def run_sim(number_neurons=default_number_neurons,
connection_probability=default_connection_probability,
synaptic_weights=default_synaptic_weights,
synaptic_time_constant=default_synaptic_time_constant,
tend=300):
'''run a simulation of a population of leaky integrate-and-fire excitatory neurons that are
randomly connected. The population is injected with a transient current.'''
from brian.units import mvolt, msecond, namp, Mohm
import brian
brian.clear()
El = 0 * mvolt
tau_m = 30 * msecond
tau_syn = synaptic_time_constant * msecond
R = 20 * Mohm
v_threshold = 30 * mvolt
v_reset = 0 * mvolt
tau_refractory = 4 * msecond
eqs = brian.Equations('''
dv/dt = (-(v - El) + R*I)/tau_m : volt
I = I_syn + I_stim : amp
dI_syn/dt = -I_syn/tau_syn : amp
I_stim : amp
''')
external_current = np.zeros(tend)
external_current[np.arange(0, 100)] = 5 * namp
group = brian.NeuronGroup(
model=eqs,
N=number_neurons, threshold=v_threshold, reset=v_reset, refractory=tau_refractory)
group.I_stim = brian.TimedArray(external_current, dt=1*msecond)
connections = brian.Connection(group, group, 'I_syn')
connections.connect_random(sparseness=connection_probability, weight=synaptic_weights*namp)
spike_monitor = brian.SpikeMonitor(group)
population_rate_monitor = brian.PopulationRateMonitor(group, bin=10*msecond)
brian.reinit()
brian.run(tend * msecond)
return spike_monitor, population_rate_monitor
def build_network():
global fig_num
neuron_groups['e'] = b.NeuronGroup(n_e_total, neuron_eqs_e, threshold=v_thresh_e, \
refractory=refrac_e, reset=scr_e, compile=True, freeze=True)
neuron_groups['i'] = b.NeuronGroup(n_e_total, neuron_eqs_i, threshold=v_thresh_i, \
refractory=refrac_i, reset=v_reset_i, compile=True, freeze=True)
for name in population_names:
print '...Creating neuron group:', name
# get a subgroup of size 'n_e' from all exc
neuron_groups[name + 'e'] = neuron_groups['e'].subgroup(conv_features *
n_e)
# get a subgroup of size 'n_i' from the inhibitory layer
neuron_groups[name + 'i'] = neuron_groups['i'].subgroup(conv_features *
n_e)
# start the membrane potentials of these groups 40mV below their resting potentials
neuron_groups[name + 'e'].v = v_rest_e - 40. * b.mV
neuron_groups[name + 'i'].v = v_rest_i - 40. * b.mV
print '...Creating recurrent connections'
for name in population_names:
neuron_groups['e'].theta = np.load(
os.path.join(best_weights_dir,
'_'.join(['theta_A', ending + '_best.npy'])))
for conn_type in recurrent_conn_names:
if conn_type == 'ei':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(
neuron_groups[conn_name[0:2]],
neuron_groups[conn_name[2:4]],
structure='sparse',
state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(conv_features):
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
feature * n_e + n] = 10.4
elif conn_type == 'ie':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# load weight matrix
weight_matrix = np.load(
os.path.join(best_weights_dir,
'_'.join([conn_name, ending, 'best.npy'])))
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(
neuron_groups[conn_name[0:2]],
neuron_groups[conn_name[2:4]],
structure='sparse',
state='g' + conn_type[0])
# define the actual synaptic connections and strengths
for feature in xrange(conv_features):
for other_feature in xrange(conv_features):
if feature != other_feature:
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
other_feature * n_e +
n] = inhibition_level
print '...Creating monitors for:', name
# spike rate monitors for excitatory and inhibitory neuron populations
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
neuron_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
rate_monitors[name + 'i'] = b.PopulationRateMonitor(
neuron_groups[name + 'i'],
bin=(single_example_time + resting_time) / b.second)
spike_counters[name + 'e'] = b.SpikeCounter(neuron_groups[name + 'e'])
# record neuron population spikes if specified
if record_spikes and do_plot:
spike_monitors[name + 'e'] = b.SpikeMonitor(neuron_groups[name +
'e'])
spike_monitors[name + 'i'] = b.SpikeMonitor(neuron_groups[name +
'i'])
if record_spikes and do_plot:
b.figure(fig_num, figsize=(8, 6))
b.ion()
b.subplot(211)
b.raster_plot(spike_monitors['Ae'],
refresh=1000 * b.ms,
showlast=1000 * b.ms,
title='Excitatory spikes per neuron')
b.subplot(212)
b.raster_plot(spike_monitors['Ai'],
refresh=1000 * b.ms,
showlast=1000 * b.ms,
title='Inhibitory spikes per neuron')
b.tight_layout()
fig_num += 1
# creating Poission spike train from input image (784 vector, 28x28 image)
for name in input_population_names:
input_groups[name + 'e'] = b.PoissonGroup(n_input, 0)
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
input_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
# creating connections from input Poisson spike train to excitatory neuron population(s)
for name in input_connection_names:
print '\n...Creating connections between', name[0], 'and', name[1]
# for each of the input connection types (in this case, excitatory -> excitatory)
for conn_type in input_conn_names:
# saved connection name
conn_name = name[0] + conn_type[0] + name[1] + conn_type[1]
# get weight matrix depending on training or test phase
weight_matrix = np.load(
os.path.join(best_weights_dir,
'_'.join([conn_name, ending + '_best.npy'])))
# create connections from the windows of the input group to the neuron population
input_connections[conn_name] = b.Connection(input_groups['Xe'], neuron_groups[name[1] + conn_type[1]], \
structure='sparse', state='g' + conn_type[0], delay=True, max_delay=delay[conn_type][1])
for feature in xrange(conv_features):
for n in xrange(n_e):
for idx in xrange(conv_size**2):
input_connections[conn_name][convolution_locations[n][idx], feature * n_e + n] = \
weight_matrix[convolution_locations[n][idx], feature * n_e + n]
if do_plot:
plot_2d_input_weights()
fig_num += 1
print '\n'
neuron_groups[connName[2:4]],
weightMatrix)
if ee_STDP_on:
if 'ee' in recurrent_conn_names:
stdp_methods[name + 'e' + name + 'e'] = b.STDP(
connections[name + 'e' + name + 'e' + ending],
eqs=eqs_stdp_ee,
pre=eqs_stdp_pre_ee,
post=eqs_stdp_post_ee,
wmin=0.,
wmax=wmax_ee)
print 'create monitors for', name
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
neuron_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
rate_monitors[name + 'i'] = b.PopulationRateMonitor(
neuron_groups[name + 'i'],
bin=(single_example_time + resting_time) / b.second)
spike_counters[name + 'e'] = b.SpikeCounter(neuron_groups[name + 'e'])
if record_spikes:
spike_monitors[name + 'e'] = b.SpikeMonitor(neuron_groups[name + 'e'])
spike_monitors[name + 'i'] = b.SpikeMonitor(neuron_groups[name + 'i'])
if record_spikes:
b.figure(fig_num)
fig_num += 1
b.ion()
b.subplot(211)
def __init__(mode, connectivity, weight_dependence, post_pre, conv_size, conv_stride, conv_features, weight_sharing, lattice_structure, random_inhibition_prob, top_percent):
'''
Network initialization.
'''
# setting input parameters
this.mode = mode
this.connectivity = connectivity
this.weight_dependence = weight_dependence
this.post_pre = post_pre
this.conv_size = conv_size
this.conv_features = conv_features
this.weight_sharing = weight_sharing
this.lattice_structure = lattice_structure
this.random_inhibition_prob = random_inhibition_prob
# load training or testing data
if mode == 'train':
start = time.time()
this.data = get_labeled_data(MNIST_data_path + 'training')
end = time.time()
print 'time needed to load training set:', end - start
else:
start = time.time()
this.data = get_labeled_data(MNIST_data_path + 'testing', bTrain = False)
end = time.time()
print 'time needed to load test set:', end - start
# set parameters for simulation based on train / test mode
if test_mode:
weight_path = top_level_path + 'weights/conv_patch_connectivity_weights/'
this.num_examples = 10000 * 1
this.do_plot_performance = False
ee_STDP_on = False
else:
weight_path = top_level_path + 'random/conv_patch_connectivity_random/'
this.num_examples = 60000 * 1
this.do_plot_performance = True
ee_STDP_on = True
# plotting or not
do_plot = True
# number of inputs to the network
this.n_input = 784
this.n_input_sqrt = int(math.sqrt(n_input))
# number of neurons parameters
this.n_e = ((n_input_sqrt - conv_size) / conv_stride + 1) ** 2
this.n_e_total = n_e * conv_features
this.n_e_sqrt = int(math.sqrt(n_e))
this.n_i = n_e
this.conv_features_sqrt = int(math.sqrt(conv_features))
# time (in seconds) per data example presentation and rest period in between, used to calculate total runtime
this.single_example_time = 0.35 * b.second
this.resting_time = 0.15 * b.second
runtime = num_examples * (single_example_time + resting_time)
# set the update interval
if test_mode:
this.update_interval = num_examples
else:
