def compute_z_moments(w_s, eta_old, H_old, psi_old):
''' Compute the first moment and the variance of the latent variable
w_s (list of length s1): The path probabilities for all s in S1
eta_old (list of nb_layers elements of shape (K_l x r_{l-1}, 1)): eta
estimators of the previous iteration for each layer
H_old (list of nb_layers elements of shape (K_l x r_l-1, r_l)): Lambda
estimators of the previous iteration for each layer
psi_old (list of nb_layers elements of shape (K_l x r_l-1, r_l-1)): Psi
estimators of the previous iteration for each layer
-------------------------------------------------------------------------
returns (tuple of length 2): E(z^{(l)}) and Var(z^{(l)})
'''
k = [eta.shape[0] for eta in eta_old]
L = len(eta_old)
Ez = [[] for l in range(L)]
AT = [[] for l in range(L)]
w_reshaped = w_s.reshape(*k, order='C')
for l in reversed(range(L)):
# Compute E(z^{(l)})
idx_to_sum = tuple(set(range(L)) - set([l]))
wl = w_reshaped.sum(idx_to_sum)[..., n_axis, n_axis]
Ezl = (wl * eta_old[l]).sum(0, keepdims=True)
Ez[l] = Ezl
etaTeta = eta_old[l] @ t(eta_old[l], (0, 2, 1))
HlHlT = H_old[l] @ t(H_old[l], (0, 2, 1))
E_zlzlT = (wl * (HlHlT + psi_old[l] + etaTeta)).sum(0, keepdims=True)
var_zl = E_zlzlT - Ezl @ t(Ezl, (0, 2, 1))
try:
var_zl = ensure_psd([var_zl])[0] # Numeric stability check
except:
print(var_zl)
raise RuntimeError('Var z1 was not psd')
AT_l = cholesky(var_zl)
AT[l] = AT_l
return Ez, AT
def MDGMM(y, n_clusters, r, k, init, var_distrib, nj, it = 50, \
eps = 1E-05, maxstep = 100, seed = None, perform_selec = True):
''' Fit a Generalized Linear Mixture of Latent Variables Model (GLMLVM)
y (numobs x p ndarray): The observations containing mixed variables
n_clusters (int or str): The number of clusters to look for in the data or the use mode of the MDGMM
r (dict): The dimension of latent variables through the first 2 layers
k (dict): The number of components of the latent Gaussian mixture layers
init (dict): The initialisation parameters for the algorithm
var_distrib (p 1darray): An array containing the types of the variables in y
nj (p 1darray): For binary/count data: The maximum values that the variable can take.
For ordinal data: the number of different existing categories for each variable
For categorical data: the number of different existing categories for each variable
it (int): The maximum number of MCEM iterations of the algorithm
eps (float): If the likelihood increase by less than eps then the algorithm stops
maxstep (int): The maximum number of optimisation step for each variable
seed (int): The random state seed to set (Only for numpy generated data for the moment)
perform_selec (Bool): Whether to perform architecture selection or not
------------------------------------------------------------------------------------------------
returns (dict): The predicted classes, the likelihood through the EM steps
and a continuous representation of the data
'''
# Break the reference link
k = deepcopy(k)
r = deepcopy(r)
best_k = deepcopy(k)
best_r = deepcopy(r)
# Add other checks for the other variables
check_inputs(k, r)
prev_lik = - 1E15
best_lik = -1E15
tol = 0.01
max_patience = 1
patience = 0
#====================================================
# Initialize the parameters
#====================================================
eta_c, eta_d, H_c, H_d, psi_c, psi_d = dispatch_dgmm_init(init)
lambda_bin, lambda_ord, lambda_categ = dispatch_gllvm_init(init)
w_s_c, w_s_d = dispatch_paths_init(init)
numobs = len(y)
likelihood = []
it_num = 0
ratio = 1000
np.random.seed = seed
#====================================================
