def general_WienerCont(err=1e-4,
n_st=2,
n_sz=2,
use_adaptive=1,
simps_err=1e-3):
_like = lambda value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max, err=err, n_st=n_st, n_sz=n_sz, use_adaptive=use_adaptive, simps_err=simps_err: wiener_like_contaminant(
value,
cont_x,
v,
sv,
a,
z,
sz,
t,
st,
t_min,
t_max,
err=err,
n_st=n_st,
n_sz=n_sz,
use_adaptive=use_adaptive,
simps_err=simps_err,
)
_like.__doc__ = wiener_like_contaminant.__doc__
return stochastic_from_dist(name="Wiener Diffusion Contaminant Process",
logp=_like)
def general_WienerCont(err=1e-4, n_st=2, n_sz=2, use_adaptive=1, simps_err=1e-3):
_like = lambda value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max, err=err, n_st=n_st, n_sz=n_sz, \
use_adaptive=use_adaptive, simps_err=simps_err: \
wiener_like_contaminant(value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max,\
err=err, n_st=n_st, n_sz=n_sz, use_adaptive=use_adaptive, simps_err=simps_err)
_like.__doc__ = wiener_like_contaminant.__doc__
return stochastic_from_dist(name="Wiener Diffusion Contaminant Process",
logp=_like)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
sampling_method <string> - an argument used by hddm.generate.gen_rts
cdf_range <sequance> - an argument used by hddm.generate.gen_rts
sampling_dt <float> - an argument used by hddm.generate.gen_rts
Ouput:
wfpt <class> - the wfpt stochastic
"""
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1}
wp = wiener_params
#create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
return hddm.wfpt.wiener_like(x['rt'].values, v, sv, a, z, sz, t, st, p_outlier=p_outlier, **wp)
#create random function
def random(self):
return hddm.utils.flip_errors(hddm.generate.gen_rts(method=sampling_method,
size=self.shape, dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
#create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
#create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x, w_outlier=wp['w_outlier'], **self.parents)
#create wfpt class
wfpt = stochastic_from_dist('wfpt', wfpt_like)
#add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(time=cdf_range[1], **dict(self.parents.items() + wp.items()))
wfpt.cdf = cdf
wfpt.random = random
#add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
def generate_wfpt_reg_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1}
wp = wiener_params
def wiener_multi_like(value, v, sv, a, z, sz, t, st, reg_outcomes, p_outlier=0):
"""Log-likelihood for the full DDM using the interpolation method"""
params = {'v': v, 'sv': sv, 'a': a, 'z': z, 'sz': sz, 't': t, 'st': st}
for reg_outcome in reg_outcomes:
params[reg_outcome] = params[reg_outcome].loc[value['rt'].index].values
return hddm.wfpt.wiener_like_multi(value['rt'].values,
params['v'], params['sv'], params['a'], params['z'],
params['sz'], params['t'], params['st'], 1e-4,
reg_outcomes,
p_outlier=p_outlier)
def random(self):
param_dict = deepcopy(self.parents.value)
del param_dict['reg_outcomes']
sampled_rts = self.value.copy()
#print(sampled_rts)
#print(self.value.index)
for i in self.value.index:
#get current params
#print(i)
for p in self.parents['reg_outcomes']:
param_dict[p] = np.asscalar(self.parents.value[p].loc[i])
#sample
samples = hddm.generate.gen_rts(method=sampling_method,
size=1, dt=sampling_dt, **param_dict)
sampled_rts.at[i, 'rt'] = hddm.utils.flip_errors(samples).rt
return sampled_rts
stoch = stochastic_from_dist('wfpt_reg', wiener_multi_like)
stoch.random = random
return stoch
def generate_wfpt_reg_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1}
wp = wiener_params
def wiener_multi_like(value, v, sv, a, z, sz, t, st, reg_outcomes, p_outlier=0):
"""Log-likelihood for the full DDM using the interpolation method"""
params = {'v': v, 'sv': sv, 'a': a, 'z': z, 'sz': sz, 't': t, 'st': st}
for reg_outcome in reg_outcomes:
params[reg_outcome] = params[reg_outcome].ix[value['rt'].index].values
return hddm.wfpt.wiener_like_multi(value['rt'].values,
params['v'], params['sv'], params['a'], params['z'],
params['sz'], params['t'], params['st'], 1e-4,
reg_outcomes,
p_outlier=p_outlier)
def random(self):
param_dict = deepcopy(self.parents.value)
del param_dict['reg_outcomes']
sampled_rts = self.value.copy()
for i in self.value.index:
#get current params
for p in self.parents['reg_outcomes']:
param_dict[p] = np.asscalar(self.parents.value[p].ix[i])
#sample
samples = hddm.generate.gen_rts(method=sampling_method,
size=1, dt=sampling_dt, **param_dict)
sampled_rts.ix[i]['rt'] = hddm.utils.flip_errors(samples).rt
return sampled_rts
stoch = stochastic_from_dist('wfpt_reg', wiener_multi_like)
stoch.random = random
return stoch
def make_mlp_likelihood_rlssm(
model=None, model_config=None, model_config_rl=None, wiener_params=None, **kwargs
):
"""Defines the likelihoods for the MLP networks for RLSSMs.
:Arguments:
model: str <default='ddm'>
String that determines which model you would like to fit your data to.
Currently available models are: 'ddm', 'full_ddm', 'angle', 'weibull', 'ornstein', 'levy'
model_config: dict <default=None>
Config dictionary for the sequential sampling model, necessary for construction of likelihood. In the style of what you find under hddm.model_config.
model_config_rl: dict <default=None>
Config dictionary for the reinforcement learning model, necessary for construction of likelihood. In the style of what you find under hddm.model_config_rl.
kwargs: dict
Dictionary of additional keyword arguments.
Importantly here, this carries the preloaded CNN.