this.update_interval = 100
# rest potential parameters, reset potential parameters, threshold potential parameters, and refractory periods
v_rest_e, v_rest_i = -65. * b.mV, -60. * b.mV
v_reset_e, v_reset_i = -65. * b.mV, -45. * b.mV
v_thresh_e, v_thresh_i = -52. * b.mV, -40. * b.mV
refrac_e, refrac_i = 5. * b.ms, 2. * b.ms
# dictionaries for weights and delays
weight, delay = {}, {}
# populations, connections, saved connections, etc.
input_population_names = [ 'X' ]
population_names = [ 'A' ]
input_connection_names = [ 'XA' ]
save_conns = [ 'XeAe', 'AeAe' ]
# weird and bad names for variables, I think
input_conn_names = [ 'ee_input' ]
recurrent_conn_names = [ 'ei', 'ie', 'ee' ]
# setting weight, delay, and intensity parameters
weight['ee_input'] = (conv_size ** 2) * 0.175
delay['ee_input'] = (0 * b.ms, 10 * b.ms)
delay['ei_input'] = (0 * b.ms, 5 * b.ms)
input_intensity = start_input_intensity = 2.0
# time constants, learning rates, max weights, weight dependence, etc.
tc_pre_ee, tc_post_ee = 20 * b.ms, 20 * b.ms
nu_ee_pre, nu_ee_post = 0.0001, 0.01
wmax_ee = 1.0
exp_ee_post = exp_ee_pre = 0.2
w_mu_pre, w_mu_post = 0.2, 0.2
# setting up differential equations (depending on train / test mode)
if test_mode:
scr_e = 'v = v_reset_e; timer = 0*ms'
else:
tc_theta = 1e7 * b.ms
theta_plus_e = 0.05 * b.mV
scr_e = 'v = v_reset_e; theta += theta_plus_e; timer = 0*ms'
offset = 20.0 * b.mV
v_thresh_e = '(v>(theta - offset + ' + str(v_thresh_e) + ')) * (timer>refrac_e)'
# equations for neurons
neuron_eqs_e = '''
dv/dt = ((v_rest_e - v) + (I_synE + I_synI) / nS) / (100 * ms) : volt
I_synE = ge * nS * -v : amp
I_synI = gi * nS * (-100.*mV-v) : amp
dge/dt = -ge/(1.0*ms) : 1
dgi/dt = -gi/(2.0*ms) : 1
'''
if test_mode:
neuron_eqs_e += '\n theta :volt'
else:
neuron_eqs_e += '\n dtheta/dt = -theta / (tc_theta) : volt'
neuron_eqs_e += '\n dtimer/dt = 100.0 : ms'
neuron_eqs_i = '''
dv/dt = ((v_rest_i - v) + (I_synE + I_synI) / nS) / (10*ms) : volt
I_synE = ge * nS * -v : amp
I_synI = gi * nS * (-85.*mV-v) : amp
dge/dt = -ge/(1.0*ms) : 1
dgi/dt = -gi/(2.0*ms) : 1
'''
# creating dictionaries for various objects
this.neuron_groups = {}
this.input_groups = {}
this.connections = {}
this.input_connections = {}
this.stdp_methods = {}
this.rate_monitors = {}
this.spike_monitors = {}
this.spike_counters = {}
# creating excitatory, inhibitory populations
this.neuron_groups['e'] = b.NeuronGroup(n_e_total, neuron_eqs_e, threshold=v_thresh_e, refractory=refrac_e, reset=scr_e, compile=True, freeze=True)
this.neuron_groups['i'] = b.NeuronGroup(n_e_total, neuron_eqs_i, threshold=v_thresh_i, refractory=refrac_i, reset=v_reset_i, compile=True, freeze=True)
# creating subpopulations of excitatory, inhibitory neurons
for name in population_names:
print '...creating neuron group:', name
# get a subgroup of size 'n_e' from all exc
neuron_groups[name + 'e'] = neuron_groups['e'].subgroup(conv_features * n_e)
# get a subgroup of size 'n_i' from the inhibitory layer
neuron_groups[name + 'i'] = neuron_groups['i'].subgroup(conv_features * n_e)
# start the membrane potentials of these groups 40mV below their resting potentials
neuron_groups[name + 'e'].v = v_rest_e - 40. * b.mV
neuron_groups[name + 'i'].v = v_rest_i - 40. * b.mV
print '...creating recurrent connections'
for name in population_names:
# if we're in test mode / using some stored weights
if mode == 'test' or weight_path[-8:] == 'weights/conv_patch_connectivity_weights/':
# load up adaptive threshold parameters
neuron_groups['e'].theta = np.load(weight_path + 'theta_A' + '_' + ending +'.npy')
else:
# otherwise, set the adaptive additive threshold parameter at 20mV
neuron_groups['e'].theta = np.ones((n_e_total)) * 20.0 * b.mV
for conn_type in recurrent_conn_names:
if conn_type == 'ei':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(neuron_groups[conn_name[0:2]], neuron_groups[conn_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(conv_features):
for n in xrange(n_e):
connections[conn_name][feature * n_e + n, feature * n_e + n] = 10.4
elif conn_type == 'ie':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(neuron_groups[conn_name[0:2]], neuron_groups[conn_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(conv_features):
for other_feature in xrange(conv_features):
if feature != other_feature:
for n in xrange(n_e):
connections[conn_name][feature * n_e + n, other_feature * n_e + n] = 17.4
if random_inhibition_prob != 0.0:
for feature in xrange(conv_features):
for other_feature in xrange(conv_features):
for n_this in xrange(n_e):
for n_other in xrange(n_e):
if n_this != n_other:
if b.random() < random_inhibition_prob:
connections[conn_name][feature * n_e + n_this, other_feature * n_e + n_other] = 17.4
elif conn_type == 'ee':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# get weights from file if we are in test mode
if mode == 'test':
weight_matrix = get_matrix_from_file(weight_path + conn_name + '_' + ending + '.npy', conv_features * n_e, conv_features * n_e)
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(neuron_groups[conn_name[0:2]], neuron_groups[conn_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
if connectivity == 'all':
for feature in xrange(conv_features):
for other_feature in xrange(conv_features):
if feature != other_feature:
for this_n in xrange(n_e):
for other_n in xrange(n_e):
if is_lattice_connection(n_e_sqrt, this_n, other_n):
if mode == 'test':
connections[conn_name][feature * n_e + this_n, other_feature * n_e + other_n] = weight_matrix[feature * n_e + this_n, other_feature * n_e + other_n]
else:
connections[conn_name][feature * n_e + this_n, other_feature * n_e + other_n] = (b.random() + 0.01) * 0.3
elif connectivity == 'pairs':
for feature in xrange(conv_features):
if feature % 2 == 0:
for this_n in xrange(n_e):
for other_n in xrange(n_e):
if is_lattice_connection(n_e_sqrt, this_n, other_n):
if mode == 'test':
connections[conn_name][feature * n_e + this_n, (feature + 1) * n_e + other_n] = weight_matrix[feature * n_e + this_n, (feature + 1) * n_e + other_n]
else:
connections[conn_name][feature * n_e + this_n, (feature + 1) * n_e + other_n] = (b.random() + 0.01) * 0.3
elif feature % 2 == 1:
for this_n in xrange(n_e):
for other_n in xrange(n_e):
if is_lattimode == 'test'ce_connection(n_e_sqrt, this_n, other_n):
if mode == 'test':
connections[conn_name][feature * n_e + this_n, (feature - 1) * n_e + other_n] = weight_matrix[feature * n_e + this_n, (feature - 1) * n_e + other_n]
else:
connections[conn_name][feature * n_e + this_n, (feature - 1) * n_e + other_n] = (b.random() + 0.01) * 0.3
elif connectivity == 'none':
pass
# if STDP from excitatory -> excitatory is on and this connection is excitatory -> excitatory
if ee_STDP_on and 'ee' in recurrent_conn_names:
stdp_methods[name + 'e' + name + 'e'] = b.STDP(connections[name + 'e' + name + 'e'], eqs=eqs_stdp_ee, pre=eqs_stdp_pre_ee, post=eqs_stdp_post_ee, wmin=0., wmax=wmax_ee)
print '...creating monitors for:', name
# spike rate monitors for excitatory and inhibitory neuron populations
rate_monitors[name + 'e'] = b.PopulationRateMonitor(neuron_groups[name + 'e'], bin=(single_example_time + resting_time) / b.second)
rate_monitors[name + 'i'] = b.PopulationRateMonitor(neuron_groups[name + 'i'], bin=(single_example_time + resting_time) / b.second)
spike_counters[name + 'e'] = b.SpikeCounter(neuron_groups[name + 'e'])
# record neuron population spikes if specified
spike_monitors[name + 'e'] = b.SpikeMonitor(neuron_groups[name + 'e'])
spike_monitors[name + 'i'] = b.SpikeMonitor(neuron_groups[name + 'i'])
def build_network():
global fig_num, assignments
neuron_groups['e'] = b.NeuronGroup(n_e_total,
neuron_eqs_e,
threshold=v_thresh_e,
refractory=refrac_e,
reset=scr_e,
compile=True,
freeze=True)
neuron_groups['i'] = b.NeuronGroup(n_e_total,
neuron_eqs_i,
threshold=v_thresh_i,
refractory=refrac_i,
reset=v_reset_i,
compile=True,
freeze=True)
for name in population_names:
print '...Creating neuron group:', name
# get a subgroup of size 'n_e' from all exc
neuron_groups[name + 'e'] = neuron_groups['e'].subgroup(conv_features *
n_e)
# get a subgroup of size 'n_i' from the inhibitory layer
neuron_groups[name + 'i'] = neuron_groups['i'].subgroup(conv_features *
n_e)
# start the membrane potentials of these groups 40mV below their resting potentials
neuron_groups[name + 'e'].v = v_rest_e - 40. * b.mV
neuron_groups[name + 'i'].v = v_rest_i - 40. * b.mV
print '...Creating recurrent connections'
for name in population_names:
# if we're in test mode / using some stored weights
if test_mode:
# load up adaptive threshold parameters
if save_best_model:
neuron_groups['e'].theta = np.load(
os.path.join(best_weights_dir,
'_'.join(['theta_A', ending + '_best.npy'])))
else:
neuron_groups['e'].theta = np.load(
os.path.join(end_weights_dir,
'_'.join(['theta_A', ending + '_end.npy'])))
else:
# otherwise, set the adaptive additive threshold parameter at 20mV
neuron_groups['e'].theta = np.ones((n_e_total)) * 20.0 * b.mV
for conn_type in recurrent_conn_names:
