def test_lif(num, device):
print('Scale:{}, Model:LIF, Device:{}, '.format(num, device), end='')
st_build = time.time()
bp.profile.set(jit=True,
device=device,
dt=0.1,
numerical_method='exponential')
V_rest = -52.0
V_reset = -60.0
V_th = -50.0
neu = bpmodels.neurons.get_LIF(V_rest=V_rest,
V_reset=V_reset,
V_th=V_th,
noise=0.,
mode='scalar')
syn = bpmodels.synapses.get_exponential(tau_decay=2.0, mode='scalar')
num_exc = int(num / 2)
num_inh = int(num / 2)
prob = 0.01
JE = 1 / np.sqrt(prob * num_exc)
JI = 1 / np.sqrt(prob * num_inh)
group = bp.NeuGroup(neu, geometry=num_exc + num_inh, monitors=['spike'])
group.ST['V'] = np.random.random(num_exc + num_inh) * (V_th -
V_rest) + V_rest
exc_conn = bp.SynConn(syn,
pre_group=group[:num_exc],
post_group=group,
conn=bp.connect.FixedProb(prob=prob))
exc_conn.ST['g'] = JE
inh_conn = bp.SynConn(syn,
pre_group=group[num_exc:],
post_group=group,
conn=bp.connect.FixedProb(prob=prob))
exc_conn.ST['g'] = -JI
net = bp.Network(group, exc_conn, inh_conn)
ed_build = time.time()
st_run = time.time()
net.run(duration=1000., inputs=(group, 'ST.input', 3.))
ed_run = time.time()
build_time = float(ed_build - st_build)
run_time = float(ed_run - st_run)
print('BuildT:{:.2f}s, RunT:{:.2f}s'.format(build_time, run_time))
return run_time, build_time
if pre['sp'][pre_id] > 0.:
post_ids = pre2post[pre_id]
post['gi'][post_ids] += wi
exc_syn = bp.SynType('exc_syn', steps=exc_update, ST=bp.types.SynState([]))
inh_syn = bp.SynType('inh_syn', steps=inh_update, ST=bp.types.SynState([]))
group = bp.NeuGroup(neuron, geometry=num_exc + num_inh, monitors=['sp'])
group.ST['V'] = El + (np.random.randn(num_exc + num_inh) * 5 - 5)
group.ST['ge'] = (np.random.randn(num_exc + num_inh) * 1.5 + 4) * 10. / unit
group.ST['gi'] = (np.random.randn(num_exc + num_inh) * 12 + 20) * 10. / unit
exc_conn = bp.SynConn(exc_syn,
pre_group=group[:num_exc],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
inh_conn = bp.SynConn(inh_syn,
pre_group=group[num_exc:],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
net = bp.Network(group, exc_conn, inh_conn)
t0 = time.time()
net.run(10 * 1000., report=True)
print('Used time {} s.'.format(time.time() - t0))
bp.visualize.raster_plot(net.ts, group.mon.sp, show=True)
def run_brianpy(num_neu, duration, device='cpu'):
num_inh = int(num_neu / 5)
num_exc = num_neu - num_inh
bp.profile.set(jit=True, device=device, dt=dt)
# Parameters
taum = 20
taue = 5
taui = 10
Vt = -50
Vr = -60
El = -60
Erev_exc = 0.
Erev_inh = -80.
I = 20.
we = 0.6 # excitatory synaptic weight (voltage)
wi = 6.7 # inhibitory synaptic weight
ref = 5.0
neu_ST = bp.types.NeuState({
'sp_t': -1e7,
'V': Vr,
'spike': 0.,
'ge': 0.,
'gi': 0.
})
@bp.integrate
def int_ge(ge, t):
return -ge / taue
@bp.integrate
def int_gi(gi, t):
return -gi / taui
@bp.integrate
def int_V(V, t, ge, gi):
return (ge * (Erev_exc - V) + gi * (Erev_inh - V) +
(El - V) + I) / taum
def neu_update(ST, _t):
ST['ge'] = int_ge(ST['ge'], _t)
ST['gi'] = int_gi(ST['gi'], _t)
ST['spike'] = 0.
if (_t - ST['sp_t']) > ref:
V = int_V(ST['V'], _t, ST['ge'], ST['gi'])
ST['spike'] = 0.
if V >= Vt:
ST['V'] = Vr
ST['spike'] = 1.