:Returns:
Returns a pymc.object stochastic object as defined by PyMC2
"""
def make_likelihood():
likelihood_str = make_likelihood_str_mlp_rlssm(
model=model,
config=model_config,
config_rl=model_config_rl,
wiener_params=wiener_params,
)
exec(likelihood_str)
my_fun = locals()["custom_likelihood"]
return my_fun
likelihood_ = make_likelihood()
wfpt_nn_rl = stochastic_from_dist(
"WienernnRL_" + model, partial(likelihood_, **kwargs)
)
return wfpt_nn_rl
'w_outlier': 0.1
}
wp = wiener_params
#with open("weights.pickle", "rb") as tmp_file:
# weights = pickle.load(tmp_file)
#with open('biases.pickle', 'rb') as tmp_file:
# biases = pickle.load(tmp_file)
#with open('activations.pickle', 'rb') as tmp_file:
# activations = pickle.load(tmp_file)
#print('hei')
nn_response = x['nn_response'].values.astype(int)
return wiener_like_nn_collapsing_keras(np.absolute(x['rt'].values),
nn_response,
v,
sv,
a,
alpha,
beta,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
Wienernn_collapsing_keras = stochastic_from_dist(
'Wienernn_collapsing_keras', wienernn_like_collapsing_keras)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
sampling_method <string> - an argument used by hddm.generate.gen_rts
cdf_range <sequance> - an argument used by hddm.generate.gen_rts
sampling_dt <float> - an argument used by hddm.generate.gen_rts
Ouput:
wfpt <class> - the wfpt stochastic
"""
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1}
wp = wiener_params
#create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
if x['rt'].abs().max() < 998:
return hddm.wfpt.wiener_like(x['rt'].values, v, sv, a, z, sz, t, st,
p_outlier=p_outlier, **wp)
else: # for missing RTs. Currently undocumented.
noresponse = x['rt'].abs() >= 999
## get sum of log p for trials with RTs as usual ##
LLH_resp = hddm.wfpt.wiener_like(x.loc[-noresponse, 'rt'].values,
v, sv, a, z, sz, t, st, p_outlier=p_outlier, **wp)
## get sum of log p for no-response trials from p(upper_boundary|parameters) ##
# this function assumes following format for the RTs:
# - accuracy coding such that correct responses have a 1 and incorrect responses a 0
# - usage of HDDMStimCoding for z
# - missing RTs are coded as 999/-999
# - note that hddm will flip RTs, such that error trials have negative RTs
# so that the miss-trial in the go condition and comission error
# in the no-go condition will have negative RTs
# get number of no-response trials
n_noresponse = sum(noresponse)
# percentage correct according to probability to get to upper boundary
if v == 0:
p_correct = z
else:
p_correct = (np.exp(-2 * a * z * v) - 1) / (np.exp(-2 * a * v) - 1)
# calculate percent no-response trials from % correct
if sum(x.loc[noresponse, 'rt']) > 0:
p_noresponse = p_correct # when no-response trials have a positive RT
# we are looking at nogo Trials
else:
p_noresponse = 1 - p_correct # when no-response trials have a
# negative RT we are looking at go Trials
# likelihood for no-response trials
LLH_noresp = np.log(p_noresponse)*n_noresponse
return LLH_resp + LLH_noresp
#create random function
def random(self):
return hddm.utils.flip_errors(hddm.generate.gen_rts(method=sampling_method,
size=self.shape, dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
#create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
#create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x, w_outlier=wp['w_outlier'], **self.parents)
#create wfpt class
wfpt = stochastic_from_dist('wfpt', wfpt_like)
#add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(time=cdf_range[1], **dict(list(self.parents.items()) + list(wp.items())))
wfpt.cdf = cdf
wfpt.random = random
#add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
# initialize problem
states = len(data.state.unique())
actions = len(data.action.unique())
V = 1./actions * np.ones((states, actions))
logp = 0
for t, (s, a, reward) in data[['state', 'action', 'reward']].iterrows():
# get proba and add it to the log likelihood
proba = softmax_proba(V[s,:], a, invtemp)
logp += np.log(proba)
V[s, a] += lrate * (reward - V[s, a])
return logp
RL_like = stochastic_from_dist(name="QLearn likelihood",
logp=RL_likelihood,
random=RL_generate)
def check_params_valid(**params):
lrate = params.get('lrate', .1)
invtemp = params.get('invtemp', 5)
return (0 < lrate) and (lrate < 1) and (invtemp > 0)
def gen_data(params=None, **kwargs):
if params is None:
params = {'lrate': .1, 'invtemp': 10}
return kabuki.generate.gen_rand_data(RL_generate, params,
check_valid_func=check_params_valid,
**kwargs)
'n_st': 2,
'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1
}
wp = wiener_params
response = x['response'].values.astype(int)
q = x['q_init'].iloc[0]
feedback = x['feedback'].values