if conn_type == 'ei':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(
neuron_groups[conn_name[0:2]],
neuron_groups[conn_name[2:4]],
structure='sparse',
state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(conv_features):
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
feature * n_e + n] = 10.4
elif conn_type == 'ie':
# create connection name (composed of population and connections types)
conn_name = name + conn_type[0] + name + conn_type[
1] + '_' + ending
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(
neuron_groups[conn_name[0:2]],
neuron_groups[conn_name[2:4]],
structure='sparse',
state='g' + conn_type[0])
# instantiate the created connection with the 'weightMatrix' loaded from file
for feature in xrange(conv_features):
for other_feature in xrange(conv_features):
if feature != other_feature:
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
other_feature * n_e +
n] = 17.4
print '...Creating monitors for:', name
# spike rate monitors for excitatory and inhibitory neuron populations
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
neuron_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
rate_monitors[name + 'i'] = b.PopulationRateMonitor(
neuron_groups[name + 'i'],
bin=(single_example_time + resting_time) / b.second)
spike_counters[name + 'e'] = b.SpikeCounter(neuron_groups[name + 'e'])
# record neuron population spikes if specified
if record_spikes or plot:
spike_monitors[name + 'e'] = b.SpikeMonitor(neuron_groups[name +
'e'])
spike_monitors[name + 'i'] = b.SpikeMonitor(neuron_groups[name +
'i'])
if record_spikes and plot:
b.figure(fig_num, figsize=(8, 6))
fig_num += 1
b.ion()
b.subplot(211)
b.raster_plot(spike_monitors['Ae'],
refresh=1000 * b.ms,
showlast=1000 * b.ms,
title='Excitatory spikes per neuron')
b.subplot(212)
b.raster_plot(spike_monitors['Ai'],
refresh=1000 * b.ms,
showlast=1000 * b.ms,
title='Inhibitory spikes per neuron')
b.tight_layout()
# creating Poission spike train from input image (784 vector, 28x28 image)
for name in input_population_names:
input_groups[name + 'e'] = b.PoissonGroup(n_input, 0)
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
input_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
# creating connections from input Poisson spike train to excitatory neuron population(s)
for name in input_connection_names:
print '\n...Creating connections between', name[0], 'and', name[1]
# for each of the input connection types (in this case, excitatory -> excitatory)
for conn_type in input_conn_names:
# saved connection name
conn_name = name[0] + conn_type[0] + name[1] + conn_type[1]
# get weight matrix depending on training or test phase
if test_mode:
if save_best_model:
weight_matrix = np.load(
os.path.join(
best_weights_dir,
'_'.join([conn_name, ending + '_best.npy'])))
else:
weight_matrix = np.load(
os.path.join(
end_weights_dir,
'_'.join([conn_name, ending + '_end.npy'])))
# create connections from the windows of the input group to the neuron population
input_connections[conn_name] = b.Connection(input_groups['Xe'], neuron_groups[name[1] + conn_type[1]], \
structure='sparse', state='g' + conn_type[0], delay=True, max_delay=delay[conn_type][1])
if test_mode:
for feature in xrange(conv_features):
for n in xrange(n_e):
for idx in xrange(conv_size**2):
input_connections[conn_name][convolution_locations[n][idx], feature * n_e + n] = \
weight_matrix[convolution_locations[n][idx], feature * n_e + n]
else:
for feature in xrange(conv_features):
for n in xrange(n_e):
for idx in xrange(conv_size**2):
input_connections[conn_name][
convolution_locations[n][idx],
feature * n_e + n] = (b.random() + 0.01) * 0.3
if test_mode:
if plot:
plot_weights_and_assignments(assignments)
fig_num += 1
# if excitatory -> excitatory STDP is specified, add it here (input to excitatory populations)
if not test_mode:
print '...Creating STDP for connection', name
# STDP connection name
conn_name = name[0] + conn_type[0] + name[1] + conn_type[1]
# create the STDP object
stdp_methods[conn_name] = b.STDP(input_connections[conn_name], eqs=eqs_stdp_ee, \
pre=eqs_stdp_pre_ee, post=eqs_stdp_post_ee, wmin=0., wmax=wmax_ee)
print '\n'
def __init__(self,
n_input=784,
conv_size=16,
conv_stride=4,
conv_features=50,
connectivity='all',
weight_dependence=False,
post_pre=True,
weight_sharing=False,
lattice_structure='4',
random_lattice_prob=0.0,
random_inhibition_prob=0.0):
'''
Constructor for the spiking convolutional neural network model.
n_input: (flattened) dimensionality of the input data
conv_size: side length of convolution windows used
conv_stride: stride (horizontal and vertical) of convolution windows used
conv_features: number of convolution features (or patches) used
connectivity: connection style between patches; one of 'none', 'pairs', all'; more to be added
weight_dependence: whether to use weight STDP with weight dependence
post_pre: whether to use STDP with both post- and pre-synpatic traces
weight_sharing: whether to impose that all neurons within a convolution patch share a common set of weights
lattice_structure: lattice connectivity pattern between patches; one of 'none', '4', '8', and 'all'
random_lattice_prob: probability of adding random additional lattice connections between patches
random_inhibition_prob: probability of adding random additional inhibition edges from the inhibitory to excitatory population
'''
self.n_input, self.conv_size, self.conv_stride, self.conv_features, self.connectivity, self.weight_dependence, \
self.post_pre, self.weight_sharing, self.lattice_structure, self.random_lattice_prob, self.random_inhibition_prob = \
n_input, conv_size, conv_stride, conv_features, connectivity, weight_dependence, post_pre, weight_sharing, lattice_structure, \
random_lattice_prob, random_inhibition_prob
# number of inputs to the network
self.n_input_sqrt = int(math.sqrt(self.n_input))
self.n_excitatory_patch = (
(self.n_input_sqrt - self.conv_size) / self.conv_stride + 1)**2
self.n_excitatory = self.n_excitatory_patch * self.conv_features
self.n_excitatory_patch_sqrt = int(math.sqrt(self.n_excitatory_patch))
self.n_inhibitory_patch = self.n_excitatory_patch
self.n_inhibitory = self.n_excitatory
self.conv_features_sqrt = int(math.ceil(math.sqrt(self.conv_features)))
# time (in seconds) per data example presentation and rest period in between
self.single_example_time = 0.35 * b.second
self.resting_time = 0.15 * b.second
# set update intervals
self.update_interval = 100
self.weight_update_interval = 10
self.print_progress_interval = 10
# rest potential parameters, reset potential parameters, threshold potential parameters, and refractory periods
v_rest_e, v_rest_i = -65. * b.mV, -60. * b.mV
v_reset_e, v_reset_i = -65. * b.mV, -45. * b.mV
v_thresh_e, v_thresh_i = -52. * b.mV, -40. * b.mV
refrac_e, refrac_i = 5. * b.ms, 2. * b.ms
# time constants, learning rates, max weights, weight dependence, etc.
tc_pre_ee, tc_post_ee = 20 * b.ms, 20 * b.ms
nu_ee_pre, nu_ee_post = 0.0001, 0.01
exp_ee_post = exp_ee_pre = 0.2
w_mu_pre, w_mu_post = 0.2, 0.2
# parameters for neuron equations
tc_theta = 1e7 * b.ms
theta_plus = 0.05 * b.mV
scr_e = 'v = v_reset_e; theta += theta_plus; timer = 0*ms'
offset = 20.0 * b.mV
v_thresh_e = '(v>(theta - offset + ' + str(
v_thresh_e) + ')) * (timer>refrac_e)'
# equations for neurons
neuron_eqs_e = '''
dv / dt = ((v_rest_e - v) + (I_synE + I_synI) / nS) / (100 * ms) : volt
I_synE = ge * nS * - v : amp
I_synI = gi * nS * (-100. * mV - v) : amp
dge / dt = -ge / (1.0*ms) : 1
dgi / dt = -gi / (2.0*ms) : 1
dtheta / dt = -theta / (tc_theta) : volt
dtimer / dt = 100.0 : ms
'''
neuron_eqs_i = '''
dv/dt = ((v_rest_i - v) + (I_synE + I_synI) / nS) / (10*ms) : volt
I_synE = ge * nS * -v : amp
I_synI = gi * nS * (-85.*mV-v) : amp
dge/dt = -ge/(1.0*ms) : 1
dgi/dt = -gi/(2.0*ms) : 1
'''
# STDP synaptic traces
eqs_stdp_ee = '''
dpre / dt = -pre / tc_pre_ee : 1.0
dpost / dt = -post / tc_post_ee : 1.0
'''
# dictionaries for weights and delays
self.weight, self.delay = {}, {}
# setting weight, delay, and intensity parameters
self.weight['ee_input'] = (conv_size**2) * 0.175
self.delay['ee_input'] = (0 * b.ms, 10 * b.ms)
self.delay['ei_input'] = (0 * b.ms, 5 * b.ms)
self.input_intensity = self.start_input_intensity = 2.0
self.wmax_ee = 1.0
# populations, connections, saved connections, etc.
self.input_population_names = ['X']
self.population_names = ['A']
self.input_connection_names = ['XA']
self.save_connections = ['XeAe', 'AeAe']
self.input_connection_names = ['ee_input']
self.recurrent_connection_names = ['ei', 'ie', 'ee']
# setting STDP update rule
if weight_dependence:
if post_pre:
eqs_stdp_pre_ee = 'pre = 1.; w -= nu_ee_pre * post * w ** exp_ee_pre'
eqs_stdp_post_ee = 'w += nu_ee_post * pre * (wmax_ee - w) ** exp_ee_post; post = 1.'
else:
eqs_stdp_pre_ee = 'pre = 1.'
eqs_stdp_post_ee = 'w += nu_ee_post * pre * (wmax_ee - w) ** exp_ee_post; post = 1.'
else:
if post_pre:
eqs_stdp_pre_ee = 'pre = 1.; w -= nu_ee_pre * post'
eqs_stdp_post_ee = 'w += nu_ee_post * pre; post = 1.'
else:
eqs_stdp_pre_ee = 'pre = 1.'