# Dispatch variables between categories
#====================================================
y_bin = y[:, np.logical_or(var_distrib == 'bernoulli',\
var_distrib == 'binomial')]
nj_bin = nj[np.logical_or(var_distrib == 'bernoulli',\
var_distrib == 'binomial')]
nj_bin = nj_bin.astype(int)
nb_bin = len(nj_bin)
y_ord = y[:, var_distrib == 'ordinal']
nj_ord = nj[var_distrib == 'ordinal']
nj_ord = nj_ord.astype(int)
nb_ord = len(nj_ord)
y_categ = y[:, var_distrib == 'categorical']
nj_categ = nj[var_distrib == 'categorical'].astype(int)
nb_categ = len(nj_categ)
yc = y[:, var_distrib == 'continuous']
ss = StandardScaler()
yc = ss.fit_transform(yc)
nb_cont = yc.shape[1]
# *_1L standsds for quantities going through all the network (head + tail)
k_1L, L_1L, L, bar_L, S_1L = nb_comps_and_layers(k)
r_1L = {'c': r['c'] + r['t'], 'd': r['d'] + r['t'], 't': r['t']}
best_sil = [-1.1 for l in range(L['t'] - 1)] if n_clusters == 'multi' else -1.1
new_sil = [-1.1 for l in range(L['t'] - 1)] if n_clusters == 'multi' else -1.1
M = M_growth(1, r_1L, numobs)
if nb_bin + nb_ord + nb_categ == 0: # Create the InputError class and change this
raise ValueError('Input does not contain discrete variables,\
consider using a regular DGMM')
if nb_cont == 0: # Create the InputError class and change this
raise ValueError('Input does not contain continuous values,\
consider using a DDGMM')
# Compute the Gower matrix
cat_features = np.logical_or(var_distrib == 'categorical', var_distrib == 'bernoulli')
dm = gower_matrix(y, cat_features = cat_features)
while (it_num < it) & ((ratio > eps) | (patience <= max_patience)):
print(it_num)
# The clustering layer is the one used to perform the clustering
# i.e. the layer l such that k[l] == n_clusters
if not(isnumeric(n_clusters)):
if n_clusters == 'auto':
clustering_layer = 0
elif n_clusters == 'multi':
clustering_layer = list(range(L['t'] - 1))
else:
raise ValueError('Please enter an int, auto or multi for n_clusters')
else:
assert (np.array(k['t']) == n_clusters).any()
clustering_layer = np.argmax(np.array(k['t']) == n_clusters)
#####################################################################################
################################# MC step ############################################
#####################################################################################
#=====================================================================
# Draw from f(z^{l} | s, Theta) for both heads and tail
#=====================================================================
mu_s_c, sigma_s_c = compute_path_params(eta_c, H_c, psi_c)
sigma_s_c = ensure_psd(sigma_s_c)
mu_s_d, sigma_s_d = compute_path_params(eta_d, H_d, psi_d)
sigma_s_d = ensure_psd(sigma_s_d)
z_s_c, zc_s_c, z_s_d, zc_s_d = draw_z_s_all_network(mu_s_c, sigma_s_c,\
mu_s_d, sigma_s_d, yc, eta_c, eta_d, S_1L, L, M)
#========================================================================
# Draw from f(z^{l+1} | z^{l}, s, Theta) for l >= 1
#========================================================================
# Create wrapper as before and after
chsi_c = compute_chsi(H_c, psi_c, mu_s_c, sigma_s_c)
chsi_c = ensure_psd(chsi_c)
rho_c = compute_rho(eta_c, H_c, psi_c, mu_s_c, sigma_s_c, zc_s_c, chsi_c)
chsi_d = compute_chsi(H_d, psi_d, mu_s_d, sigma_s_d)
chsi_d = ensure_psd(chsi_d)
rho_d = compute_rho(eta_d, H_d, psi_d, mu_s_d, sigma_s_d, zc_s_d, chsi_d)
# In the following z2 and z1 will denote z^{l+1} and z^{l} respectively
z2_z1s_c, z2_z1s_d = draw_z2_z1s_network(chsi_c, chsi_d, rho_c, \
rho_d, M, r_1L, L)
#=======================================================================