split_by = x['split_by'].values
return wiener_like_rlddm(x['rt'].values,
response,
feedback,
split_by,
q,
alpha,
pos_alpha,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
WienerRL = stochastic_from_dist('wienerRL', wienerRL_like)
def generate_wfpt_rl_reg_stochastic_class(wiener_params=None,
sampling_method="cdf",
cdf_range=(-5, 5),
sampling_dt=1e-4):
# set wiener_params
if wiener_params is None:
wiener_params = {
"err": 1e-4,
"n_st": 2,
"n_sz": 2,
"use_adaptive": 1,
"simps_err": 1e-3,
"w_outlier": 0.1,
}
wp = wiener_params
def wienerRL_multi_like(value,
v,
sv,
a,
z,
sz,
t,
st,
alpha,
reg_outcomes,
p_outlier=0):
"""Log-likelihood for the full DDM using the interpolation method"""
response = value["response"].values.astype(int)
q = value["q_init"].iloc[0]
feedback = value["feedback"].values.astype(float)
split_by = value["split_by"].values.astype(int)
params = {
"v": v,
"sv": sv,
"a": a,
"z": z,
"sz": sz,
"t": t,
"st": st,
"alpha": alpha,
}
for reg_outcome in reg_outcomes:
params[reg_outcome] = params[reg_outcome].loc[
value["rt"].index].values
return hddm.wfpt.wiener_like_multi_rlddm(
value["rt"].values,
response,
feedback,
split_by,
q,
params["v"],
params["sv"],
params["a"],
params["z"],
params["sz"],
params["t"],
params["st"],
params["alpha"],
1e-4,
reg_outcomes,
p_outlier=p_outlier,
)
def random(self):
param_dict = deepcopy(self.parents.value)
del param_dict["reg_outcomes"]
sampled_rts = self.value.copy()
for i in self.value.index:
# get current params
for p in self.parents["reg_outcomes"]:
param_dict[p] = np.asscalar(self.parents.value[p].loc[i])
# sample
samples = hddm.generate.gen_rts(method=sampling_method,
size=1,
dt=sampling_dt,
**param_dict)
sampled_rts.loc[i, "rt"] = hddm.utils.flip_errors(samples).rt
return sampled_rts
stoch = stochastic_from_dist("wfpt_reg", wienerRL_multi_like)
stoch.random = random
return stoch
def generate_wfpt_nn_reg_stochastic_class(wiener_params=None,
sampling_method='cdf',
cdf_range=(-5, 5),
sampling_dt=1e-4):
#set wiener_params
if wiener_params is None:
wiener_params = {
'err': 1e-4,
'n_st': 2,
'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1
}
wp = wiener_params
def wienerNN_multi_like(value,
v,
sv,
a,
z,
sz,
t,
st,
alpha,
beta,
reg_outcomes,
p_outlier=0):
"""Log-likelihood for the full DDM using the interpolation method"""
nn_response = value['nn_response'].values.astype(int)
with open("weights.pickle", "rb") as tmp_file:
weights = pickle.load(tmp_file)
with open('biases.pickle', 'rb') as tmp_file:
biases = pickle.load(tmp_file)
with open('activations.pickle', 'rb') as tmp_file:
activations = pickle.load(tmp_file)
params = {
'v': v,
'sv': sv,
'a': a,
'z': z,
'sz': sz,
't': t,
'st': st,
'alpha': alpha,
'beta': beta
}
for reg_outcome in reg_outcomes:
params[reg_outcome] = params[reg_outcome].loc[
value['rt'].index].values
return hddm.wfpt.wiener_like_multi_nnddm(np.absolute(
value['rt'].values),
nn_response,
activations,
weights,
biases,
params['v'],
params['sv'],
params['a'],
params['z'],
params['sz'],
params['t'],
params['st'],
params['alpha'],
params['beta'],
1e-4,
reg_outcomes,
p_outlier=p_outlier)
def random(self):
param_dict = deepcopy(self.parents.value)
del param_dict['reg_outcomes']
sampled_rts = self.value.copy()
for i in self.value.index:
#get current params
for p in self.parents['reg_outcomes']:
param_dict[p] = np.asscalar(self.parents.value[p].loc[i])
#sample
samples = hddm.generate.gen_rts(method=sampling_method,
size=1,
dt=sampling_dt,
**param_dict)
sampled_rts.loc[i, 'rt'] = hddm.utils.flip_errors(samples).rt
return sampled_rts
stoch = stochastic_from_dist('wfpt_reg', wienerNN_multi_like)
stoch.random = random
return stoch
**wfpt_parents)
def wienernn_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
wiener_params = {
'err': 1e-4,
'n_st': 2,
'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1
}
wp = wiener_params
nn_response = x['nn_response'].values.astype(int)
return wiener_like_nn(np.absolute(x['rt'].values),
nn_response,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
Wienernn = stochastic_from_dist('wienernn', wienernn_like)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
sampling_method <string> - an argument used by hddm.generate.gen_rts
cdf_range <sequance> - an argument used by hddm.generate.gen_rts
sampling_dt <float> - an argument used by hddm.generate.gen_rts
Ouput:
wfpt <class> - the wfpt stochastic
"""
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1,
}
wp = wiener_params
#create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
if x['rt'].abs().max() < 998:
return hddm.wfpt.wiener_like(x['rt'].values, v, sv, a, z, sz, t, st,
p_outlier=p_outlier, **wp)
else: # for missing RTs. Currently undocumented.