eqs_stdp_post_ee = 'w += nu_ee_post * pre; post = 1.'
print '\n'
# for filesaving purposes
stdp_input = ''
if self.weight_dependence:
stdp_input += 'weight_dependence_'
else:
stdp_input += 'no_weight_dependence_'
if self.post_pre:
stdp_input += 'post_pre'
else:
stdp_input += 'no_post_pre'
if self.weight_sharing:
use_weight_sharing = 'weight_sharing'
else:
use_weight_sharing = 'no_weight_sharing'
# set ending of filename saves
self.ending = self.connectivity + '_' + str(self.conv_size) + '_' + str(self.conv_stride) + '_' + str(self.conv_features) + \
'_' + str(self.n_excitatory_patch) + '_' + stdp_input + '_' + \
use_weight_sharing + '_' + str(self.lattice_structure) + '_' + str(self.random_lattice_prob) + \
'_' + str(self.random_inhibition_prob)
self.fig_num = 1
# creating dictionaries for various objects
self.neuron_groups, self.input_groups, self.connections, self.input_connections, self.stdp_methods, self.rate_monitors, \
self.spike_monitors, self.spike_counters, self.output_numbers = {}, {}, {}, {}, {}, {}, {}, {}, {}
# creating convolution locations inside the input image
self.convolution_locations = {}
for n in xrange(self.n_excitatory_patch):
self.convolution_locations[n] = [ ((n % self.n_excitatory_patch_sqrt) * self.conv_stride + (n // self.n_excitatory_patch_sqrt) \
* self.n_input_sqrt * self.conv_stride) + (x * self.n_input_sqrt) + y \
for y in xrange(self.conv_size) for x in xrange(self.conv_size) ]
# instantiating neuron spike / votes monitor
self.result_monitor = np.zeros(
(self.update_interval, self.conv_features,
self.n_excitatory_patch))
# creating overarching neuron populations
self.neuron_groups['e'] = b.NeuronGroup(self.n_excitatory, neuron_eqs_e, threshold=v_thresh_e, \
refractory=refrac_e, reset=scr_e, compile=True, freeze=True)
self.neuron_groups['i'] = b.NeuronGroup(self.n_inhibitory, neuron_eqs_i, threshold=v_thresh_i, \
refractory=refrac_i, reset=v_reset_i, compile=True, freeze=True)
# create neuron subpopulations
for name in self.population_names:
print '...creating neuron group:', name
# get a subgroup of size 'n_e' from all exc
self.neuron_groups[name + 'e'] = self.neuron_groups['e'].subgroup(
self.conv_features * self.n_excitatory_patch)
# get a subgroup of size 'n_i' from the inhibitory layer
self.neuron_groups[name + 'i'] = self.neuron_groups['i'].subgroup(
self.conv_features * self.n_excitatory_patch)
# start the membrane potentials of these groups 40mV below their resting potentials
self.neuron_groups[name + 'e'].v = v_rest_e - 40. * b.mV
self.neuron_groups[name + 'i'].v = v_rest_i - 40. * b.mV
print '...creating recurrent connections'
for name in self.population_names:
# set the adaptive additive threshold parameter at 20mV
self.neuron_groups['e'].theta = np.ones(
(self.n_excitatory)) * 20.0 * b.mV
for connection_type in self.recurrent_connection_names:
if connection_type == 'ei':
# create connection name (composed of population and connection types)
connection_name = name + connection_type[
0] + name + connection_type[1]
# create a connection from the first group in conn_name with the second group
self.connections[connection_name] = b.Connection(self.neuron_groups[connection_name[0:2]], \
self.neuron_groups[connection_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(self.conv_features):
for n in xrange(self.n_excitatory_patch):
self.connections[conn_name][feature * self.n_excitatory_patch + n, \
feature * self.n_excitatory_patch + n] = 10.4
elif connection_type == 'ie':
# create connection name (composed of population and connection types)
connection_name = name + connection_type[
0] + name + connection_type[1]
# create a connection from the first group in conn_name with the second group
self.connections[connection_name] = b.Connection(self.neuron_groups[connection_name[0:2]], \
self.neuron_groups[connection_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(self.conv_features):
for other_feature in xrange(self.conv_features):
if feature != other_feature:
for n in xrange(self.n_excitatory_patch):
self.connections[connection_name][feature * self.n_excitatory_patch + n, \
other_feature * self.n_excitatory_patch + n] = 17.4
# adding random inhibitory connections as specified
if self.random_inhibition_prob != 0.0:
for feature in xrange(self.conv_features):
for other_feature in xrange(self.conv_features):
for n_this in xrange(self.n_excitatory_patch):
for n_other in xrange(
self.n_excitatory_patch):
if n_this != n_other:
if b.random(
) < self.random_inhibition_prob:
self.connections[connection_name][feature * self.n_excitatory_patch + n_this, \
other_feature * self.n_excitatory_patch + n_other] = 17.4
elif connection_type == 'ee':
# create connection name (composed of population and connection types)
connection_name = name + connection_type[
0] + name + connection_type[1]
# create a connection from the first group in conn_name with the second group
self.connections[connection_name] = b.Connection(self.neuron_groups[connection_name[0:2]], \
self.neuron_groups[connection_name[2:4]], structure='sparse', state='g' + connection_type[0])
# instantiate the created connection
if self.connectivity == 'all':
for feature in xrange(self.conv_features):
for other_feature in xrange(self.conv_features):
if feature != other_feature:
for this_n in xrange(
self.n_excitatory_patch):
for other_n in xrange(
self.n_excitatory_patch):
if is_lattice_connection(
self.
n_excitatory_patch_sqrt,
this_n, other_n):
self.connections[connection_name][feature * self.n_excitatory_patch + this_n, \
other_feature * self.n_excitatory_patch + other_n] = \
(b.random() + 0.01) * 0.3
elif self.connectivity == 'pairs':
for feature in xrange(self.conv_features):
if feature % 2 == 0:
for this_n in xrange(self.n_excitatory_patch):
for other_n in xrange(
self.n_excitatory_patch):
if is_lattice_connection(
self.n_excitatory_patch_sqrt,
this_n, other_n):
self.connections[connection_name][feature * self.n_excitatory_patch + this_n, \
(feature + 1) * self.n_excitatory_patch + other_n] = (b.random() + 0.01) * 0.3
elif feature % 2 == 1:
for this_n in xrange(self.n_excitatory_patch):
for other_n in xrange(
self.n_excitatory_patch):
if is_lattice_connection(
self.n_excitatory_patch_patch,
this_n, other_n):
self.connections[connection_name][feature * self.n_excitatory_patch + this_n, \
(feature - 1) * self.n_excitatory_patch + other_n] = (b.random() + 0.01) * 0.3
elif connectivity == 'linear':
for feature in xrange(self.conv_features):
if feature != self.conv_features - 1:
for this_n in xrange(self.n_excitatory_patch):
for other_n in xrange(
self.n_excitatory_patch):
if is_lattice_connection(
self.n_excitatory_patch_sqrt,
this_n, other_n):
self.connections[connection_name][feature * self.n_excitatory_patch + this_n, \
(feature + 1) * self.n_excitatory_patch + other_n] = \
(b.random() + 0.01) * 0.3
if feature != 0:
for this_n in xrange(self.n_excitatory_patch):
for other_n in xrange(
self.n_excitatory_patch):
if is_lattice_connection(
self.n_excitatory_patch_sqrt,
this_n, other_n):
self.connections[connection_name][feature * self.n_excitatory_patch + this_n, \
(feature - 1) * self.n_excitatory_patch + other_n] = \
(b.random() + 0.01) * 0.3
elif self.connectivity == 'none':
pass
# if STDP from excitatory -> excitatory is on and this connection is excitatory -> excitatory
if 'ee' in self.recurrent_conn_names:
self.stdp_methods[name + 'e' + name + 'e'] = b.STDP(self.connections[name + 'e' + name + 'e'], \
eqs=eqs_stdp_ee, pre=eqs_stdp_pre_ee, \
post=eqs_stdp_post_ee, wmin=0., wmax=self.wmax_ee)
print '...creating monitors for:', name
# spike rate monitors for excitatory and inhibitory neuron populations
self.rate_monitors[name + 'e'] = b.PopulationRateMonitor(self.neuron_groups[name + 'e'], \
bin=(self.single_example_time + self.resting_time) / b.second)
self.rate_monitors[name + 'i'] = b.PopulationRateMonitor(self.neuron_groups[name + 'i'], \
bin=(self.single_example_time + self.resting_time) / b.second)
self.spike_counters[name + 'e'] = b.SpikeCounter(
self.neuron_groups[name + 'e'])
# record neuron population spikes
self.spike_monitors[name + 'e'] = b.SpikeMonitor(
self.neuron_groups[name + 'e'])
self.spike_monitors[name + 'i'] = b.SpikeMonitor(
self.neuron_groups[name + 'i'])
if do_plot:
b.figure(self.fig_num)
fig_num += 1
b.ion()
b.subplot(211)
b.raster_plot(self.spike_monitors['Ae'],
refresh=1000 * b.ms,
showlast=1000 * b.ms)
b.subplot(212)
b.raster_plot(self.spike_monitors['Ai'],
refresh=1000 * b.ms,
showlast=1000 * b.ms)
