][i], spike_generators_1,
# d_time + 3.0, d_time + settings['h_time'] + 3.0,
# settings['h_time'], settings['h'])
spike_times = []
for neuron_number in data['input'][i]:
if data['input'][i][neuron_number]:
spike_times.append(data['input'][i][neuron_number][0])
if settings['learning']['use_teacher']:
if settings['topology']['n_layer_out'] == 1:
set_teacher_input(
np.min(spike_times) \
+ d_time \
+ settings['network']['h'] \
+ settings['learning']['reinforce_delta'],
teacher_1,
settings
)
else:
set_teacher_input(
np.min(spike_times) \
+ d_time \
+ settings['network']['h'] \
+ settings['learning']['reinforce_delta'],
[teacher_1[data['class'][i]]],
settings
)
if settings['network']['noise_after_pattern']:
nest.SetStatus(
poisson_layer,
{'start': d_time + np.max(spike_times),
'stop': float(d_time + settings['network']['h_time']),
'rate': settings['network']['noise_freq']}
)
nest.Simulate(settings['network']['h_time'])
ex_class = data['class'][i]
spikes = nest.GetStatus(spike_detector_1, keys="events")[0]['times']
senders = nest.GetStatus(spike_detector_1, keys="events")[0]['senders']
mask = spikes > d_time
spikes = spikes[mask]
senders = senders[mask]
tmp_dict = {
'latency': spikes - d_time,
'senders': senders,
'class': ex_class
}
output_latency.append(tmp_dict)
d_time += settings['network']['h_time']
if i + hi + 1 > len(data['input']):
i = 0
else:
i += hi
if settings['network']['save_history']:
if settings['topology']['two_layers']:
tmp_weights = save_weigths_two_layers(parrot_layer, layer_hid,
layer_out, settings)
tmp_norm_hid = weight_norm(tmp_weights['layer_hid'])
tmp_norm_out = weight_norm(tmp_weights['layer_out'])
tmp_norm = np.linalg.norm([tmp_norm_hid, tmp_norm_out])
norm_history.append(tmp_norm)
else:
tmp_weights = save_weights_one_layer(parrot_layer, layer_out,
settings)
tmp_norm_out = weight_norm(tmp_weights['layer_out'])
norm_history.append(tmp_norm_out)
weights_history.append(tmp_weights)
# if len(norm_history) > 5 * len(data['input']) and settings['early_stop']:
# early_stop = np.std(norm_history[-5 * len(data['input']):]) < 0.025
# else:
early_stop = d_time > full_time
if settings['topology']['two_layers']:
weights = save_weigths_two_layers(
parrot_layer,
layer_hid,
layer_out,
settings
)
else:
weights = save_weights_one_layer(
parrot_layer,
layer_out,
settings
)
# print(weights['layer_out'].keys())
# with open('weights' + str(weights['layer_out'].keys()) + '.json', 'w') as outfile:
# json.dump(weights, outfile, indent=4)
devices = {
'voltmeter': voltmeter,
'spike_detector_1': spike_detector_1,
'spike_detector_2': spike_detector_2,
'spike_detector_3': spike_detector_3,
}
return weights, output_latency, devices, weights_history, norm_history
def test(settings, data, weights):
np.random.seed()
rank = nest.Rank()
rng = np.random.randint(500)
num_v_procs = settings['network']['num_threads'] \
* settings['network']['num_procs']
nest.ResetKernel()
nest.SetKernelStatus({
'local_num_threads': settings['network']['num_threads'],
'total_num_virtual_procs': num_v_procs,
'resolution': settings['network']['h'],
'rng_seeds': range(rng, rng + num_v_procs)
})
layer_out = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_out'])
if settings['topology']['two_layers']:
layer_hid = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_hid'])
spike_generators_1 = nest.Create('spike_generator',
settings['topology']['n_input'])
poisson_layer = nest.Create('poisson_generator',
settings['topology']['n_input'])
parrot_layer = nest.Create('parrot_neuron',
settings['topology']['n_input'])
spike_detector_1 = nest.Create('spike_detector')
spike_detector_2 = nest.Create('spike_detector')