noresponse = x['rt'].abs() >= 999
## get sum of log p for trials with RTs as usual ##
logp_resp = hddm.wfpt.wiener_like(x.loc[~noresponse, 'rt'].values,
v, sv, a, z, sz, t, st, p_outlier=p_outlier, **wp)
# get number of no-response trials
n_noresponse = sum(noresponse)
k_upper = sum(x.loc[noresponse, 'rt'] > 0)
# percentage correct according to probability to get to upper boundary
if v == 0:
p_upper = z
else:
p_upper = (np.exp(-2 * a * z * v) - 1) / (np.exp(-2 * a * v) - 1)
logp_noresp = stats.binom.logpmf(k_upper, n_noresponse, p_upper)
return logp_resp + logp_noresp
#create random function
def random(self):
return hddm.utils.flip_errors(hddm.generate.gen_rts(method=sampling_method,
size=self.shape, dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
#create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
#create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x, w_outlier=wp['w_outlier'], **self.parents)
#create wfpt class
wfpt = stochastic_from_dist('wfpt', wfpt_like)
#add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(time=cdf_range[1], **dict(list(self.parents.items()) + list(wp.items())))
wfpt.cdf = cdf
wfpt.random = random
#add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
from time import time
import unittest
from kabuki.utils import stochastic_from_dist
def multi_normal_like(values, vec_mu, tau):
"""logp for multi normal"""
logp = 0
for i in range(len(vec_mu)):
logp += pm.normal_like(values[i, :], vec_mu[i], tau)
return logp
MN = stochastic_from_dist(name="MultiNormal", logp=multi_normal_like)
class TestStepMethods(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(TestStepMethods, self).__init__(*args, **kwargs)
self.uniform_lb = 1e-10
self.uniform_ub = 1e10
def runTest(self):
return
def assert_results(self,
node,
true_value,
true_mean,
'w_outlier': 0.1
}
wp = wiener_params
#with open("weights.pickle", "rb") as tmp_file:
# weights = pickle.load(tmp_file)
#with open('biases.pickle', 'rb') as tmp_file:
# biases = pickle.load(tmp_file)
#with open('activations.pickle', 'rb') as tmp_file:
# activations = pickle.load(tmp_file)
#print('hei')
nn_response = x['nn_response'].values.astype(int)
return wiener_like_nn_weibull(np.absolute(x['rt'].values),
nn_response,
v,
sv,
a,
alpha,
beta,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
Wienernn_weibull = stochastic_from_dist('Wienernn_weibull',
wienernn_like_weibull)
rt1 = np.inf
if rt0 < rt1:
sampled_rts[i_sample] = rt0
else:
sampled_rts[i_sample] = -rt1
data = pd.DataFrame(sampled_rts, columns=['rt'])
data['response'] = 1.
data['response'][data['rt']<0] = 0.
data['rt'] = np.abs(data['rt'])
return data
lba_class = stochastic_from_dist(name='lba_like', logp=lba_like, random=lba_random)
lba_class.pdf = pdf
def gen_single_params_set():
"""Returns a dict of DDM parameters with random values for a singel conditin
the function is used by gen_rand_params.
"""
params = {}
params['s'] = 2.5*rand()
params['b'] = 0.5+rand()*1.5
params['A'] = rand() * params['b']
params['v'] = rand()
params['t'] = 0.2+rand()*0.3
return params
def generate_wfpt_stochastic_class(wiener_params=None,
sampling_method="cssm",
cdf_range=(-5, 5),
sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
:Arguments:
wiener_params: dict <default=None>
dictonary of wiener_params for wfpt likelihoods
sampling_method: str <default='cssm'>
an argument used by hddm.generate.gen_rts
cdf_range: sequence <default=(-5,5)>
an argument used by hddm.generate.gen_rts
sampling_dt: float <default=1e-4>
an argument used by hddm.generate.gen_rts
:Output:
wfpt: class
the wfpt stochastic
"""
# set wiener_params
if wiener_params is None:
wiener_params = {
"err": 1e-4,
"n_st": 2,
"n_sz": 2,
"use_adaptive": 1,
"simps_err": 1e-3,
"w_outlier": 0.1,
}
wp = wiener_params
# create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
if x["rt"].abs().max() < 998:
return hddm.wfpt.wiener_like(x["rt"].values,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
else: # for missing RTs. Currently undocumented.
noresponse = x["rt"].abs() >= 999
## get sum of log p for trials with RTs as usual ##
logp_resp = hddm.wfpt.wiener_like(x.loc[~noresponse, "rt"].values,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
# get number of no-response trials
n_noresponse = sum(noresponse)
k_upper = sum(x.loc[noresponse, "rt"] > 0)
# percentage correct according to probability to get to upper boundary
if v == 0:
p_upper = z
else:
p_upper = (np.exp(-2 * a * z * v) - 1) / (np.exp(-2 * a * v) -
1)
logp_noresp = stats.binom.logpmf(k_upper, n_noresponse, p_upper)
return logp_resp + logp_noresp
# create random function
def random(
self,
keep_negative_responses=True,
add_model=False,
add_outliers=False,
add_model_parameters=False,
keep_subj_idx=False,
):
# print(self.value)
# print(type(self.value))
assert sampling_method in [
"cdf",
"drift",
"cssm",
], "Sampling method is invalid!"
if sampling_method == "cdf" or sampling_method == "drift":
return hddm.utils.flip_errors(
hddm.generate.gen_rts(method=sampling_method,
size=self.shape,
dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
elif sampling_method == "cssm":
keys_tmp = self.parents.value.keys()
cnt = 0
theta = np.zeros(len(list(keys_tmp)), dtype=np.float32)
for param in model_config["full_ddm_vanilla"]["params"]:
theta[cnt] = np.array(self.parents.value[param]).astype(
np.float32)
cnt += 1
sim_out = simulator(theta=theta,
model="full_ddm_vanilla",
n_samples=self.shape[0],
max_t=20)
if add_outliers:
if self.parents.value["p_outlier"] > 0.0:
sim_out = hddm_dataset_generators._add_outliers(
sim_out=sim_out,
p_outlier=self.parents.value["p_outlier"],
max_rt_outlier=1 / wiener_params["w_outlier"],
)
sim_out_proc = hddm_preprocess(
sim_out,
keep_negative_responses=keep_negative_responses,
keep_subj_idx=keep_subj_idx,
add_model_parameters=add_model_parameters,
)
if add_model:
if ((self.parents.value["sz"] == 0)
and (self.parents.value["sv"] == 0)
and (self.parents.value["st"] == 0)):
sim_out_proc["model"] = "ddm_vanilla"
else:
sim_out_proc["model"] = "full_ddm_vanilla"
sim_out_proc = hddm.utils.flip_errors(
sim_out_proc) # ['rt'] * sim_out_proc['response']
return sim_out_proc
# create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
# create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x,
w_outlier=wp["w_outlier"],
**self.parents)
# create wfpt class
wfpt = stochastic_from_dist("wfpt", wfpt_like)
# add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(
time=cdf_range[1],
**dict(list(self.parents.items()) + list(wp.items())))
wfpt.cdf = cdf
wfpt.random = random
# add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
def generate_wfpt_reg_stochastic_class(wiener_params=None,
sampling_method="cdf",
cdf_range=(-5, 5),
sampling_dt=1e-4):
# set wiener_params
if wiener_params is None:
wiener_params = {
"err": 1e-4,
"n_st": 2,
"n_sz": 2,
"use_adaptive": 1,
"simps_err": 1e-3,
"w_outlier": 0.1,
}
wp = wiener_params
def wiener_multi_like(value,
v,
sv,
a,
z,
sz,
t,
st,
reg_outcomes,
p_outlier=0.05):
"""Log-likelihood for the full DDM using the interpolation method"""
params = {"v": v, "sv": sv, "a": a, "z": z, "sz": sz, "t": t, "st": st}
for reg_outcome in reg_outcomes:
params[reg_outcome] = params[reg_outcome].loc[
value["rt"].index].values
return hddm.wfpt.wiener_like_multi(
value["rt"].values,
params["v"],
params["sv"],
params["a"],
params["z"],
params["sz"],
params["t"],
params["st"],
1e-4,
reg_outcomes,
w_outlier=wp["w_outlier"],
p_outlier=p_outlier,
)
def random(
self,
keep_negative_responses=True,
add_model_parameters=False,
keep_subj_idx=False,
):
assert sampling_method in ["drift",
"cssm"], "Sampling method is invalid!"