# specifying locations of lattice connections
self.lattice_locations = {}
if self.connectivity == 'all':
for this_n in xrange(self.conv_features * self.n_excitatory_patch):
self.lattice_locations[this_n] = [ other_n for other_n in xrange(self.conv_features * self.n_excitatory_patch) \
if is_lattice_connection(self.n_excitatory_patch_sqrt, \
this_n % self.n_excitatory_patch, other_n % self.n_excitatory_patch) ]
elif self.connectivity == 'pairs':
for this_n in xrange(self.conv_features * self.n_excitatory_patch):
self.lattice_locations[this_n] = []
for other_n in xrange(self.conv_features *
self.n_excitatory_patch):
if this_n // self.n_excitatory_patch % 2 == 0:
if is_lattice_connection(self.n_excitatory_patch_sqrt, this_n % self.n_excitatory_patch, \
other_n % self.n_excitatory_patch) and \
other_n // self.n_excitatory_patch == this_n // self.n_excitatory_patch + 1:
self.lattice_locations[this_n].append(other_n)
elif this_n // self.n_excitatory_patch % 2 == 1:
if is_lattice_connection(self.n_excitatory_patch_sqrt, this_n % self.n_excitatory_patch, \
other_n % self.n_excitatory_patch) and \
other_n // self.n_excitatory_patch == this_n // self.n_excitatory_patch - 1:
self.lattice_locations[this_n].append(other_n)
elif self.connectivity == 'linear':
for this_n in xrange(self.conv_features * self.n_excitatory_patch):
self.lattice_locations[this_n] = []
for other_n in xrange(conv_features * self.n_excitatory_patch):
if this_n // self.n_excitatory_patch != self.conv_features - 1:
if is_lattice_connection(self.n_excitatory_patch_sqrt, this_n % self.n_excitatory_patch, \
other_n % self.n_excitatory_patch) and \
other_n // self.n_excitatory_patch == this_n // self.n_excitatory_patch + 1:
self.lattice_locations[this_n].append(other_n)
elif this_n // self.n_excitatory_patch != 0:
if is_lattice_connection(self.n_excitatory_patch_sqrt, this_n % self.n_excitatory_patch, \
other_n % self.n_excitatory_patch) and \
other_n // self.n_excitatory_patch == this_n // self.n_excitatory_patch - 1:
self.lattice_locations[this_n].append(other_n)
# setting up parameters for weight normalization between patches
num_lattice_connections = sum(
[len(value) for value in lattice_locations.values()])
self.weight['ee_recurr'] = (num_lattice_connections /
self.conv_features) * 0.15
# creating Poission spike train from input image (784 vector, 28x28 image)
for name in self.input_population_names:
self.input_groups[name + 'e'] = b.PoissonGroup(self.n_input, 0)
self.rate_monitors[name + 'e'] = b.PopulationRateMonitor(self.input_groups[name + 'e'], \
bin=(self.single_example_time + self.resting_time) / b.second)
# creating connections from input Poisson spike train to convolution patch populations
for name in self.input_connection_names:
print '\n...creating connections between', name[0], 'and', name[1]
# for each of the input connection types (in this case, excitatory -> excitatory)
for connection_type in self.input_conn_names:
# saved connection name
connection_name = name[0] + connection_type[0] + name[
1] + connection_type[1]
# create connections from the windows of the input group to the neuron population
self.input_connections[connection_name] = b.Connection(self.input_groups['Xe'], \
self.neuron_groups[name[1] + connection_type[1]], structure='sparse', \
state='g' + connection_type[0], delay=True, max_delay=self.delay[connection_type][1])
for feature in xrange(self.conv_features):
for n in xrange(self.n_excitatory_patch):
for idx in xrange(self.conv_size**2):
self.input_connections[connection_name][self.convolution_locations[n][idx], \
feature * self.n_excitatory_patch + n] = (b.random() + 0.01) * 0.3
# if excitatory -> excitatory STDP is specified, add it here (input to excitatory populations)
print '...creating STDP for connection', name
# STDP connection name
connection_name = name[0] + connection_type[0] + name[
1] + connection_type[1]
# create the STDP object
self.stdp_methods[connection_name] = b.STDP(self.input_connections[connection_name], \
eqs=eqs_stdp_ee, pre=eqs_stdp_pre_ee, post=eqs_stdp_post_ee, wmin=0., wmax=self.wmax_ee)
print '\n'
def fft_std(delta_u, run_num, new_connectivity, osc, rep):
#bn.seed(int(time.time()))
bn.reinit_default_clock()
#bn.seed(1412958308+2)
bn.defaultclock.dt = 0.5 * bn.ms
#==============================================================================
# Define constants for the model.
#==============================================================================
fft_file = './std_fft_p20_'
rate_file = './std_rate_p20_'
print delta_u
print run_num
print new_connectivity
print rep
if osc:
T = 5.5 * bn.second
else:
T = 2.5 * bn.second
n_tsteps = T / bn.defaultclock.dt
fft_start = 0.5 * bn.second / bn.defaultclock.dt # Time window for the FFT computation
ro = 1.2 * bn.Hz
SEE1 = 1.0
SEE2 = 1.0
qee1 = 1.00 # Fraction of NMDA receptors for e to e connections
qee2 = 0.00
qie1 = 1.00 # Fraction of NMDA receptors for e to i connections
qie2 = 0.00
uee1 = 0.2 - delta_u
uee2 = 0.2 + delta_u
uie1 = 0.2
uie2 = 0.2
trec1 = 1000.0 * bn.ms
trec2 = 1000.0 * bn.ms
k = 0.65
#Jeo_const = 1.0#*bn.mV # Base strength of o (external) to e connections
Ne = 3200 # number of excitatory neurons
Ni = 800 # number of inhibitory neurons
No = 20000 # number of external neurons
N = Ne + Ni
pcon = 0.2 # probability of connection
Jee = 10.0 / (Ne * pcon)
Jie = 10.0 / (Ne * pcon)
Jii = k * 10.0 / (Ni * pcon)
Jei = k * 10.0 / (Ni * pcon)
Jeo = 1.0
El = -60.0 * bn.mV # leak reversal potential
Vreset = -52.0 * bn.mV # reversal potential
Vthresh = -40.0 * bn.mV # spiking threshold
tref = 2.0 * bn.ms # refractory period
te = 20.0 * bn.ms # membrane time constant of excitatory neurons
ti = 10.0 * bn.ms # membrane time constant of inhibitory neruons
tee_ampa = 10.0 * bn.ms # time const of ampa currents at excitatory neurons
tee_nmda = 100.0 * bn.ms # time const of nmda currents at excitatory neurons
tie_ampa = 10.0 * bn.ms # time const of ampa currents at inhibitory neurons
tie_nmda = 100.0 * bn.ms # time const of nmda currents at inhibitory neurons
tii_gaba = 10.0 * bn.ms # time const of GABA currents at inhibitory neurons
tei_gaba = 10.0 * bn.ms # time const of GABA currents at excitatory neurons
teo_input = 100.0 * bn.ms
#==============================================================================
# Define model structure
#==============================================================================
model = '''
dV/dt = (-(V-El)+J_ampa1*I_ampa1+J_nmda1*I_nmda1+J_ampa2*I_ampa2+J_nmda2*I_nmda2-J_gaba*I_gaba+J_input*I_input+eta)/tm : bn.volt
dI_ampa1/dt = -I_ampa1/t_ampa : bn.volt
dI_nmda1/dt = -I_nmda1/t_nmda : bn.volt
dI_ampa2/dt = -I_ampa2/t_ampa : bn.volt
dI_nmda2/dt = -I_nmda2/t_nmda : bn.volt
dI_gaba/dt = -I_gaba/t_gaba : bn.volt
dI_input/dt = (-I_input+mu)/t_input : bn.volt
dx1/dt = (1-x1)/t1_rec : 1
dx2/dt = (1-x2)/t2_rec : 1
u1 : 1
t1_rec : bn.second
u2 : 1
t2_rec : bn.second
mu : bn.volt
eta : bn.volt
J_ampa1 : 1
J_nmda1 : 1
J_ampa2 : 1
J_nmda2 : 1
J_gaba : 1
J_input : 1
tm : bn.second
t_ampa : bn.second
t_nmda : bn.second
t_gaba : bn.second
t_input : bn.second
'''
P_reset = "V=-52*bn.mV;x1+=-u1*x1;x2+=-u2*x2"
Se_model = '''
we_ampa1 : bn.volt
we_nmda1 : bn.volt
we_ampa2 : bn.volt
we_nmda2 : bn.volt
'''
Se_pre = ('I_ampa1 += x1_pre*we_ampa1', 'I_nmda1 += x1_pre*we_nmda1',
'I_ampa2 += x2_pre*we_ampa2', 'I_nmda2 += x2_pre*we_nmda2')
Si_model = '''
wi_gaba : bn.volt
'''
Si_pre = 'I_gaba += wi_gaba'
So_model = '''
wo_input : bn.volt
'''
So_pre = 'I_input += wo_input'
#==============================================================================
# Define populations
#==============================================================================
P = bn.NeuronGroup(N,
model,
threshold=Vthresh,
reset=P_reset,
refractory=tref)
Pe = P[0:Ne]
Pe.tm = te
Pe.t_ampa = tee_ampa
Pe.t_nmda = tee_nmda
Pe.t_gaba = tei_gaba
Pe.t_input = teo_input
Pe.I_ampa1 = 0 * bn.mV
Pe.I_nmda1 = 0 * bn.mV
Pe.I_ampa2 = 0 * bn.mV
Pe.I_nmda2 = 0 * bn.mV
Pe.I_gaba = 0 * bn.mV
Pe.I_input = 0 * bn.mV
Pe.V = (np.random.rand(Pe.V.size) * 12 - 52) * bn.mV
Pe.x1 = 1.0
Pe.x2 = 1.0
Pe.u1 = uee1
Pe.u2 = uee2
Pe.t1_rec = trec1
Pe.t2_rec = trec2
Pi = P[Ne:(Ne + Ni)]
Pi.tm = ti
Pi.t_ampa = tie_ampa
Pi.t_nmda = tie_nmda
Pi.t_gaba = tii_gaba
Pi.t_input = teo_input
Pi.I_ampa1 = 0 * bn.mV
Pi.I_nmda1 = 0 * bn.mV
Pi.I_ampa2 = 0 * bn.mV
Pi.I_nmda2 = 0 * bn.mV
Pi.I_gaba = 0 * bn.mV
Pi.I_input = 0 * bn.mV
Pi.V = (np.random.rand(Pi.V.size) * 12 - 52) * bn.mV
Pi.x1 = 1.0
Pi.x2 = 1.0
