def nf_target(params, data, likelihood_min = 1e-10):
return np.sum(np.maximum(np.log(batch_fptd(data[:, 0] * data[:, 1] * (- 1),
params[0],
params[1] * 2,
params[2],
params[3])),
np.log(likelihood_min)))
def make_fptd_data(data=[],
params=[],
metadata=[],
keep_file=0,
n_kde=100,
n_unif_up=100,
n_unif_down=100,
idx=0):
out = np.zeros((n_kde + n_unif_up + n_unif_down, 3))
tmp_kde = kde_class.logkde((data[:, 0], data[:, 1], metadata))
# Get kde part
samples_kde = tmp_kde.kde_sample(n_samples=n_kde)
out[:n_kde, 0] = samples_kde[0].ravel()
out[:n_kde, 1] = samples_kde[1].ravel()
# If we have 4 parameters we know we have the ddm --> use default sdv = 0
if len(params) == 4:
out[:n_kde, 2] = np.log(
batch_fptd(out[:n_kde, 0] * out[:n_kde, 1] * (-1), params[0],
params[1] * 2, params[2], params[3]))
# If we have 5 parameters but analytic we know we need to use the ddm_sdv --> supply sdv value to batch_fptd
if len(params) == 5:
out[:n_kde, 2] = np.log(
batch_fptd(out[:n_kde, 0] * out[:n_kde, 1] * (-1), params[0],
params[1] * 2, params[2], params[3], params[4]))
# Get positive uniform part:
choice_tmp = np.random.choice(metadata['possible_choices'], size=n_unif_up)
if metadata['max_t'] < 100:
rt_tmp = np.random.uniform(low=0.0001,
high=metadata['max_t'],
size=n_unif_up)
else:
rt_tmp = np.random.uniform(low=0.0001, high=100, size=n_unif_up)
likelihoods_unif = tmp_kde.kde_eval(data=(rt_tmp, choice_tmp)).ravel()
out[n_kde:(n_kde + n_unif_up), 0] = rt_tmp
out[n_kde:(n_kde + n_unif_up), 1] = choice_tmp
# If we have 4 parameters we know we have the ddm --> use default sdv = 0
if len(params) == 4:
out[n_kde:(n_kde + n_unif_up), 2] = np.log(
batch_fptd(
out[n_kde:(n_kde + n_unif_up), 0] *
out[n_kde:(n_kde + n_unif_up), 1] * (-1), params[0],
params[1] * 2, params[2], params[3]))
# If we have 5 parameters but analytic we know we need to use the ddm_sdv --> supply sdv value to batch_fptd
if len(params) == 5:
out[n_kde:(n_kde + n_unif_up), 2] = np.log(
batch_fptd(
out[n_kde:(n_kde + n_unif_up), 0] *
out[n_kde:(n_kde + n_unif_up), 1] * (-1), params[0],
params[1] * 2, params[2], params[3], params[4]))
# Get negative uniform part:
choice_tmp = np.random.choice(metadata['possible_choices'],
size=n_unif_down)
rt_tmp = np.random.uniform(low=-1.0, high=0.0001, size=n_unif_down)
out[(n_kde + n_unif_up):, 0] = rt_tmp
out[(n_kde + n_unif_up):, 1] = choice_tmp
out[(n_kde + n_unif_up):, 2] = -66.77497
if idx % 10 == 0:
print(idx)
return out.astype(np.float)
def kde_vs_mlp_likelihoods(ax_titles=[],
title='Likelihoods KDE - MLP',
network_dir='',
x_labels=[],
parameter_matrix=[],
cols=3,
model='angle',
data_signature='',
n_samples=10,
nreps=10,
save=True,
show=False,
machine='home',
method='mlp',
traindatanalytic=0,
plot_format='svg'):
mpl.rcParams['text.usetex'] = True
#matplotlib.rcParams['pdf.fonttype'] = 42
mpl.rcParams['svg.fonttype'] = 'none'
# Initialize rows and graph parameters
rows = int(np.ceil(len(ax_titles) / cols))
sns.set(style="white", palette="muted", color_codes=True, font_scale=2)
fig, ax = plt.subplots(rows,
cols,
figsize=(10, 10),
sharex=True,
sharey=False)
fig.suptitle(title + ': ' + model.upper().replace('_', '-'), fontsize=40)
sns.despine(right=True)
# Data template
plot_data = np.zeros((4000, 2))
plot_data[:, 0] = np.concatenate(([i * 0.0025 for i in range(2000, 0, -1)],
[i * 0.0025 for i in range(1, 2001, 1)]))
plot_data[:, 1] = np.concatenate((np.repeat(-1, 2000), np.repeat(1, 2000)))
# Load Keras model and initialize batch container
keras_model = keras.models.load_model(network_dir + 'model_final.h5')
keras_input_batch = np.zeros((4000, parameter_matrix.shape[1] + 2))
keras_input_batch[:, parameter_matrix.shape[1]:] = plot_data
for i in range(len(ax_titles)):
print('Making Plot: ', i)
row_tmp = int(np.floor(i / cols))
col_tmp = i - (cols * row_tmp)
# Get predictions from keras model
keras_input_batch[:, :parameter_matrix.shape[1]] = parameter_matrix[
i, :]
ll_out_keras = keras_model.predict(keras_input_batch, batch_size=100)
# Get prediction from navarro if traindatanalytic = 1
if traindatanalytic:
ll_out_gt = cdw.batch_fptd(plot_data[:, 0] * plot_data[:, 1],
v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3])
sns.lineplot(plot_data[:, 0] * plot_data[:, 1],
ll_out_gt,
color='black',
alpha=0.5,