# AF add: exchange this with new simulator
param_dict = deepcopy(self.parents.value)
del param_dict["reg_outcomes"]
sampled_rts = self.value.copy()
if sampling_method == "drift":
for i in self.value.index:
# get current params
for p in self.parents["reg_outcomes"]:
param_dict[p] = np.asscalar(self.parents.value[p].loc[i])
# sample
samples = hddm.generate.gen_rts(method=sampling_method,
size=1,
dt=sampling_dt,
**param_dict)
sampled_rts.loc[i, "rt"] = hddm.utils.flip_errors(
samples).rt.iloc[0]
return sampled_rts
if sampling_method == "cssm":
param_data = np.zeros(
(self.value.shape[0],
len(model_config["full_ddm_vanilla"]["params"])),
dtype=np.float32,
)
cnt = 0
for tmp_str in model_config["full_ddm_vanilla"]["params"]:
if tmp_str in self.parents["reg_outcomes"]:
param_data[:, cnt] = param_dict[tmp_str].values
# changed from iloc[self.value.index]
else:
param_data[:, cnt] = param_dict[tmp_str]
cnt += 1
sim_out = simulator(theta=param_data,
model="full_ddm_vanilla",
n_samples=1,
max_t=20)
sim_out_proc = hddm_preprocess(
sim_out,
keep_negative_responses=keep_negative_responses,
add_model_parameters=add_model_parameters,
keep_subj_idx=keep_subj_idx,
)
sim_out_proc = hddm.utils.flip_errors(sim_out_proc)
return sim_out_proc
stoch = stochastic_from_dist("wfpt_reg", wiener_multi_like)
stoch.random = random
return stoch
from nose import SkipTest
from pandas import DataFrame
from time import time
import unittest
from kabuki.utils import stochastic_from_dist
def multi_normal_like(values, vec_mu, tau):
"""logp for multi normal"""
logp = 0
for i in range(len(vec_mu)):
logp += pm.normal_like(values[i,:], vec_mu[i], tau)
return logp
MN = stochastic_from_dist(name="MultiNormal", logp=multi_normal_like)
class TestStepMethods(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(TestStepMethods, self).__init__(*args, **kwargs)
self.uniform_lb = 1e-10
self.uniform_ub = 1e10
def runTest(self):
return
def assert_results(self, node, true_value, true_mean, true_std=None,
def RL_like(x, v, alpha, pos_alpha, z=0.5, p_outlier=0):
wiener_params = {
"err": 1e-4,
"n_st": 2,
"n_sz": 2,
"use_adaptive": 1,
"simps_err": 1e-3,
"w_outlier": 0.1,
}
sum_logp = 0
wp = wiener_params
response = x["response"].values.astype(int)
q = x["q_init"].iloc[0]
feedback = x["feedback"].values.astype(float)
split_by = x["split_by"].values.astype(int)
return wiener_like_rl(response,
feedback,
split_by,
q,
alpha,
pos_alpha,
v,
z,
p_outlier=p_outlier,
**wp)
RL = stochastic_from_dist("RL", RL_like)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
sampling_method <string> - an argument used by hddm.generate.gen_rts
cdf_range <sequance> - an argument used by hddm.generate.gen_rts
sampling_dt <float> - an argument used by hddm.generate.gen_rts
Ouput:
wfpt <class> - the wfpt stochastic
"""
#set wiener_params
if wiener_params is None:
wiener_params = {'err': 1e-4, 'n_st':2, 'n_sz':2,
'use_adaptive':1,
'simps_err':1e-3,
'w_outlier': 0.1}
wp = wiener_params
#create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
if np.all(~np.isnan(x['rt'])):
return hddm.wfpt.wiener_like(x['rt'].values, v, sv, a, z, sz, t, st,
p_outlier=p_outlier, **wp)
else: # for missing RTs. Currently undocumented.