Pi.u1 = 0.0
Pi.u2 = 0.0
Pi.t1_rec = 1.0
Pi.t2_rec = 1.0
Pe.J_ampa1 = Jee * (1 - qee1) #*SEE1
Pe.J_nmda1 = Jee * qee1 #*SEE1
Pe.J_ampa2 = Jee * (1 - qee2) #*SEE2
Pe.J_nmda2 = Jee * qee2 #*SEE2
Pi.J_ampa1 = Jie * (1 - qie2) #*SEE2
Pi.J_nmda1 = Jie * qie2 #*SEE2
Pi.J_ampa2 = Jie * (1 - qie1) #*SEE1
Pi.J_nmda2 = Jie * qie1 #*SEE1
Pe.J_gaba = Jei
Pi.J_gaba = Jii
Pe.J_input = Jeo
Pi.J_input = Jeo
#==============================================================================
# Define inputs
#==============================================================================
if osc:
Pe.mu = 12.0 * bn.mV
holder = np.zeros((n_tsteps, ))
t_freq = np.linspace(0, 10, n_tsteps)
fo = 0.2 # Smallest frequency in the signal
fe = 10.0 # Largest frequency in the signal
F = int(fe / 0.2)
for m in range(1, F + 1):
holder = holder + np.cos(2 * np.pi * m * fo * t_freq - m *
(m - 1) * np.pi / F)
holder = holder / np.max(holder)
Pe.eta = bn.TimedArray(0.0 * bn.mV * holder) #, dt=0.5*bn.ms)
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Pi.mu = 0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Po = bn.PoissonGroup(No, rates=0 * bn.Hz)
else:
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
holder_pe = np.zeros((n_tsteps, ))
time_steps = np.linspace(0, T / bn.second, n_tsteps)
holder_pe[time_steps < 0.5] = 0.0 * bn.mV
holder_pe[time_steps >= 0.5] = 6.0 * bn.mV #25
holder_pe[time_steps > 1.5] = 0.0 * bn.mV #25
Pe.mu = bn.TimedArray(holder_pe)
def firing_function(t, ro):
if t > 0.5 * bn.second and t < 3.5 * bn.second:
return 0.0 * bn.Hz
else:
return 0.0 * bn.Hz
Pe.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Pi.mu = 0.0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Po = bn.PoissonGroup(No, rates=lambda t: firing_function(t, ro))
#==============================================================================
# Define synapses
#==============================================================================
See1 = bn.Synapses(Pe, Pe, model=Se_model, pre=Se_pre)
See2 = bn.Synapses(Pe, Pe, model=Se_model, pre=Se_pre)
Sie1 = bn.Synapses(Pe, Pi, model=Se_model, pre=Se_pre)
Sie2 = bn.Synapses(Pe, Pi, model=Se_model, pre=Se_pre)
Sei = bn.Synapses(Pi, Pe, model=Si_model, pre=Si_pre)
Sii = bn.Synapses(Pi, Pi, model=Si_model, pre=Si_pre)
Seo = bn.Synapses(Po, Pe, model=So_model, pre=So_pre)
#==============================================================================
# Define random connections
#==============================================================================
if new_connectivity:
See1.connect_random(Pe, Pe, sparseness=pcon / 2.0)
See2.connect_random(Pe, Pe, sparseness=pcon / 2.0)
Sie1.connect_random(Pe, Pi, sparseness=pcon / 2.0)
Sie2.connect_random(Pe, Pi, sparseness=pcon / 2.0)
Sii.connect_random(Pi, Pi, sparseness=pcon)
Sei.connect_random(Pi, Pe, sparseness=pcon)
Seo.connect_random(Po, Pe, sparseness=pcon)
print 'Saving'
See1.save_connectivity('./See1_connections_std_saver_p20_' +
str(run_num))
See2.save_connectivity('./See2_connections_std_saver_p20_' +
str(run_num))
Sie1.save_connectivity('./Sie1_connections_std_saver_p20_' +
str(run_num))
Sie2.save_connectivity('./Sie2_connections_std_saver_p20_' +
str(run_num))
Sii.save_connectivity('./Sii_connections_std_saver_p20_' +
str(run_num))
Sei.save_connectivity('./Sei_connections_std_saver_p20_' +
str(run_num))
Seo.save_connectivity('./Seo_connections_std_saver_p20_' +
str(run_num))
else:
print 'Loading'
See1.load_connectivity('./See1_connections_std_saver_p20_' +
str(run_num))
See2.load_connectivity('./See2_connections_std_saver_p20_' +
str(run_num))
Sie1.load_connectivity('./Sie1_connections_std_saver_p20_' +
str(run_num))
Sie2.load_connectivity('./Sie2_connections_std_saver_p20_' +
str(run_num))
Sii.load_connectivity('./Sii_connections_std_saver_p20_' +
str(run_num))
Sei.load_connectivity('./Sei_connections_std_saver_p20_' +
str(run_num))
Seo.load_connectivity('./Seo_connections_std_saver_p20_' +
str(run_num))
See1.we_ampa1 = SEE1 * 1.0 * bn.mV / tee_ampa
See1.we_nmda1 = SEE1 * 1.0 * bn.mV / tee_nmda
See1.we_ampa2 = 0.0 * bn.mV / tee_ampa
See1.we_nmda2 = 0.0 * bn.mV / tee_nmda
See2.we_ampa1 = 0.0 * bn.mV / tee_ampa
See2.we_nmda1 = 0.0 * bn.mV / tee_nmda
See2.we_ampa2 = SEE2 * 1.0 * bn.mV / tee_ampa
See2.we_nmda2 = SEE2 * 1.0 * bn.mV / tee_nmda
Sie1.we_ampa1 = 0.0 * bn.mV / tie_ampa
Sie1.we_nmda1 = 0.0 * bn.mV / tie_nmda
Sie1.we_ampa2 = SEE1 * 1.0 * bn.mV / tie_ampa
Sie1.we_nmda2 = SEE1 * 1.0 * bn.mV / tie_nmda
Sie2.we_ampa1 = SEE2 * 1.0 * bn.mV / tie_ampa
Sie2.we_nmda1 = SEE2 * 1.0 * bn.mV / tie_nmda
Sie2.we_ampa2 = 0.0 * bn.mV / tie_ampa
Sie2.we_nmda2 = 0.0 * bn.mV / tie_nmda
Sei.wi_gaba = 1.0 * bn.mV / tei_gaba
Sii.wi_gaba = 1.0 * bn.mV / tii_gaba
Seo.wo_input = 1.0 * bn.mV / teo_input
#==============================================================================
# Define monitors
#==============================================================================
Pe_mon_V = bn.StateMonitor(Pe, 'V', timestep=10, record=True)
Pe_mon_eta = bn.StateMonitor(Pe, 'eta', timestep=1, record=True)
Pe_mon_ampa1 = bn.StateMonitor(Pe, 'I_ampa1', timestep=1, record=True)
Pe_mon_nmda1 = bn.StateMonitor(Pe, 'I_nmda1', timestep=1, record=True)
Pe_mon_ampa2 = bn.StateMonitor(Pe, 'I_ampa2', timestep=1, record=True)
Pe_mon_nmda2 = bn.StateMonitor(Pe, 'I_nmda2', timestep=1, record=True)
Pe_mon_gaba = bn.StateMonitor(Pe, 'I_gaba', timestep=1, record=True)
Pe_mon_input = bn.StateMonitor(Pe, 'I_input', timestep=10, record=True)
See1_mon_x = bn.StateMonitor(Pe, 'x1', timestep=10, record=True)
See2_mon_x = bn.StateMonitor(Pe, 'x2', timestep=10, record=True)
Pe_ratemon = bn.PopulationRateMonitor(Pe, bin=10.0 * bn.ms)
Pi_ratemon = bn.PopulationRateMonitor(Pi, bin=10.0 * bn.ms)
#==============================================================================
# Run model
#==============================================================================
timer = 0 * bn.second
t_start = time.time()
bn.run(T, report='graphical')
timer = timer + T
print '-------------------------------------------------------'
print 'Time is ' + str(timer) + ' seconds'
t_end = time.time()
print 'Time to compute last ' +str(T)+' seconds is: ' + \
str(t_end - t_start) + ' seconds'
print '-------------------------------------------------------\n'
Pe_mon_ampa1_vals = Pe.J_ampa1[0] * np.mean(Pe_mon_ampa1.values.T, axis=1)
Pe_mon_nmda1_vals = Pe.J_nmda1[0] * np.mean(Pe_mon_nmda1.values.T, axis=1)
Pe_mon_ampa2_vals = Pe.J_ampa2[0] * np.mean(Pe_mon_ampa2.values.T, axis=1)
Pe_mon_nmda2_vals = Pe.J_nmda2[0] * np.mean(Pe_mon_nmda2.values.T, axis=1)
Pe_mon_ampa_vals = Pe_mon_ampa1_vals + Pe_mon_ampa2_vals
Pe_mon_nmda_vals = Pe_mon_nmda1_vals + Pe_mon_nmda2_vals
Pe_mon_gaba_vals = Pe.J_gaba[0] * np.mean(Pe_mon_gaba.values.T, axis=1)
Pe_mon_input_vals = Pe.J_input[0] * np.mean(Pe_mon_input.values.T, axis=1)
Pe_mon_V_vals = np.mean(Pe_mon_V.values.T, axis=1)
Pe_mon_all_vals = Pe_mon_ampa_vals + Pe_mon_nmda_vals - Pe_mon_gaba_vals
See1_mon_x_vals = np.mean(See1_mon_x.values.T, axis=1)
See2_mon_x_vals = np.mean(See2_mon_x.values.T, axis=1)
#==============================================================================
# Save into a Matlab file
#==============================================================================
if osc:
Pe_output = Pe.J_ampa1[0]*Pe_mon_ampa1.values+Pe.J_nmda1[0]*Pe_mon_nmda1.values + \
Pe.J_ampa2[0]*Pe_mon_ampa2.values+Pe.J_nmda2[0]*Pe_mon_nmda2.values-Pe.J_gaba[0]*Pe_mon_gaba.values
Pe_output = Pe_output[:, fft_start:, ]
Pe_V = Pe_mon_V.values[:, fft_start:, ]
Pe_glut = Pe.J_ampa1[0]*Pe_mon_ampa1.values+Pe.J_nmda1[0]*Pe_mon_nmda1.values + \
Pe.J_ampa2[0]*Pe_mon_ampa2.values+Pe.J_nmda2[0]*Pe_mon_nmda2.values
Pe_glut = Pe_glut[:, fft_start:, ]
Pe_gaba = Pe.J_gaba[0] * Pe_mon_gaba.values
Pe_gaba = Pe_gaba[:, fft_start:, ]
Pe_input = Pe_mon_eta[:, fft_start:, ]
T_step = bn.defaultclock.dt
holder = {
'Pe_output': Pe_output,
'Pe_input': Pe_input,
'Pe_V': Pe_V,
'Pe_glut': Pe_glut,
'Pe_gaba': Pe_gaba,
'T_step': T_step
}
scipy.io.savemat(fft_file + 'delta_u' + str(delta_u) + '_' + str(rep),
mdict=holder)
else:
holder = {
'Pe_rate': Pe_ratemon.rate,
'Pe_time': Pe_ratemon.times,
'uee1': uee1,
'uee2': uee2,
'uie1': uie1,
'uie2': uie2
}
scipy.io.savemat(rate_file + 'delta_q_' + str(delta_u) + '_' +
str(run_num) + 'rep' + str(rep),
mdict=holder)
bn.clear(erase=True, all=True)
def fft_nostd(qee, run_num, new_connectivity, osc, rep):
#bn.seed(int(time.time()))
# bn.seed(1412958308+2)
bn.reinit_default_clock()
