def set_measured_activity(self):
"""
Set the full measured activity, from nonlinear response.
"""
# Learned background firing only utilizes average background signal
self.Yy0 = receptor_activity(self.Ss0, self.Kk1, self.Kk2, self.eps,
self.binding_competitive,
self.num_binding_sites)
self.Yy = receptor_activity(self.Ss, self.Kk1, self.Kk2, self.eps,
self.binding_competitive,
self.num_binding_sites)
self.Yy += sp.random.normal(0, self.meas_noise, self.Mm)
# Apply temporal kernel
if self.temporal_run == False:
pass
else:
kernel_params = [
self.kernel_T, self.kernel_dt, self.kernel_tau_1,
self.kernel_tau_2, self.kernel_shape_1, self.kernel_shape_2,
self.kernel_alpha, self.kernel_scale
]
self.Yy0, self.memory_Yy0 = temporal_kernel(
self.Yy0, self.memory_Yy0, self.signal_trace_Tt, kernel_params)
self.Yy, self.memory_Yy = temporal_kernel(self.Yy, self.memory_Yy,
self.signal_trace_Tt,
kernel_params)
# Nonlinearities
self.Yy0 *= self.NL_scale * (self.Yy > self.NL_threshold)
self.Yy *= self.NL_scale * (self.Yy > self.NL_threshold)
self.Yy0 = sp.minimum(self.Yy0, self.firing_max)
self.Yy = sp.minimum(self.Yy, self.firing_max)
# Measured response above background
self.dYy = self.Yy - self.Yy0
# Add effects of divisive normalization if called.
if self.divisive_normalization == True:
self.Yy0 = inhibitory_normalization(self.Yy0, self.inh_C,
self.inh_D, self.inh_eta,
self.inh_R)
self.Yy = inhibitory_normalization(self.Yy, self.inh_C, self.inh_D,
self.inh_eta, self.inh_R)
self.dYy = self.Yy - self.Yy0
def manual_Kk_replace(self):
"""
Manually add high responders to Kk2 matrix
"""
# First get the epsilon -- needed to calculate activities to find
# weak responders.
self.set_normal_free_energy()
# Get tuning curves
tuning_curves = sp.zeros((self.Mm, self.Nn))
for iN in range(self.Nn):
tuning_Ss = sp.zeros(self.Nn)
tuning_Ss[iN] = self.manual_Kk_replace_Ss
tuning_curves[:, iN] = receptor_activity(tuning_Ss, self.Kk1,
self.Kk2, self.eps,
self.binding_competitive,
self.num_binding_sites)
# Add specialist responses to weak responders
for iM in range(self.Mm):
if sp.mean(tuning_curves[iM, :]) < self.manual_Kk_replace_min_act:
self.Kk2[iM, sp.random.randint(self.Nn)] = \
10.**sp.random.uniform(self.manual_Kk_replace_lo,
self.manual_Kk_replace_hi)
def set_mean_response_array(self):
"""
Set the mean receptor responses for the signal array.
"""
self.Yy = receptor_activity(self.Ss, self.Kk1, self.Kk2, self.eps)
self.Yy *= self.NL_scale * (self.Yy > self.NL_threshold)
self.Yy = sp.minimum(self.Yy, self.firing_max)
def set_measured_activity(self): # True receptor activity self.Yy = receptor_activity(self.Ss, self.Kk1, self.Kk2, self.eps) # Learned background activity only utilizes average background signal self.Yy0 = bkgrnd_activity(self.Ss0, self.Kk1, self.Kk2, self.eps) # Measured response above background self.dYy = self.Yy - self.Yy0
def set_temporal_adapted_epsilon(self):
"""
Set adapted epsilon based on current value and adaptation rate.
The adapted value is set by linear decay rate equation,
d(eps)/dt = beta*(a_0 - a). a_0 is set by passing the manually
chosen variables temporal_adaptation_mu_eps and
temporal_adaptation_mu_Ss0 to the activity.
"""
# Perfectly adapted activity level is set manually
activity_stats = [
self.adapted_activity_mu, self.adapted_activity_sigma
]
perfect_adapt_Yy = random_matrix([self.Mm],
params=activity_stats,
seed=self.seed_adapted_activity)
beta_scale_factors = sp.random.uniform(self.adaptive_beta_scaling_min,
self.adaptive_beta_scaling_max,
self.Mm)