label='TRUE',
ax=ax[row_tmp, col_tmp])
# Get predictions from simulations /kde
if not traindatanalytic:
for j in range(nreps):
if model == 'ddm' or model == 'ddm_analytic':
out = cds.ddm_flexbound(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.constant,
boundary_multiplicative=True,
boundary_params={})
if model == 'ddm_sdv':
out = cds.ddm_sdv(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3],
sdv=parameter_matrix[i, 4],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.constant,
boundary_multiplicative=True,
boundary_params={})
if model == 'full_ddm' or model == 'full_ddm2':
out = cds.full_ddm(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3],
dw=parameter_matrix[i, 4],
sdv=parameter_matrix[i, 5],
dndt=parameter_matrix[i, 6],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.constant,
boundary_multiplicative=True,
boundary_params={})
if model == 'angle' or model == 'angle2':
out = cds.ddm_flexbound(
v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.angle,
boundary_multiplicative=False,
boundary_params={'theta': parameter_matrix[i, 4]})
if model == 'weibull_cdf' or model == 'weibull_cdf2':
out = cds.ddm_flexbound(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
ndt=parameter_matrix[i, 3],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.weibull_cdf,
boundary_multiplicative=True,
boundary_params={
'alpha': parameter_matrix[i,
4],
'beta': parameter_matrix[i, 5]
})
if model == 'levy':
out = cds.levy_flexbound(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
alpha_diff=parameter_matrix[i, 3],
ndt=parameter_matrix[i, 4],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.constant,
boundary_multiplicative=True,
boundary_params={})
if model == 'ornstein':
out = cds.ornstein_uhlenbeck(v=parameter_matrix[i, 0],
a=parameter_matrix[i, 1],
w=parameter_matrix[i, 2],
g=parameter_matrix[i, 3],
ndt=parameter_matrix[i, 4],
s=1,
delta_t=0.001,
max_t=20,
n_samples=n_samples,
print_info=False,
boundary_fun=bf.constant,
boundary_multiplicative=True,
boundary_params={})
mykde = kdec.logkde((out[0], out[1], out[2]))
ll_out_gt = mykde.kde_eval((plot_data[:, 0], plot_data[:, 1]))
# Plot kde predictions
if j == 0:
sns.lineplot(plot_data[:, 0] * plot_data[:, 1],
np.exp(ll_out_gt),
color='black',
alpha=0.5,
label='KDE',
ax=ax[row_tmp, col_tmp])
elif j > 0:
sns.lineplot(plot_data[:, 0] * plot_data[:, 1],
np.exp(ll_out_gt),
color='black',
alpha=0.5,
ax=ax[row_tmp, col_tmp])
# Plot keras predictions
sns.lineplot(plot_data[:, 0] * plot_data[:, 1],
np.exp(ll_out_keras[:, 0]),
color='green',
label='MLP',
alpha=1,
ax=ax[row_tmp, col_tmp])
# Legend adjustments
if row_tmp == 0 and col_tmp == 0:
ax[row_tmp, col_tmp].legend(loc='upper left',
fancybox=True,
shadow=True,
fontsize=12)
else:
ax[row_tmp, col_tmp].legend().set_visible(False)
if row_tmp == rows - 1:
ax[row_tmp, col_tmp].set_xlabel('rt', fontsize=24)
else:
ax[row_tmp, col_tmp].tick_params(color='white')
if col_tmp == 0:
ax[row_tmp, col_tmp].set_ylabel('likelihood', fontsize=24)
ax[row_tmp, col_tmp].set_title(ax_titles[i], fontsize=20)
ax[row_tmp, col_tmp].tick_params(axis='y', size=16)
ax[row_tmp, col_tmp].tick_params(axis='x', size=16)
for i in range(len(ax_titles), rows * cols, 1):
row_tmp = int(np.floor(i / cols))
col_tmp = i - (cols * row_tmp)
ax[row_tmp, col_tmp].axis('off')
if save == True:
if machine == 'home':
fig_dir = "/users/afengler/OneDrive/git_repos/nn_likelihoods/figures/" + method + "/likelihoods/"
if not os.path.isdir(fig_dir):
os.mkdir(fig_dir)
figure_name = 'mlp_vs_kde_likelihood_'
plt.subplots_adjust(top=0.9)
plt.subplots_adjust(hspace=0.3, wspace=0.3)
if traindatanalytic == 1:
if plot_format == 'svg':
plt.savefig(fig_dir + '/' + figure_name + model +
data_signature + '_' + train_data_type + '.svg',
format='svg',
transparent=True,
frameon=False)
if plot_format == 'png':
plt.savefig(fig_dir + '/' + figure_name + model + '_analytic' +
'.png',
dpi=300) #, bbox_inches = 'tight')
else:
if plot_format == 'svg':
plt.savefig(fig_dir + '/' + figure_name + model + '_kde' +
'.svg',
format='svg',
transparent=True,
frameon=False)
if plot_format == 'png':
plt.savefig(fig_dir + '/' + figure_name + model + '_kde' +
'.png',
dpi=300) #, bbox_inches = 'tight')
if show:
return plt.show()
else:
plt.close()
return 'finished'