bn.defaultclock.dt = 0.5 * bn.ms
#==============================================================================
# Define constants for the model.
#==============================================================================
fft_file = './nostd_fft_p20_'
rate_file = './nostd_rate_p20_'
if osc:
T = 8.0 * bn.second
else:
T = 3.5 * bn.second
n_tsteps = T / bn.defaultclock.dt
fft_start = 3.0 * bn.second / bn.defaultclock.dt # Time window for the FFT computation
#run_num = 10
ro = 1.2 * bn.Hz
#==============================================================================
# Need to do all others besides 0.2 and 0.5
#==============================================================================
print qee
print run_num
print new_connectivity
print rep
qie = 0.3 # Fraction of NMDA receptors for e to i connections
k = 0.65
Jeo_const = 1.0 #*bn.mV # Base strength of o (external) to e connections
Ne = 3200 # number of excitatory neurons
Ni = 800 # number of inhibitory neurons
No = 2000 # number of external neurons
N = Ne + Ni
pcon = 0.2 # probability of connection
Jee = 5.0 / (Ne * pcon)
Jie = 5.0 / (Ne * pcon)
Jii = k * 5.0 / (Ni * pcon)
Jei = k * 5.0 / (Ni * pcon)
Jeo = 1.0
El = -60.0 * bn.mV # leak reversal potential
Vreset = -52.0 * bn.mV # reversal potential
Vthresh = -40.0 * bn.mV # spiking threshold
tref = 2.0 * bn.ms # refractory period
te = 20.0 * bn.ms # membrane time constant of excitatory neurons
ti = 10.0 * bn.ms # membrane time constant of inhibitory neruons
tee_ampa = 10.0 * bn.ms # time const of ampa currents at excitatory neurons
tee_nmda = 100.0 * bn.ms # time const of nmda currents at excitatory neurons
tie_ampa = 10.0 * bn.ms # time const of ampa currents at inhibitory neurons
tie_nmda = 100.0 * bn.ms # time const of nmda currents at inhibitory neurons
tii_gaba = 10.0 * bn.ms # time const of GABA currents at inhibitory neurons
tei_gaba = 10.0 * bn.ms # time const of GABA currents at excitatory neurons
teo_input = 100.0 * bn.ms
#==============================================================================
# Define model structure
#==============================================================================
model = '''
dV/dt = (-(V-El)+J_ampa*I_ampa+J_nmda*I_nmda-J_gaba*I_gaba+J_input*I_input+eta+eta_corr)/tm : bn.volt
dI_ampa/dt = -I_ampa/t_ampa : bn.volt
dI_nmda/dt = -I_nmda/t_nmda : bn.volt
dI_gaba/dt = -I_gaba/t_gaba : bn.volt
dI_input/dt = (-I_input+mu)/t_input : bn.volt
J_ampa : 1
J_nmda : 1
J_gaba : 1
J_input : 1
mu : bn.volt
eta : bn.volt
eta_corr : bn.volt
tm : bn.second
t_ampa : bn.second
t_nmda : bn.second
t_gaba : bn.second
t_input : bn.second
'''
P_reset = "V=-52*bn.mV"
Se_model = '''
we_ampa : bn.volt
we_nmda : bn.volt
'''
Se_pre = ('I_ampa += we_ampa', 'I_nmda += we_nmda')
Si_model = '''
wi_gaba : bn.volt
'''
Si_pre = 'I_gaba += wi_gaba'
So_model = '''
wo_input : bn.volt
'''
So_pre = 'I_input += wo_input'
#==============================================================================
# Define populations
#==============================================================================
P = bn.NeuronGroup(N,
model,
threshold=Vthresh,
reset=P_reset,
refractory=tref)
Pe = P[0:Ne]
Pe.tm = te
Pe.t_ampa = tee_ampa
Pe.t_nmda = tee_nmda
Pe.t_gaba = tei_gaba
Pe.t_input = teo_input
Pe.I_ampa = 0 * bn.mV
Pe.I_nmda = 0 * bn.mV
Pe.I_gaba = 0 * bn.mV
Pe.I_input = 0 * bn.mV
Pe.V = (np.random.rand(Pe.V.size) * 12 - 52) * bn.mV
Pi = P[Ne:(Ne + Ni)]
Pi.tm = ti
Pi.t_ampa = tie_ampa
Pi.t_nmda = tie_nmda
Pi.t_gaba = tii_gaba
Pi.t_input = teo_input
Pi.I_ampa = 0 * bn.mV
Pi.I_nmda = 0 * bn.mV
Pi.I_gaba = 0 * bn.mV
Pi.I_input = 0 * bn.mV
Pi.V = (np.random.rand(Pi.V.size) * 12 - 52) * bn.mV
Pe.J_ampa = Jee * (1 - qee) #*SEE1
Pe.J_nmda = Jee * qee #*SEE1
Pi.J_ampa = Jie * (1 - qie) #*SEE1
Pi.J_nmda = Jie * qie #*SEE1
Pe.J_gaba = Jei
Pi.J_gaba = Jii
Pe.J_input = Jeo
Pi.J_input = Jeo
#==============================================================================
# Define inputs
#==============================================================================
if osc:
Pe.mu = 2.0 * bn.mV
holder = np.zeros((n_tsteps, ))
t_freq = np.linspace(0, 10, n_tsteps)
fo = 0.2 # Smallest frequency in the signal
fe = 10.0 # Largest frequency in the signal
F = int(fe / 0.2)
for m in range(1, F + 1):
holder = holder + np.cos(2 * np.pi * m * fo * t_freq - m *
(m - 1) * np.pi / F)
holder = holder / np.max(holder)
Pe.eta = bn.TimedArray(0.0 * bn.mV * holder) #, dt=0.5*bn.ms)
Pe.eta_corr = 0 * bn.mV
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Pi.mu = 0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Pi.eta_corr = 0 * bn.mV
Po = bn.PoissonGroup(No, rates=0 * bn.Hz)
else:
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
holder_pe = np.zeros((n_tsteps, ))
time_steps = np.linspace(0, T / bn.second, n_tsteps)
holder_pe[time_steps < 0.5] = 0.0 * bn.mV
holder_pe[time_steps >= 0.5] = 3.0 * bn.mV # 35.0/Jeo *bn.mV #25
Pe.mu = bn.TimedArray(holder_pe)
def firing_function(t, ro):
if t > 0.5 * bn.second and t < 3.5 * bn.second:
return 0.0 * bn.Hz
else:
return 0.0 * bn.Hz
# Pe.mu = 0*bn.mV
Pe.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Pi.mu = 0.0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Po = bn.PoissonGroup(No, rates=lambda t: firing_function(t, ro))
#==============================================================================
# Define synapses
#==============================================================================
See = bn.Synapses(Pe, Pe, model=Se_model, pre=Se_pre)
Sie = bn.Synapses(Pe, Pi, model=Se_model, pre=Se_pre)
Sei = bn.Synapses(Pi, Pe, model=Si_model, pre=Si_pre)
Sii = bn.Synapses(Pi, Pi, model=Si_model, pre=Si_pre)
Seo = bn.Synapses(Po, Pe, model=So_model, pre=So_pre)
#==============================================================================
# Define monitors
#==============================================================================
Pe_mon_V = bn.StateMonitor(Pe, 'V', timestep=1, record=True)
Pe_mon_eta = bn.StateMonitor(Pe, 'eta', timestep=1, record=True)
Pe_mon_ampa = bn.StateMonitor(Pe, 'I_ampa', timestep=1, record=True)
Pe_mon_nmda = bn.StateMonitor(Pe, 'I_nmda', timestep=1, record=True)
Pe_mon_gaba = bn.StateMonitor(Pe, 'I_gaba', timestep=1, record=True)
Pe_ratemon = bn.PopulationRateMonitor(Pe, bin=10.0 * bn.ms)
#==============================================================================
# Define random connections
#==============================================================================
if new_connectivity:
See.connect_random(Pe, Pe, sparseness=pcon)
Sie.connect_random(Pe, Pi, sparseness=pcon)
Sii.connect_random(Pi, Pi, sparseness=pcon)
Sei.connect_random(Pi, Pe, sparseness=pcon)
Seo.connect_random(Po, Pe, sparseness=pcon)
print 'Saving'
See.save_connectivity('./See_connections_nostd_saver_p20' +
str(run_num))
Sie.save_connectivity('./Sie_connections_nostd_saver_p20' +
str(run_num))
Sii.save_connectivity('./Sii_connections_nostd_saver_p20' +
str(run_num))
Sei.save_connectivity('./Sei_connections_nostd_saver_p20' +
str(run_num))
Seo.save_connectivity('./Seo_connections_nostd_saver_p20' +
str(run_num))
else:
print 'Loading'
See.load_connectivity('./See_connections_nostd_saver_p20' +
str(run_num))
Sie.load_connectivity('./Sie_connections_nostd_saver_p20' +
str(run_num))
Sii.load_connectivity('./Sii_connections_nostd_saver_p20' +
str(run_num))
Sei.load_connectivity('./Sei_connections_nostd_saver_p20' +
str(run_num))
Seo.load_connectivity('./Seo_connections_nostd_saver_p20' +
str(run_num))
See.we_ampa = 1.0 * bn.mV / tee_ampa
See.we_nmda = 1.0 * bn.mV / tee_nmda
Sie.we_ampa = 1.0 * bn.mV / tie_ampa