# This is a kind of hacky way to incorporate WL breaking.
# Requires Kk1 to be small
Kk2_sum = sp.dot(self.Kk2**-1.0, self.Ss).T
den = perfect_adapt_Yy.T*(1 - (1/Kk2_sum)**beta_scale_factors)\
+ (1/Kk2_sum)**beta_scale_factors
perfect_adapt_Yy = (perfect_adapt_Yy.T / den)
# Make adaptation rate into a vector if it has not yet been set.
try:
self.temporal_adaptation_rate_vector
except AttributeError:
assert self.temporal_adaptation_rate_sigma == 0, "Before "\
"setting new epsilon with set_temporal_adapted_epsilon, "\
"you must call set_ordered_temporal_adaptation_rate, since "\
"temporal_adaptation_rate_sigma is nonzero"
self.temporal_adaptation_rate_vector = sp.ones(self.Mm)*\
self.temporal_adaptation_rate
# Receptor activity used for adaptation is not firing rate; just
# get the Or/Orco activity, w/o LN functions at backend.
current_Yy = receptor_activity(self.Ss, self.Kk1, self.Kk2, self.eps,
self.binding_competitive,
self.num_binding_sites)
if self.temporal_adaptation_type == 'imperfect':
d_eps_dt = (self.temporal_adaptation_rate_vector*\
(current_Yy.T - perfect_adapt_Yy)).T
delta_t = self.signal_trace_Tt[1] - self.signal_trace_Tt[0]
self.eps += delta_t * d_eps_dt
elif self.temporal_adaptation_type == 'perfect':
self.eps = free_energy(self.Ss, self.Kk1, self.Kk2,
perfect_adapt_Yy)
# Enforce epsilon limits
self.eps = sp.maximum(self.eps.T, self.min_eps).T
self.eps = sp.minimum(self.eps.T, self.max_eps).T
def set_measured_activity(self):
"""
Set the full measured activity, from nonlinear response.
"""
# True receptor activity
self.Yy = receptor_activity(self.Ss, self.Kk1, self.Kk2, self.eps)
# Learned background activity only utilizes average background signal
self.Yy0 = receptor_activity(self.Ss0, self.Kk1, self.Kk2, self.eps)
# Measured response above background
self.dYy = self.Yy - self.Yy0
# Add effects of divisive normalization if called.
if self.divisive_normalization == True:
self.Yy0 = inhibitory_normalization(self.Yy0, self.inh_C,
self.inh_D, self.inh_eta,
self.inh_R)
self.Yy = inhibitory_normalization(self.Yy, self.inh_C, self.inh_D,
self.inh_eta, self.inh_R)
self.dYy = self.Yy - self.Yy0
def set_temporal_adapted_epsilon(self):
"""
Set adapted epsilon based on current value and adaptation rate.
The adapted value is set by linear decay rate equation,
d(eps)/dt = beta*(a_0 - a). a_0 is set by passing the manually
chosen variables temporal_adaptation_mu_eps and
temporal_adaptation_mu_Ss0 to the activity.
"""
# Perfectly adapted activity level is based on the variables:
# temporal_adaptation_mu_eps, temporal_adaptation_sigma_eps,
# temporal_adaptation_mu_Ss0. These functions take the activity
# level set by these variables at that signal intensity, to
# adapt epsilon to the current Ss
perfect_adapt_eps_base = sp.ones(self.Mm)*\
self.temporal_adaptation_mu_eps + random_matrix(self.Mm,
params=[0, self.temporal_adaptation_sigma_eps],
seed=self.seed_eps)
perfect_adapt_Ss = sp.zeros(self.Nn)
perfect_adapt_Ss[self.Ss0 != 0] = self.temporal_adaptation_mu_Ss0
perfect_adapt_Yy = receptor_activity(perfect_adapt_Ss, self.Kk1,
self.Kk2, perfect_adapt_eps_base)
# Make adaptation rate into a vector if it has not yet been set.
try:
self.temporal_adaptation_rate_vector
except AttributeError:
assert self.temporal_adaptation_rate_sigma == 0, "Before "\
"setting new epsilon with set_temporal_adapted_epsilon, "\
"you must call set_ordered_temporal_adaptation_rate, since "\
"temporal_adaptation_rate_sigma is nonzero"
self.temporal_adaptation_rate_vector = sp.ones(self.Mm)*\
self.temporal_adaptation_rate
if self.temporal_adaptation_type == 'imperfect':
d_eps_dt = self.temporal_adaptation_rate_vector*\
(self.Yy - perfect_adapt_Yy)
delta_t = self.signal_trace_Tt[1] - self.signal_trace_Tt[0]
self.eps += delta_t * d_eps_dt
elif self.temporal_adaptation_type == 'perfect':
self.eps = free_energy(self.Ss, self.Kk1, self.Kk2,
perfect_adapt_Yy)
def decode_nonlinear_CS(
obj,
opt_type="L1_strong",
precision='None',
init_params=[sp.random.rand() * -0.1,
sp.random.rand() * 0.1]):
"""
Run CS decoding with L1 norm, using full activity with no linearization.
Args:
Rr: numpy array; measurement matrix.
Yy: numpy array; Measured signal.
Optional args:
opt_type: String for type of L1 minimization "L1_strong" or "L1_weak".
precision: Float, for L1_weak, the multiplier of the squared error.
init_params: List; initialization point for the optimization.
"""
def L1_strong(x):
return sp.sum(abs(x))
from kinetics import receptor_activity
if opt_type == "L1_strong":
constraints = ({
'type':
'eq',
'fun':
lambda x: receptor_activity(x, obj.Kk1, obj.Kk2, obj.eps) - obj.Yy
})
res = minimize(
L1_strong,
obj.Ss * sp.random.normal(1, 0.1, obj.Nn),
#sp.random.normal(init_params[0], init_params[1], obj.Nn),
method='SLSQP',
constraints=constraints)
else:
print('Unknown optimization type')
quit()
return res.x