ST['sp_t'] = _t
else:
ST['V'] = V
neuron = bp.NeuType(name='COBA',
ST=neu_ST,
steps=neu_update,
mode='scalar')
def syn_update1(pre, post, pre2post):
for pre_id in range(len(pre2post)):
if pre['spike'][pre_id] > 0.:
post_ids = pre2post[pre_id]
for i in post_ids:
post['ge'][i] += we
exc_syn = bp.SynType('exc_syn',
steps=syn_update1,
ST=bp.types.SynState([]),
mode='vector')
def syn_update2(pre, post, pre2post):
for pre_id in range(len(pre2post)):
if pre['spike'][pre_id] > 0.:
post_ids = pre2post[pre_id]
for i in post_ids:
post['gi'][i] += wi
inh_syn = bp.SynType('inh_syn',
steps=syn_update2,
ST=bp.types.SynState([]),
mode='vector')
group = bp.NeuGroup(neuron, geometry=num_exc + num_inh)
group.ST['V'] = np.random.randn(num_exc + num_inh) * 5. - 55.
exc_conn = bp.SynConn(exc_syn,
pre_group=group[:num_exc],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
inh_conn = bp.SynConn(inh_syn,
pre_group=group[num_exc:],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
net = bp.Network(group, exc_conn, inh_conn)
t0 = time.time()
net.run(duration)
t = time.time() - t0
print(f'BrainPy ({device}) used time {t} s.')
return t
# Set pre & post NeuGroup
pre = bp.NeuGroup(LIF_neuron,
geometry=(10, ),
monitors=['V', 'input', 'spike'])
pre.runner.set_schedule(['input', 'update', 'monitor', 'reset'])
pre.ST['V'] = -65.
post = bp.NeuGroup(LIF_neuron,
geometry=(10, ),
monitors=['V', 'input', 'spike'])
post.runner.set_schedule(['input', 'update', 'monitor', 'reset'])
pre.ST['V'] = -65.
# Set synapse connection & network
two_exponentials = bp.SynConn(model=two_exponentials_syn,
pre_group=pre,
post_group=post,
conn=bp.connect.All2All(),
monitors=['g'],
delay=10.)
two_exponentials.runner.set_schedule(
['input', 'update', 'output', 'monitor'])
net = bp.Network(pre, two_exponentials, post)
current = bp.inputs.spike_current([5., 10., 15., 20.],
bp.profile._dt,
1.,
duration=duration)
net.run(duration=duration,
inputs=[two_exponentials, 'pre.spike', current, "="],
report=True)
# Figure
def test_hh(num, device):
print('Scale:{}, Model:HH, Device:{}, '.format(num, device), end='')
st_build = time.time()
bp.profile.set(jit=True,
device=device,
dt=0.1,
numerical_method='exponential')
num_exc = int(num * 0.8)
num_inh = int(num * 0.2)
num = num_exc + num_inh
Cm = 200 # Membrane Capacitance [pF]
gl = 10. # Leak Conductance [nS]
El = -60. # Resting Potential [mV]
g_Na = 20. * 1000
ENa = 50. # reversal potential (Sodium) [mV]
g_Kd = 6. * 1000 # K Conductance [nS]
EK = -90. # reversal potential (Potassium) [mV]
VT = -63.
Vt = -20.
# Time constants
taue = 5. # Excitatory synaptic time constant [ms]
taui = 10. # Inhibitory synaptic time constant [ms]
# Reversal potentials
Ee = 0. # Excitatory reversal potential (mV)
Ei = -80. # Inhibitory reversal potential (Potassium) [mV]
# excitatory synaptic weight
we = 6.0 * np.sqrt(3200) / np.sqrt(
num_exc) # excitatory synaptic conductance [nS]
# inhibitory synaptic weight
wi = 67.0 * np.sqrt(800) / np.sqrt(
num_inh) # inhibitory synaptic conductance [nS]
inf = 0.05
neu_ST = bp.types.NeuState('V', 'm', 'n', 'h', 'sp', 'ge', 'gi')
@bp.integrate
def int_ge(ge, t):
return -ge / taue
@bp.integrate
def int_gi(gi, t):
return -gi / taui
@bp.integrate
def int_m(m, t, V):
a = 13.0 - V + VT
b = V - VT - 40.0
m_alpha = 0.32 * a / (exp(a / 4.) - 1.)