Sie.we_nmda = 1.0 * bn.mV / tie_nmda
Sei.wi_gaba = 1.0 * bn.mV / tei_gaba
Sii.wi_gaba = 1.0 * bn.mV / tii_gaba
Seo.wo_input = 1.0 * bn.mV / teo_input
#==============================================================================
# Run model
#==============================================================================
timer = 0 * bn.second
t_start = time.time()
bn.run(T, report='graphical')
timer = timer + T
print '-------------------------------------------------------'
print 'Time is ' + str(timer) + ' seconds'
t_end = time.time()
print 'Time to compute last ' +str(T)+' seconds is: ' + \
str(t_end - t_start) + ' seconds'
print '-------------------------------------------------------\n'
#==============================================================================
# Save into a Matlab file
#==============================================================================
if osc:
Pe_output = Pe.J_ampa[0] * Pe_mon_ampa.values + Pe.J_nmda[
0] * Pe_mon_nmda.values - Pe.J_gaba[0] * Pe_mon_gaba.values
Pe_output = Pe_output[:, fft_start:, ]
Pe_glut = Pe.J_ampa[0] * Pe_mon_ampa.values + Pe.J_nmda[
0] * Pe_mon_nmda.values
Pe_glut = Pe_glut[:, fft_start:, ]
Pe_gaba = Pe.J_gaba[0] * Pe_mon_gaba.values[:, fft_start:, ]
Pe_V = Pe_mon_V.values[:, fft_start:, ]
Pe_input = Pe_mon_eta[:, fft_start:, ]
T_step = bn.defaultclock.dt
holder = {
'Pe_output': Pe_output,
'Pe_input': Pe_input,
'Pe_V': Pe_V,
'Pe_glut': Pe_glut,
'Pe_gaba': Pe_gaba,
'T_step': T_step
}
scipy.io.savemat(fft_file + 'qee' + str(qee) + '_' + str(rep),
mdict=holder)
else:
holder = {'Pe_rate': Pe_ratemon.rate, 'Pe_time': Pe_ratemon.times}
scipy.io.savemat(rate_file + 'qee_' + str(qee) + '_' + str(run_num) +
'rep' + str(rep),
mdict=holder)
def build_network():
global fig_num
neuron_groups['e'] = b.NeuronGroup(n_e_total,
neuron_eqs_e,
threshold=v_thresh_e,
refractory=refrac_e,
reset=scr_e,
compile=True,
freeze=True)
neuron_groups['i'] = b.NeuronGroup(n_e_total,
neuron_eqs_i,
threshold=v_thresh_i,
refractory=refrac_i,
reset=v_reset_i,
compile=True,
freeze=True)
for name in ['A']:
print '...Creating neuron group:', name
# get a subgroup of size 'n_e' from all exc
neuron_groups[name + 'e'] = neuron_groups['e'].subgroup(conv_features *
n_e)
# get a subgroup of size 'n_i' from the inhibitory layer
neuron_groups[name + 'i'] = neuron_groups['i'].subgroup(conv_features *
n_e)
# start the membrane potentials of these groups 40mV below their resting potentials
neuron_groups[name + 'e'].v = v_rest_e - 40. * b.mV
neuron_groups[name + 'i'].v = v_rest_i - 40. * b.mV
print '...Creating recurrent connections'
for name in ['A']:
neuron_groups['e'].theta = np.load(
os.path.join(best_weights_dir,
'_'.join(['theta_A', ending + '_best.npy'])))
for conn_type in ['ei', 'ie']:
if conn_type == 'ei':
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(neuron_groups[conn_name[0:2]], \
neuron_groups[conn_name[2:4]], structure='sparse', state='g' + conn_type[0])
# instantiate the created connection
for feature in xrange(conv_features):
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
feature * n_e + n] = 10.4
elif conn_type == 'ie' and not remove_inhibition:
# create connection name (composed of population and connection types)
conn_name = name + conn_type[0] + name + conn_type[1]
# create a connection from the first group in conn_name with the second group
connections[conn_name] = b.Connection(neuron_groups[conn_name[0:2]], \
neuron_groups[conn_name[2:4]], structure='sparse', state='g' + conn_type[0])
# define the actual synaptic connections and strengths
for feature in xrange(conv_features):
if inhib_scheme in ['far', 'strengthen']:
for other_feature in set(range(conv_features)) - set(
neighbor_mapping[feature]):
if inhib_scheme == 'far':
for n in xrange(n_e):
connections[conn_name][feature * n_e + n,
other_feature *
n_e + n] = 17.4
elif inhib_scheme == 'strengthen':
if n_e == 1:
x, y = feature // np.sqrt(
n_e_total), feature % np.sqrt(
n_e_total)
x_, y_ = other_feature // np.sqrt(
n_e_total), other_feature % np.sqrt(
n_e_total)
else:
x, y = feature // np.sqrt(
conv_features), feature % np.sqrt(
conv_features)
x_, y_ = other_feature // np.sqrt(
conv_features
), other_feature % np.sqrt(conv_features)
for n in xrange(n_e):
connections[conn_name][feature * n_e + n, other_feature * n_e + n] = \
min(17.4, inhib_const * np.sqrt(euclidean([x, y], [x_, y_])))
elif inhib_scheme == 'increasing':
for other_feature in xrange(conv_features):
if n_e == 1:
x, y = feature // np.sqrt(
n_e_total), feature % np.sqrt(n_e_total)
x_, y_ = other_feature // np.sqrt(
n_e_total), other_feature % np.sqrt(
n_e_total)
else:
x, y = feature // np.sqrt(
conv_features), feature % np.sqrt(
conv_features)
x_, y_ = other_feature // np.sqrt(
conv_features), other_feature % np.sqrt(
conv_features)
if feature != other_feature:
for n in xrange(n_e):
connections[conn_name][feature * n_e + n, other_feature * n_e + n] = \
min(17.4, inhib_const * np.sqrt(euclidean([x, y], [x_, y_])))
else:
raise Exception(
'Expecting one of "far", "increasing", or "strengthen" for argument "inhib_scheme".'
)
# spike rate monitors for excitatory and inhibitory neuron populations
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
neuron_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
rate_monitors[name + 'i'] = b.PopulationRateMonitor(
neuron_groups[name + 'i'],
bin=(single_example_time + resting_time) / b.second)
spike_counters[name + 'e'] = b.SpikeCounter(neuron_groups[name + 'e'])
# record neuron population spikes if specified
if record_spikes:
spike_monitors[name + 'e'] = b.SpikeMonitor(neuron_groups[name +
'e'])
spike_monitors[name + 'i'] = b.SpikeMonitor(neuron_groups[name +
'i'])
if record_spikes and do_plot:
if reset_state_vars:
time_window = single_example_time * 1000
else:
time_window = (single_example_time + resting_time) * 1000
b.figure(fig_num, figsize=(8, 6))
b.ion()
b.subplot(211)
b.raster_plot(spike_monitors['Ae'],
refresh=time_window * b.ms,
showlast=time_window * b.ms,
title='Excitatory spikes per neuron')
b.subplot(212)
b.raster_plot(spike_monitors['Ai'],
refresh=time_window * b.ms,
showlast=time_window * b.ms,
title='Inhibitory spikes per neuron')
b.tight_layout()
fig_num += 1
# creating Poission spike train from input image (784 vector, 28x28 image)
for name in ['X']:
input_groups[name + 'e'] = b.PoissonGroup(n_input, 0)
rate_monitors[name + 'e'] = b.PopulationRateMonitor(
input_groups[name + 'e'],
bin=(single_example_time + resting_time) / b.second)
# creating connections from input Poisson spike train to convolution patch populations
for name in ['XA']:
print '\n...Creating connections between', name[0], 'and', name[1]
# for each of the input connection types (in this case, excitatory -> excitatory)
for conn_type in ['ee_input']:
# saved connection name
conn_name = name[0] + conn_type[0] + name[1] + conn_type[1]
# get weight matrix depending on training or test phase
weight_matrix = np.load(
os.path.join(best_weights_dir,
'_'.join([conn_name, ending + '_best.npy'])))
# create connections from the windows of the input group to the neuron population
input_connections[conn_name] = b.Connection(input_groups['Xe'], neuron_groups[name[1] + \
conn_type[1]], structure='sparse', state='g' + conn_type[0], delay=True, max_delay=delay[conn_type][1])
for feature in xrange(conv_features):
for n in xrange(n_e):
for idx in xrange(conv_size**2):
input_connections[conn_name][convolution_locations[n][idx], feature * n_e + n] = \
weight_matrix[convolution_locations[n][idx], feature * n_e + n]
if do_plot:
plot_2d_input_weights()
fig_num += 1