# Compute the p(y^D| z1) for all discrete variables
#=======================================================================
py_zl1_d = fy_zl1(lambda_bin, y_bin, nj_bin, lambda_ord, y_ord, nj_ord,\
lambda_categ, y_categ, nj_categ, z_s_d[0])
#========================================================================
# Draw from p(z1 | y, s) proportional to p(y | z1) * p(z1 | s) for all s
#========================================================================
zl1_ys_d = draw_zl1_ys(z_s_d, py_zl1_d, M['d'])
#####################################################################################
################################# E step ############################################
#####################################################################################
#=====================================================================
# Compute quantities necessary for E steps of both heads and tail
#=====================================================================
# Discrete head quantities
pzl1_ys_d, ps_y_d, py_d = E_step_GLLVM(z_s_d[0], mu_s_d[0], sigma_s_d[0], w_s_d, py_zl1_d)
py_s_d = ps_y_d * py_d / w_s_d[n_axis]
# Continuous head quantities
ps_y_c, py_s_c, py_c = continuous_lik(yc, mu_s_c[0], sigma_s_c[0], w_s_c)
pz_s_d = fz_s(z_s_d, mu_s_d, sigma_s_d)
pz_s_c = fz_s(z_s_c, mu_s_c, sigma_s_c)
#=====================================================================
# Compute p(z^{(l)}| s, y). Equation (5) of the paper
#=====================================================================
# Compute pz2_z1s_d and pz2_z1s_d for the tail indices whereas it is useless
pz2_z1s_d = fz2_z1s(t(pzl1_ys_d, (1, 0, 2)), z2_z1s_d, chsi_d, rho_d, S_1L['d'])
pz_ys_d = fz_ys(t(pzl1_ys_d, (1, 0, 2)), pz2_z1s_d)
pz2_z1s_c = fz2_z1s([], z2_z1s_c, chsi_c, rho_c, S_1L['c'])
pz_ys_c = fz_ys([], pz2_z1s_c)
pz2_z1s_t = fz2_z1s([], z2_z1s_c[bar_L['c']:], chsi_c[bar_L['c']:], \
rho_c[bar_L['c']:], S_1L['t'])
# Junction layer computations
# Compute p(zC |s)
py_zs_d = fy_zs(pz_ys_d, py_s_d)
py_zs_c = fy_zs(pz_ys_c, py_s_c)
# Compute p(zt | yC, yD, sC, SD)
pzt_yCyDs = fz_yCyDs(py_zs_c, pz_ys_d, py_s_c, M, S_1L, L)
#=====================================================================
# Compute MFA expectations
#=====================================================================
# Discrete head.
Ez_ys_d, E_z1z2T_ys_d, E_z2z2T_ys_d, EeeT_ys_d = \
E_step_DGMM_d(zl1_ys_d, H_d, z_s_d, zc_s_d, z2_z1s_d, pz_ys_d,\
pz2_z1s_d, S_1L['d'], L['d'])
# Continuous head
Ez_ys_c, E_z1z2T_ys_c, E_z2z2T_ys_c, EeeT_ys_c = \
E_step_DGMM_c(H_c, z_s_c, zc_s_c, z2_z1s_c, pz_ys_c,\
pz2_z1s_c, S_1L['c'], L['c'])
# Junction layers
Ez_ys_t, E_z1z2T_ys_t, E_z2z2T_ys_t, EeeT_ys_t = \
E_step_DGMM_t(H_c[bar_L['c']:], \
z_s_c[bar_L['c']:], zc_s_c[bar_L['c']:], z2_z1s_c[bar_L['c']:],\
pzt_yCyDs, pz2_z1s_t, S_1L, L, k_1L)
# Error here for the first two terms: p(y^h | z^t, s^C) != p(y^h | z^t, s^{1C:L})
pst_yCyD = fst_yCyD(py_zs_c, py_zs_d, pz_s_d, w_s_c, w_s_d, k_1L, L)
###########################################################################
############################ M step #######################################
###########################################################################
#=======================================================
# Compute DGMM Parameters
#=======================================================
# Discrete head
w_s_d = np.mean(ps_y_d, axis = 0)
eta_d_barL, H_d_barL, psi_d_barL = M_step_DGMM(Ez_ys_d, E_z1z2T_ys_d, E_z2z2T_ys_d, \
EeeT_ys_d, ps_y_d, H_d, k_1L['d'][:-1],\
L_1L['d'], r_1L['d'])
# Add dispatching function here
eta_d[:bar_L['d']] = eta_d_barL
H_d[:bar_L['d']] = H_d_barL
psi_d[:bar_L['d']] = psi_d_barL