noresponse = np.isnan(x['rt'])
## get sum of log p for trials with RTs as usual ##
LLH_resp = hddm.wfpt.wiener_like(x.loc[-noresponse, 'rt'].values,
v, sv, a, z, sz, t, st, p_outlier=p_outlier, **wp)
## get sum of log p for no-response trials from p(upper_boundary|parameters) ##
# this function assumes following format for the RTs:
# - accuracy coding such that correct responses have a 1 and incorrect responses a 0
# - usage of HDDMStimCoding for z
# - missing RTs are coded as 999/-999
# - note that hddm will flip RTs, such that error trials have negative RTs
# so that the miss-trial in the go condition and comission error
# in the no-go condition will have negative RTs
# get number of no-response trials
n_noresponse = sum(noresponse)
# percentage correct according to probability to get to upper boundary
if v == 0:
p_correct = z
else:
p_correct = (np.exp(-2 * a * z * v) - 1) / (np.exp(-2 * a * v) - 1)
# calculate percent no-response trials from % correct
if sum(x.loc[noresponse, 'rt']) > 0:
p_noresponse = p_correct # when no-response trials have a positive RT
# we are looking at nogo Trials
else:
p_noresponse = 1 - p_correct # when no-response trials have a
# negative RT we are looking at go Trials
# likelihood for no-response trials
LLH_noresp = np.log(p_noresponse)*n_noresponse
return LLH_resp + LLH_noresp
#create random function
def random(self):
return hddm.utils.flip_errors(hddm.generate.gen_rts(method=sampling_method,
size=self.shape, dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
#create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
#create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x, w_outlier=wp['w_outlier'], **self.parents)
#create wfpt class
wfpt = stochastic_from_dist('wfpt', wfpt_like)
#add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(time=cdf_range[1], **dict(list(self.parents.items()) + list(wp.items())))
wfpt.cdf = cdf
wfpt.random = random
#add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
def _create_wfpt_parents_dict(self, knodes):
wfpt_parents = super(HDDMnn_collapsing, self)._create_wfpt_parents_dict(knodes)
wfpt_parents['beta'] = knodes['beta_bottom']
wfpt_parents['alpha'] = knodes['alpha_bottom'] if self.k else 3.00
return wfpt_parents
def _create_wfpt_knode(self, knodes):
wfpt_parents = self._create_wfpt_parents_dict(knodes)
return Knode(self.wfpt_nn_collapsing_class, 'wfpt', observed=True, col_name=['nn_response', 'rt'], **wfpt_parents)
def wienernn_like_collapsing(x, v, sv, a, alpha, beta, z, sz, t, st, p_outlier=0): #theta
wiener_params = {'err': 1e-4, 'n_st': 2, 'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1}
wp = wiener_params
with open("weights.pickle", "rb") as tmp_file:
weights = pickle.load(tmp_file)
with open('biases.pickle', 'rb') as tmp_file:
biases = pickle.load(tmp_file)
with open('activations.pickle', 'rb') as tmp_file:
activations = pickle.load(tmp_file)
nn_response = x['nn_response'].values.astype(int)
return wiener_like_nn_collapsing(np.absolute(x['rt'].values), nn_response, activations, weights, biases, v, sv, a, alpha, beta, z, sz, t, st, p_outlier=p_outlier, **wp)
Wienernn_collapsing = stochastic_from_dist('Wienernn_collapsing', wienernn_like_collapsing)
"n_st": 2,
"n_sz": 2,
"use_adaptive": 1,
"simps_err": 1e-3,
"w_outlier": 0.1,
}
wp = wiener_params
response = x["response"].values.astype(int)
q = x["q_init"].iloc[0]
feedback = x["feedback"].values.astype(float)
split_by = x["split_by"].values.astype(int)
return wiener_like_rlddm(x["rt"].values,
response,
feedback,
split_by,
q,
alpha,
pos_alpha,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
WienerRL = stochastic_from_dist("wienerRL", wienerRL_like)
def generate_wfpt_stochastic_class(wiener_params=None,
sampling_method='cdf',
cdf_range=(-5, 5),
sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
sampling_method <string> - an argument used by hddm.generate.gen_rts
cdf_range <sequance> - an argument used by hddm.generate.gen_rts
sampling_dt <float> - an argument used by hddm.generate.gen_rts
Ouput:
wfpt <class> - the wfpt stochastic
"""
#set wiener_params
if wiener_params is None:
wiener_params = {
'err': 1e-4,
'n_st': 2,
'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1
}
wp = wiener_params
#create likelihood function
def wfpt_like(x, v, sv, a, z, sz, t, st, p_outlier=0):
return hddm.wfpt.wiener_like(x['rt'].values,
v,
sv,
a,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
#create random function
def random(self):
return hddm.utils.flip_errors(
hddm.generate.gen_rts(method=sampling_method,
size=self.shape,
dt=sampling_dt,
range_=cdf_range,
structured=True,
**self.parents.value))
#create pdf function
def pdf(self, x):
out = hddm.wfpt.pdf_array(x, **self.parents)
return out
#create cdf function
def cdf(self, x):
return hddm.cdfdif.dmat_cdf_array(x,
w_outlier=wp['w_outlier'],
**self.parents)
#create wfpt class
wfpt = stochastic_from_dist('wfpt', wfpt_like)
#add pdf and cdf_vec to the class