spike_detector_3 = nest.Create('spike_detector')
voltmeter = nest.Create(
'voltmeter', 1,
{'withgid': True,
'withtime': True}
)
nest.Connect(spike_generators_1, parrot_layer,
'one_to_one', syn_spec='static_synapse')
if settings['network']['test_with_noise']:
nest.SetStatus(poisson_layer,
{'rate': settings['network']['noise_freq']})
nest.Connect(poisson_layer, parrot_layer,
'one_to_one', syn_spec='static_synapse')
nest.Connect(layer_out, spike_detector_1, 'all_to_all')
nest.Connect(parrot_layer, spike_detector_2, 'all_to_all')
nest.Connect(voltmeter, layer_out)
nest.SetStatus(layer_out, settings['model']['neuron_out'])
if settings['topology']['two_layers']:
if settings['topology']['use_inhibition']:
interconnect_layer(layer_hid, settings['model']['syn_dict_inh'])
# nest.Connect(layer_out, layer_hid,
# 'all_to_all', syn_spec=settings['syn_dict_inh'])
nest.Connect(parrot_layer, layer_hid,
'all_to_all', syn_spec='static_synapse')
nest.Connect(layer_hid, layer_out,
'all_to_all', syn_spec='static_synapse')
nest.Connect(layer_hid, spike_detector_3, 'all_to_all')
nest.SetStatus(layer_hid, settings['model']['neuron_hid'])
else:
if settings['topology']['use_inhibition']:
interconnect_layer(layer_out, settings['model']['syn_dict_inh'])
nest.Connect(parrot_layer, layer_out,
'all_to_all', syn_spec='static_synapse')
if settings['topology']['two_layers']:
for neuron_id in weights['layer_hid']:
connection = nest.GetConnections(parrot_layer, target=[neuron_id])
nest.SetStatus(connection, 'weight', weights['layer_hid'][neuron_id])
for neuron_id in weights['layer_out']:
connection = nest.GetConnections(layer_hid, target=[neuron_id])
nest.SetStatus(connection, 'weight', weights['layer_out'][neuron_id])
else:
for neuron_id in weights['layer_out']:
connection = nest.GetConnections(parrot_layer, target=[neuron_id])
nest.SetStatus(connection, 'weight', weights['layer_out'][neuron_id])
np.random.seed(500)
output_latency = []
d_time = settings['network']['start_delta']
nest.Simulate(settings['network']['start_delta'])
for example, examples_class in zip(data['input'], data['class']):
set_spike_in_generators(
example,
spike_generators_1,
d_time,
d_time + settings['network']['h_time'],
settings['network']['h_time'],
settings['network']['h'])
# nest.SetStatus(poisson_layer, {'start': 30.})
nest.Simulate(settings['network']['h_time'])
d_time += settings['network']['h_time']
spikes = nest.GetStatus(spike_detector_1, keys="events")[0]['times'].tolist()
senders = nest.GetStatus(spike_detector_1, keys="events")[0]['senders'].tolist()
output_latency = {
'spikes': spikes,
'senders': senders
}
devices = {
'voltmeter': voltmeter,
'spike_detector_1': spike_detector_1,
'spike_detector_2': spike_detector_2,
'spike_detector_3': spike_detector_3,
}
return output_latency, devices
def test_network_acc(data, settings):
comm = MPI.COMM_WORLD
data_train = data['train']['full']
weights, \
latency_train, devices_train, \
weights_history, norm_history = train(settings, data_train)
fitness = 0
if settings['data']['use_valid']:
data_valid = data['valid']['full']
raw_latency_valid, devices_valid = test(settings, data_valid, weights)
all_latency_valid = comm.allgather(raw_latency_valid)
comm.Barrier()
raw_latency_valid = merge_raw_latency(all_latency_valid)
latency_valid = create_latency(raw_latency_valid, data_valid, settings)
full_latency_valid = create_full_latency(latency_valid, settings)
if settings['learning']['use_fitness_func'] \
and settings['learning']['fitness_func'] == 'exp':
fitness, fit_list = fitness_func_exp(full_latency_valid, data_valid)
elif settings['learning']['use_fitness_func'] \
and settings['learning']['fitness_func'] == 'sigma':