m_beta = 0.28 * b / (exp(b / 5.) - 1.)
dmdt = (m_alpha * (1. - m) - m_beta * m)
return dmdt
@bp.integrate
def int_m_zeroa(m, t, V):
b = V - VT - 40.0
m_alpha = 0.32
m_beta = 0.28 * b / (exp(b / 5.) - 1.)
dmdt = (m_alpha * (1. - m) - m_beta * m)
return dmdt
@bp.integrate
def int_m_zerob(m, t, V):
a = 13.0 - V + VT
m_alpha = 0.32 * a / (exp(a / 4.) - 1.)
m_beta = 0.28
dmdt = (m_alpha * (1. - m) - m_beta * m)
return dmdt
@bp.integrate
def int_h(h, t, V):
h_alpha = 0.128 * exp((17. - V + VT) / 18.)
h_beta = 4. / (1. + exp(-(V - VT - 40.) / 5.))
dhdt = (h_alpha * (1. - h) - h_beta * h)
return dhdt
@bp.integrate
def int_n(n, t, V):
c = 15. - V + VT
n_alpha = 0.032 * c / (exp(c / 5.) - 1.)
n_beta = .5 * exp((10. - V + VT) / 40.)
dndt = (n_alpha * (1. - n) - n_beta * n)
return dndt
@bp.integrate
def int_n_zero(n, t, V):
n_alpha = 0.032
n_beta = .5 * exp((10. - V + VT) / 40.)
dndt = (n_alpha * (1. - n) - n_beta * n)
return dndt
@bp.integrate
def int_V(V, t, m, h, n, ge, gi):
g_na_ = g_Na * (m * m * m) * h
g_kd_ = g_Kd * (n * n * n * n)
dvdt = (gl * (El - V) + ge * (Ee - V) + gi * (Ei - V) - g_na_ *
(V - ENa) - g_kd_ * (V - EK)) / Cm
return dvdt
def neu_update(ST, _t):
ST['ge'] = int_ge(ST['ge'], _t)
ST['gi'] = int_gi(ST['gi'], _t)
if abs(ST['V'] - (40.0 + VT)) < inf:
ST['m'] = int_m_zerob(ST['m'], _t, ST['V'])
elif abs(ST['V'] - (13.0 + VT)) < inf:
ST['m'] = int_m_zeroa(ST['m'], _t, ST['V'])
else:
ST['m'] = int_m(ST['m'], _t, ST['V'])
ST['h'] = int_h(ST['h'], _t, ST['V'])
if abs(ST['V'] - (15.0 + VT)) > inf:
ST['n'] = int_n(ST['n'], _t, ST['V'])
else:
ST['n'] = int_n_zero(ST['n'], _t, ST['V'])
V = int_V(ST['V'], _t, ST['m'], ST['h'], ST['n'], ST['ge'], ST['gi'])
sp = ST['V'] < Vt and V >= Vt
ST['sp'] = sp
ST['V'] = V
neuron = bp.NeuType(name='CUBA-HH',
ST=neu_ST,
steps=neu_update,
mode='scalar')
requires_exc = {
'pre':
bp.types.NeuState(
['sp'], help='Pre-synaptic neuron state must have "spike" item.'),
'post':
bp.types.NeuState(
['ge'],
help='Post-synaptic neuron state must have "V" and "input" item.')
}
def update_syn_exc(ST, pre, post):
if pre['sp']:
post['ge'] += we
exc_syn = bp.SynType(name='exc_syn',
ST=bp.types.SynState(),
requires=requires_exc,
steps=update_syn_exc,
mode='scalar')
requires_inh = {
'pre':
bp.types.NeuState(
['sp'], help='Pre-synaptic neuron state must have "spike" item.'),
'post':
bp.types.NeuState(
['gi'],
help='Post-synaptic neuron state must have "V" and "input" item.')