wfpt.pdf = pdf
wfpt.cdf_vec = lambda self: hddm.wfpt.gen_cdf_using_pdf(
time=cdf_range[1],
**dict(list(self.parents.items()) + list(wp.items())))
wfpt.cdf = cdf
wfpt.random = random
#add quantiles functions
add_quantiles_functions_to_pymc_class(wfpt)
return wfpt
import numpy as np
from scipy import stats
from kabuki.utils import stochastic_from_dist
np.seterr(divide='ignore')
import hddm
def wiener_like_contaminant(value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max,
err, n_st, n_sz, use_adaptive, simps_err):
"""Log-likelihood for the simple DDM including contaminants"""
return hddm.wfpt.wiener_like_contaminant(value, cont_x.astype(np.int32), v, sv, a, z, sz, t, st,
t_min, t_max, err, n_st, n_sz, use_adaptive, simps_err)
WienerContaminant = stochastic_from_dist(name="Wiener Simple Diffusion Process",
logp=wiener_like_contaminant)
def general_WienerCont(err=1e-4, n_st=2, n_sz=2, use_adaptive=1, simps_err=1e-3):
_like = lambda value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max, err=err, n_st=n_st, n_sz=n_sz, \
use_adaptive=use_adaptive, simps_err=simps_err: \
wiener_like_contaminant(value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max,\
err=err, n_st=n_st, n_sz=n_sz, use_adaptive=use_adaptive, simps_err=simps_err)
_like.__doc__ = wiener_like_contaminant.__doc__
return stochastic_from_dist(name="Wiener Diffusion Contaminant Process",
logp=_like)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
return knodes
def _create_wfpt_parents_dict(self, knodes):
wfpt_parents = OrderedDict()
wfpt_parents['v'] = knodes['v_bottom']
wfpt_parents['alpha'] = knodes['alpha_bottom']
wfpt_parents['pos_alpha'] = knodes['pos_alpha_bottom'] if self.dual else 100.00
wfpt_parents['z'] = knodes['z_bottom'] if 'z' in self.include else 0.5
return wfpt_parents
def _create_wfpt_knode(self, knodes):
wfpt_parents = self._create_wfpt_parents_dict(knodes)
return Knode(self.rl_class, 'wfpt', observed=True, col_name=['split_by', 'feedback', 'response', 'q_init'], **wfpt_parents)
def RL_like(x, v, alpha, pos_alpha, z=0.5, p_outlier=0):
wiener_params = {'err': 1e-4, 'n_st': 2, 'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1}
sum_logp = 0
wp = wiener_params
response = x['response'].values.astype(int)
q = x['q_init'].iloc[0]
feedback = x['feedback'].values.astype(float)
split_by = x['split_by'].values.astype(int)
return wiener_like_rl(response, feedback, split_by, q, alpha, pos_alpha, v, z, p_outlier=p_outlier, **wp)
RL = stochastic_from_dist('RL', RL_like)
import numpy as np
from scipy import stats
from kabuki.utils import stochastic_from_dist
np.seterr(divide='ignore')
import hddm
def wiener_like_contaminant(value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max,
err, n_st, n_sz, use_adaptive, simps_err):
"""Log-likelihood for the simple DDM including contaminants"""
return hddm.wfpt.wiener_like_contaminant(value, cont_x.astype(np.int32), v, sv, a, z, sz, t, st,
t_min, t_max, err, n_st, n_sz, use_adaptive, simps_err)
WienerContaminant = stochastic_from_dist(name="Wiener Simple Diffusion Process",
logp=wiener_like_contaminant)
def general_WienerCont(err=1e-4, n_st=2, n_sz=2, use_adaptive=1, simps_err=1e-3):
_like = lambda value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max, err=err, n_st=n_st, n_sz=n_sz, \
use_adaptive=use_adaptive, simps_err=simps_err: \
wiener_like_contaminant(value, cont_x, v, sv, a, z, sz, t, st, t_min, t_max,\
err=err, n_st=n_st, n_sz=n_sz, use_adaptive=use_adaptive, simps_err=simps_err)
_like.__doc__ = wiener_like_contaminant.__doc__
return stochastic_from_dist(name="Wiener Diffusion Contaminant Process",
logp=_like)
def generate_wfpt_stochastic_class(wiener_params=None, sampling_method='cdf', cdf_range=(-5,5), sampling_dt=1e-4):
"""
create a wfpt stochastic class by creating a pymc nodes and then adding quantile functions.
Input:
wiener_params <dict> - dictonary of wiener_params for wfpt likelihoods
def make_mlp_likelihood(model=None,
model_config=None,
wiener_params=None,
**kwargs):
"""Defines the likelihoods for the MLP networks.
:Arguments:
model: str <default='ddm'>
String that determines which model you would like to fit your data to.
Currently available models are: 'ddm', 'full_ddm', 'angle', 'weibull', 'ornstein', 'levy'
model_config: dict <default=None>
Model config supplied via the calling HDDM class. Necessary for construction of likelihood.
Should have the structure of model_configs in the hddm.model_config.model_config dictionary.
kwargs: dict
Dictionary of additional keyword arguments.
Importantly here, this carries the preloaded CNN.
:Returns:
Returns a pymc.object stochastic object as defined by PyMC2
"""
def random(
self,
keep_negative_responses=True,
add_model=False,
add_model_parameters=False,
add_outliers=False,
keep_subj_idx=False,
):
"""
Generate random samples from a given model (the dataset matches the size of the respective observated dataset supplied as an attribute of self).
"""