# Continuous head
w_s_c = np.mean(ps_y_c, axis = 0)
eta_c_barL, H_c_barL, psi_c_barL = M_step_DGMM(Ez_ys_c, E_z1z2T_ys_c, E_z2z2T_ys_c, \
EeeT_ys_c, ps_y_c, H_c, k_1L['c'][:-1],\
L_1L['c'] + 1, r_1L['c'])
eta_c[:bar_L['c']] = eta_c_barL
H_c[:bar_L['c']] = H_c_barL
psi_c[:bar_L['c']] = psi_c_barL
# Common tail
eta_t, H_t, psi_t, Ezst_y = M_step_DGMM_t(Ez_ys_t, E_z1z2T_ys_t, E_z2z2T_ys_t, \
EeeT_ys_t, ps_y_c, ps_y_d, pst_yCyD, \
H_c[bar_L['c']:], S_1L, k_1L, \
L_1L, L, r_1L['t'])
eta_d[bar_L['d']:] = eta_t
H_d[bar_L['d']:] = H_t
psi_d[bar_L['d']:] = psi_t
eta_c[bar_L['c']:] = eta_t
H_c[bar_L['c']:] = H_t
psi_c[bar_L['c']:] = psi_t
#=======================================================
# Identifiability conditions
#=======================================================
w_s_t = np.mean(pst_yCyD, axis = 0)
eta_d, H_d, psi_d, AT_d, eta_c, H_c, psi_c, AT_c = network_identifiability(eta_d, \
H_d, psi_d, eta_c, H_c, psi_c, w_s_c, w_s_d, w_s_t, bar_L)
#=======================================================
# Compute GLLVM Parameters
#=======================================================
# We optimize each column separately as it is faster than all column jointly
# (and more relevant with the independence hypothesis)
lambda_bin = bin_params_GLLVM(y_bin, nj_bin, lambda_bin, ps_y_d, \
pzl1_ys_d, z_s_d[0], AT_d[0], tol = tol, maxstep = maxstep)
lambda_ord = ord_params_GLLVM(y_ord, nj_ord, lambda_ord, ps_y_d, \
pzl1_ys_d, z_s_d[0], AT_d[0], tol = tol, maxstep = maxstep)
lambda_categ = categ_params_GLLVM(y_categ, nj_categ, lambda_categ, ps_y_d,\
pzl1_ys_d, z_s_d[0], AT_d[0], tol = tol, maxstep = maxstep)
###########################################################################
################## Clustering parameters updating #########################
###########################################################################
new_lik = np.sum(np.log(py_d) + np.log(py_c))
likelihood.append(new_lik)
ratio = (new_lik - prev_lik)/abs(prev_lik)
if n_clusters == 'multi':
temp_classes = []
z_tail = []
classes = [[] for l in range(L['t'] - 1)]
for l in clustering_layer:
idx_to_sum = tuple(set(range(1, L['t'] + 1)) -\
set([clustering_layer[l] + 1]))
psl_y = pst_yCyD.reshape(numobs, *k['t'],\
order = 'C').sum(idx_to_sum)
temp_class_l = np.argmax(psl_y, axis = 1)
sil_l = silhouette_score(dm, temp_class_l, metric = 'precomputed')
temp_classes.append(temp_class_l)
#z_tail.append(Ezst_y[l].sum(1))
new_sil[l] = sil_l
#z_tail = []
for l in range(L['t'] - 1):
zl = Ezst_y[l].sum(1)
z_tail.append(zl)
if best_sil[l] < new_sil[l]:
# Update the quantity if the silhouette score is better
best_sil[l] = deepcopy(new_sil[l])
classes[l] = deepcopy(temp_classes[l])
if zl.shape[-1] == 3:
plot_3d(zl, classes[l])
elif zl.shape[-1] == 2:
plot_2d(zl, classes[l])
else:
idx_to_sum = tuple(set(range(1, L['t'] + 1)) - set([clustering_layer + 1]))
psl_y = pst_yCyD.reshape(numobs, *k['t'], order = 'C').sum(idx_to_sum)
temp_classes = np.argmax(psl_y, axis = 1)
try:
new_sil = silhouette_score(dm, temp_classes, metric = 'precomputed')
except:
new_sil = -1
z_tail = [Ezst_y[l].sum(1) for l in range(L['t'] - 1)]
if best_sil < new_sil:
# Update the quantity if the silhouette score is better
zl = z_tail[clustering_layer]
best_sil = deepcopy(new_sil)
classes = deepcopy(temp_classes)
if zl.shape[-1] == 3:
plot_3d(zl, classes)
elif zl.shape[-1] == 2:
plot_2d(zl, classes)
# Refresh the likelihood if best
if best_lik < new_lik:
best_lik = deepcopy(prev_lik)
if prev_lik < new_lik:
patience = 0
M = M_growth(it_num + 1, r_1L, numobs)
else:
patience += 1
###########################################################################