fitness = fitness_func_sigma(full_latency_valid, data_valid)
elif settings['learning']['use_fitness_func'] \
and settings['learning']['fitness_func'] == 'time':
fitness = fitness_func_time(full_latency_valid, data_valid)
elif settings['learning']['use_fitness_func'] \
and settings['learning']['fitness_func'] == 'acc':
fitness, out = count_acc(full_latency_valid, data_valid)
# elif settings['use_fitness_func'] and settings['fitness_func'] == 'weights':
# final_weights = list(list(weights.values())[0].values())
# np.savetxt('final_weights.txt', final_weights)
# desired_weights = np.loadtxt('../desired_weights/final_weights.txt')
# fitness = -1 * np.linalg.norm(np.subtract(final_weights, desired_weights))
raw_latency_test_train, devices_test_train = test(settings, data_train, weights)
all_latency_test_train = comm.allgather(raw_latency_test_train)
comm.Barrier()
raw_latency_test_train = merge_raw_latency(all_latency_test_train)
latency_test_train = create_latency(raw_latency_test_train, data_train, settings)
full_latency_test_train = create_full_latency(latency_test_train, settings)
acc_train, output_list_train = count_acc(full_latency_test_train, data_train)
data_test = data['test']['full']
raw_latency_test, devices_test = test(settings, data_test, weights)
all_latency_test = comm.allgather(raw_latency_test)
comm.Barrier()
raw_latency_test = merge_raw_latency(all_latency_test)
latency_test = create_latency(raw_latency_test, data_test, settings)
full_latency_test = create_full_latency(latency_test, settings)
acc_test, output_list_test = count_acc(full_latency_test, data_test)
# print(output_list_test)
comm.Barrier()
weights_all = comm.allgather(weights)
out_dict = {
'fitness': fitness,
'acc_test': acc_test,
'acc_train': acc_train,
'output_list_test': output_list_test,
'output_list_train': output_list_train,
}
return out_dict, weights_all
def test_network_acc_cv(data, settings):
def solve_fold(input_data):
data_fold = prepare_data(input_data['data'],
input_data['train_index'],
input_data['test_index'],
input_data['settings'])
return test_network_acc(data_fold, input_data['settings'])
fit = []
weights = []
acc_test = []
acc_train = []
data_list = []
skf = StratifiedKFold(n_splits=settings['learning']['n_splits'])
for train_index, test_index in skf.split(data['input'], data['class']):
input_data = {
'data': data,
'settings': settings,
'test_index': test_index,
'train_index': train_index,
}
data_list.append(input_data)
for result, weight in map(solve_fold, data_list):
acc_test.append(result['acc_test'])
acc_train.append(result['acc_train'])
fit.append(result['fitness'])
weights.append(weight)
# print(fit)
out_dict = {
'fitness': fit,
'fitness_mean': np.mean(fit),
'accs_test': acc_test,
'accs_test_mean': np.mean(acc_test),
'accs_test_std': np.std(acc_test),
'accs_train': acc_train,
'accs_train_mean': np.mean(acc_train),
'accs_train_std': np.std(acc_train),
'weights': weights,
}
return out_dict
def grid_search(data, parameters, settings):
result = {
'accuracy': [],
'std': [],
'fitness'
'parameter': [],
'parameter_name': [],
}
settings_copy = settings
for key in parameters.keys():
if isinstance(parameters[key], dict):
for key_key in parameters[key].keys():
result['parameter'].append(settings_copy[key][key_key])
result['parameter_name'].append(key_key)
acc, std = test_network_acc_cv(data, settings_copy)
result['accuracy'].append(acc)
result['std'].append(std)
settings_copy[key][key_key] += parameters[key][key_key]
else:
result['parameter'].append(settings_copy[key])
result['parameter_name'].append(key)
acc, std = test_network_acc_cv(data, settings_copy)
result['accuracy'].append(acc)
result['std'].append(std)