# This can be simplified so that we pass parameters directly to the simulator ...
theta = np.array(model_config["params_default"], dtype=np.float32)
keys_tmp = self.parents.value.keys()
cnt = 0
for param in model_config["params"]:
if param in keys_tmp:
theta[cnt] = np.array(self.parents.value[param]).astype(
np.float32)
cnt += 1
sim_out = simulator(theta=theta,
model=model,
n_samples=self.shape[0],
max_t=20)
# Add outliers:
if add_outliers:
if self.parents.value["p_outlier"] > 0.0:
sim_out = hddm_dataset_generators._add_outliers(
sim_out=sim_out,
p_outlier=self.parents.value["p_outlier"],
max_rt_outlier=1 / wiener_params["w_outlier"],
)
sim_out_proc = hddm_preprocess(
sim_out,
keep_negative_responses=keep_negative_responses,
keep_subj_idx=keep_subj_idx,
add_model_parameters=add_model_parameters,
)
if add_model:
sim_out_proc["model"] = model
return sim_out_proc
def pdf(self, x):
# Check if model supplied has only two choice options
# If yes --> check if two-dimensional input (rt, response) or one-dimensional input (rt) --> processing depends on it
# If not --> input x has to be two dimensional (rt, response) becasuse we can't deduce response from rt
x = np.array(x, dtype=np.float32)
if len(x.shape) == 1 or x.shape[1] == 1:
rt = x
response = rt / np.abs(rt)
rt = np.abs(rt)
elif x.shape[1] == 2:
rt = x[:, 0]
response = x[:, 1]
params = np.array([
self.parents[param] for param in model_config["params"]
]).astype(np.float32)
return hddm.wfpt.wiener_like_nn_mlp_pdf(
rt,
response,
params,
p_outlier=self.parents.value["p_outlier"],
w_outlier=wiener_params["w_outlier"],
network=kwargs["network"],
)
def cdf(self, x):
# TODO: Implement the CDF method for neural networks
return "Not yet implemented"
def make_likelihood():
likelihood_str = make_likelihood_str_mlp(config=model_config,
wiener_params=wiener_params)
exec(likelihood_str)
my_fun = locals()["custom_likelihood"]
return my_fun
likelihood_ = make_likelihood()
wfpt_nn = stochastic_from_dist("Wienernn_" + model,
partial(likelihood_, **kwargs))
wfpt_nn.pdf = pdf
wfpt_nn.cdf_vec = None # AF TODO: Implement this for neural nets (not a big deal actually but not yet sure where this is ever used finally)
wfpt_nn.cdf = cdf
wfpt_nn.random = random
return wfpt_nn
def make_mlp_likelihood_reg(model=None,
model_config=None,
wiener_params=None,
**kwargs):
"""Defines the regressor likelihoods for the MLP networks.
:Arguments:
model: str <default='ddm'>
String that determines which model you would like to fit your data to.
Currently available models are: 'ddm', 'full_ddm', 'angle', 'weibull', 'ornstein', 'levy'
model_config: dict <default=None>
Model config supplied via the calling HDDM class. Necessary for construction of likelihood.
Should have the structure of model_configs in the hddm.model_config.model_config dictionary.
kwargs: dict
Dictionary of additional keyword arguments.
Importantly here, this carries the preloaded CNN.
:Returns:
Returns a pymc.object stochastic object as defined by PyMC2
"""
# Prepare indirect regressors
# From dictionary that has indirect regressors as keys and links to parameters
# To dictionary that has parameters as keys and links them to any potential indirect regressor
param_links = {}
if 'indirect_regressors' in model_config:
for indirect_regressor_tmp in model_config['indirect_regressors'].keys(
):
for links_to_tmp in model_config['indirect_regressors'][
indirect_regressor_tmp]['links_to']:
if links_to_tmp in param_links.keys():
param_links[links_to_tmp].add(indirect_regressor_tmp)
else:
param_links[links_to_tmp] = set()
param_links[links_to_tmp].add(indirect_regressor_tmp)
# For remaining parameters that haven't been linked to anything
# we let them link to an empty set
# If there are not indirect_regressors, all parameters link to the empty set
for param in model_config["params"]:
if param in param_links:
pass
else:
param_links[param] = set()
print(model_config['params'])
print(param_links)
# Need to rewrite these random parts !
def random(
self,
keep_negative_responses=True,
add_model=False,
add_model_parameters=False,
add_outliers=False,
keep_subj_idx=False,
):
"""
Function to sample from a regressor based likelihood. Conditions on the covariates.
"""
param_dict = deepcopy(self.parents.value)
del param_dict["reg_outcomes"]
param_data = np.zeros(
(self.value.shape[0], len(model_config["params"])),
dtype=np.float32)
cnt = 0
for tmp_str in model_config["params"]:
if tmp_str in self.parents["reg_outcomes"]:
param_data[:, cnt] = param_dict[tmp_str].values
for linked_indirect_regressor in param_links[tmp_str]:
param_data[:, cnt] = param_data[:, cnt] + \
param_dict[linked_indirect_regressor].values
else:
param_data[:, cnt] = param_dict[tmp_str]
cnt += 1
sim_out = simulator(
theta=param_data,
model=model,
n_samples=1,
max_t=20 # n_trials = size,
)
# Add outliers:
if add_outliers:
if self.parents.value["p_outlier"] > 0.0:
sim_out = hddm_dataset_generators._add_outliers(
sim_out=sim_out,
p_outlier=self.parents.value["p_outlier"],
max_rt_outlier=1 / wiener_params["w_outlier"],
)
sim_out_proc = hddm_preprocess(
sim_out,
keep_negative_responses=keep_negative_responses,
add_model_parameters=add_model_parameters,
keep_subj_idx=keep_subj_idx,
)
if add_model:
sim_out_proc["model"] = model
return sim_out_proc
def pdf(self, x):
return "Not yet implemented"
def cdf(self, x):
# TODO: Implement the CDF method for neural networks
return "Not yet implemented"
def make_likelihood():
likelihood_str = make_reg_likelihood_str_mlp(
config=model_config,
wiener_params=wiener_params,
param_links=param_links,
)
exec(likelihood_str)
print(likelihood_str)
my_fun = locals()["custom_likelihood_reg"]
return my_fun
likelihood_ = make_likelihood()
stoch = stochastic_from_dist("wfpt_reg", partial(likelihood_, **kwargs))
stoch.pdf = pdf
stoch.cdf = cdf
stoch.random = random
return stoch
def wienernn_like_angle(x, v, sv, a, theta, z, sz, t, st, p_outlier=0):
wiener_params = {
'err': 1e-4,
'n_st': 2,
'n_sz': 2,
'use_adaptive': 1,
'simps_err': 1e-3,
'w_outlier': 0.1
}
wp = wiener_params
nn_response = x['nn_response'].values.astype(int)
return wiener_like_nn_angle(np.absolute(x['rt'].values),
nn_response,
v,
sv,
a,
theta,
z,
sz,
t,
st,
p_outlier=p_outlier,
**wp)
Wienernn_angle = stochastic_from_dist('Wienernn_angle', wienernn_like_angle)