######################## Parameter selection #############################
###########################################################################
min_nb_clusters = 2
is_not_min_specif = not(is_min_architecture_reached(k, r, min_nb_clusters))
if look_for_simpler_network(it_num) & perform_selec & is_not_min_specif:
# To add: selection according to categ
r_to_keep = r_select(y_bin, y_ord, y_categ, yc, zl1_ys_d,\
z2_z1s_d[:bar_L['d']], w_s_d, z2_z1s_c[:bar_L['c']],
z2_z1s_c[bar_L['c']:], n_clusters)
# Check layer deletion
is_c_layer_deletion = np.any([len(rl) == 0 for rl in r_to_keep['c']])
is_d_layer_deletion = np.any([len(rl) == 0 for rl in r_to_keep['d']])
is_head_layer_deletion = np.any([is_c_layer_deletion, is_d_layer_deletion])
if is_head_layer_deletion:
# Restart the algorithm
if is_c_layer_deletion:
r['c'] = [len(rl) for rl in r_to_keep['c'][:-1]]
k['c'] = k['c'][:-1]
if is_d_layer_deletion:
r['d'] = [len(rl) for rl in r_to_keep['d'][:-1]]
k['d'] = k['d'][:-1]
init = dim_reduce_init(pd.DataFrame(y), n_clusters, k, r, nj, var_distrib,\
seed = None)
eta_c, eta_d, H_c, H_d, psi_c, psi_d = dispatch_dgmm_init(init)
lambda_bin, lambda_ord, lambda_categ = dispatch_gllvm_init(init)
w_s_c, w_s_d = dispatch_paths_init(init)
# *_1L standsds for quantities going through all the network (head + tail)
k_1L, L_1L, L, bar_L, S_1L = nb_comps_and_layers(k)
r_1L = {'c': r['c'] + r['t'], 'd': r['d'] + r['t'], 't': r['t']}
M = M_growth(it_num + 1, r_1L, numobs)
prev_lik = deepcopy(new_lik)
it_num = it_num + 1
print(likelihood)
print('Restarting the algorithm')
continue
new_Lt = np.sum([len(rl) != 0 for rl in r_to_keep['t']]) #- 1
# If r_l == 0, delete the last l + 1: layers
new_Lt = np.sum([len(rl) != 0 for rl in r_to_keep['t']]) #- 1
#w_s_t = pst_yCyD.mean(0)
k_to_keep = k_select(w_s_c, w_s_d, w_s_t, k, new_Lt, clustering_layer, n_clusters)
is_selection = check_if_selection(r_to_keep, r, k_to_keep, k, L, new_Lt)
assert new_Lt > 0 # > 1 ?
if n_clusters == 'multi':
assert new_Lt == L['t']
if is_selection:
# Part to change when update also number of layers on each head
nb_deleted_layers_tail = L['t'] - new_Lt
L['t'] = new_Lt
L_1L = {keys: values - nb_deleted_layers_tail for keys, values in L_1L.items()}
eta_c, eta_d, H_c, H_d, psi_c, psi_d = dgmm_coeff_selection(eta_c,\
H_c, psi_c, eta_d, H_d, psi_d, L, r_to_keep, k_to_keep)
lambda_bin, lambda_ord, lambda_categ = gllvm_coeff_selection(lambda_bin, lambda_ord,\
lambda_categ, r, r_to_keep)
w_s_c, w_s_d = path_proba_selection(w_s_c, w_s_d, k, k_to_keep, new_Lt)
k = {h: [len(k_to_keep[h][l]) for l in range(L[h])] for h in ['d', 't']}
k['c'] = [len(k_to_keep['c'][l]) for l in range(L['c'] + 1)]
r = {h: [len(r_to_keep[h][l]) for l in range(L[h])] for h in ['d', 't']}
r['c'] = [len(r_to_keep['c'][l]) for l in range(L['c'] + 1)]
k_1L, _, L, bar_L, S_1L = nb_comps_and_layers(k)
r_1L = {'c': r['c'] + r['t'], 'd': r['d'] + r['t'], 't': r['t']}
patience = 0
best_r = deepcopy(r)
best_k = deepcopy(k)
#=======================================================
# Identifiability conditions
#=======================================================
eta_d, H_d, psi_d, AT_d, eta_c, H_c, psi_c, AT_c = network_identifiability(eta_d, \
H_d, psi_d, eta_c, H_c, psi_c, w_s_c, w_s_d, w_s_t, bar_L)
print('New architecture:')
print('k', k)
print('r', r)
print('L', L)
print('S_1L', S_1L)
print("w_s_c", len(w_s_c))
print("w_s_d", len(w_s_d))
M = M_growth(it_num + 1, r_1L, numobs)
prev_lik = deepcopy(new_lik)
print(likelihood)
print('Silhouette score:', new_sil)
it_num = it_num + 1
out = dict(likelihood = likelihood, classes = classes, \
best_r = best_r, best_k = best_k)
if n_clusters == 'multi':