}
def update_syn_inh(ST, pre, post):
if pre['sp']:
post['gi'] -= wi
inh_syn = bp.SynType(name='inh_syn',
ST=bp.types.SynState(),
requires=requires_inh,
steps=update_syn_inh,
mode='scalar')
group = bp.NeuGroup(neuron, geometry=num)
group.ST['V'] = El + (np.random.randn(num_exc + num_inh) * 5. - 5.)
group.ST['ge'] = (np.random.randn(num_exc + num_inh) * 1.5 + 4.) * 10.
group.ST['gi'] = (np.random.randn(num_exc + num_inh) * 12. + 20.) * 10.
exc_conn = bp.SynConn(exc_syn,
pre_group=group[:num_exc],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
inh_conn = bp.SynConn(inh_syn,
pre_group=group[num_exc:],
post_group=group,
conn=bp.connect.FixedProb(prob=0.02))
net = bp.Network(group, exc_conn, inh_conn)
ed_build = time.time()
st_run = time.time()
net.run(duration=1000.0)
ed_run = time.time()
build_time = float(ed_build - st_build)
run_time = float(ed_run - st_run)
print('BuildT:{:.2f}s, RunT:{:.2f}s'.format(build_time, run_time))
return run_time, build_time
pre = bp.NeuGroup(LIF_neuron,
geometry=(10, ),
monitors=['V', 'input', 'spike'])
pre.runner.set_schedule(['input', 'update', 'monitor', 'reset'])
pre.pars['V_rest'] = -65.
pre.ST['V'] = -65.
post = bp.NeuGroup(LIF_neuron,
geometry=(10, ),
monitors=['V', 'input', 'spike'])
post.runner.set_schedule(['input', 'update', 'monitor', 'reset'])
post.pars['V_rest'] = -65.
post.ST['V'] = -65.
gabaa = bp.SynConn(model=GABAa_syn,
pre_group=pre,
post_group=post,
conn=bp.connect.All2All(),
monitors=['s'],
delay=10.)
gabaa.runner.set_schedule(['input', 'update', 'output', 'monitor'])
net = bp.Network(pre, gabaa, post)
current = bp.inputs.spike_current([10, 110, 210, 300, 305, 310, 315, 320],
bp.profile._dt,
1.,
duration=duration)
net.run(duration=duration,
inputs=[gabaa, 'pre.spike', current, "="],
report=True)
# paint gabaa
bp.profile.set(dt=.1)
n_post = 1
neuron = rate_neuron()
post = bp.NeuGroup(neuron, n_post, monitors=['r'])
pre = bp.NeuGroup(neuron, 20, monitors=['r'])
#mode = 'matrix'
mode = 'vector'
print(mode)
bcm1 = get_BCM(learning_rate=0.005, w_max=w_max, mode=mode)
bcm = bp.SynConn(model=bcm1,
pre_group=pre,
post_group=post,
conn=bp.connect.All2All(),
monitors=['w', 'dwdt'],
delay=0)
bcm.r_th = np.zeros(n_post)
bcm.post_r = np.zeros(n_post)
bcm.sum_post_r = np.zeros(n_post)
net = bp.Network(pre, bcm, post)
# group selection
group1, duration = bp.inputs.constant_current(([1.5, 1], [0, 1]) * 20)
group2, duration = bp.inputs.constant_current(([0, 1], [1., 1]) * 20)
input_r = np.vstack(((group1, ) * 10, (group2, ) * 10))
# set params
pre_neu_num = 2
post_neu_num = 1
bp.profile.set(jit=True, dt=0.02, merge_steps=True, show_code=False)
# build network
fr_neu = get_fr_neu()
oja_synapse = bpmodels.learning_rules.get_Oja()
pre_neu = bp.NeuGroup(fr_neu, geometry=(pre_neu_num, ), monitors=['r'])
post_neu = bp.NeuGroup(fr_neu, geometry=(post_neu_num, ), monitors=['r'])
pre_neu.ST['r'] = 1.
post_neu.ST['r'] = 1.
syn = bp.SynConn(oja_synapse,
pre_group=pre_neu,
post_group=post_neu,
conn=bp.connect.All2All(),
monitors=['w'])
net = bp.Network(pre_neu, syn, post_neu)
# create input
current_mat_in = []
current_mat_out = []
current1, _ = bp.inputs.constant_current([(2., 20.), (0., 20.)] * 3 +
[(0., 20.), (0., 20.)] * 2)
current2, _ = bp.inputs.constant_current([(0., 20.), (2., 20.)] * 5)
current3, _ = bp.inputs.constant_current([(2., 20.), (0., 20.)] * 5)
current_mat_in = np.vstack((current1, current2))
#current_mat_out = np.vstack((current3, current3))
current_mat_out = current3