out['z'] = z_tail
else:
out['z'] = z_tail[clustering_layer]
return(out)
def DDGMM(y, n_clusters, r, k, init, var_distrib, nj, it = 50, \
eps = 1E-05, maxstep = 100, seed = None, perform_selec = True):
''' Fit a Generalized Linear Mixture of Latent Variables Model (GLMLVM)
y (numobs x p ndarray): The observations containing categorical variables
n_clusters (int): The number of clusters to look for in the data
r (list): The dimension of latent variables through the first 2 layers
k (list): The number of components of the latent Gaussian mixture layers
init (dict): The initialisation parameters for the algorithm
var_distrib (p 1darray): An array containing the types of the variables in y
nj (p 1darray): For binary/count data: The maximum values that the variable can take.
For ordinal data: the number of different existing categories for each variable
it (int): The maximum number of MCEM iterations of the algorithm
eps (float): If the likelihood increase by less than eps then the algorithm stops
maxstep (int): The maximum number of optimisation step for each variable
seed (int): The random state seed to set (Only for numpy generated data for the moment)
perform_selec (Bool): Whether to perform architecture selection or not
------------------------------------------------------------------------------------------------
returns (dict): The predicted classes, the likelihood through the EM steps
and a continuous representation of the data
'''
prev_lik = -1E16
best_lik = -1E16
tol = 0.01
max_patience = 1
patience = 0
best_k = deepcopy(k)
best_r = deepcopy(r)
best_sil = -1
new_sil = -1
# Initialize the parameters
eta = deepcopy(init['eta'])
psi = deepcopy(init['psi'])
lambda_bin = deepcopy(init['lambda_bin'])
lambda_ord = deepcopy(init['lambda_ord'])
lambda_categ = deepcopy(init['lambda_categ'])
H = deepcopy(init['H'])
w_s = deepcopy(
init['w_s']
) # Probability of path s' through the network for all s' in Omega
numobs = len(y)
likelihood = []
it_num = 0
ratio = 1000
np.random.seed = seed
# Dispatch variables between categories
y_bin = y[:,
np.logical_or(var_distrib == 'bernoulli', var_distrib ==
'binomial')]
nj_bin = nj[np.logical_or(var_distrib == 'bernoulli',
var_distrib == 'binomial')].astype(int)
nb_bin = len(nj_bin)
y_categ = y[:, var_distrib == 'categorical']
nj_categ = nj[var_distrib == 'categorical'].astype(int)
nb_categ = len(nj_categ)
y_ord = y[:, var_distrib == 'ordinal']
nj_ord = nj[var_distrib == 'ordinal'].astype(int)
nb_ord = len(nj_ord)
L = len(k)
k_aug = k + [1]
S = np.array([np.prod(k_aug[l:]) for l in range(L + 1)])
M = M_growth(1, r, numobs)
assert nb_ord + nb_bin + nb_categ > 0
# Compute the Gower matrix
cat_features = np.logical_or(var_distrib == 'categorical',
var_distrib == 'bernoulli')
dm = gower_matrix(y, cat_features=cat_features)
while (it_num < it) & ((ratio > eps) | (patience <= max_patience)):
print(it_num)
# The clustering layer is the one used to perform the clustering
# i.e. the layer l such that k[l] == n_clusters
clustering_layer = np.argmax(np.array(k) == n_clusters)
#####################################################################################
################################# S step ############################################
#####################################################################################
#=====================================================================
# Draw from f(z^{l} | s, Theta) for all s in Omega
#=====================================================================
mu_s, sigma_s = compute_path_params(eta, H, psi)
sigma_s = ensure_psd(sigma_s)
z_s, zc_s = draw_z_s(mu_s, sigma_s, eta, M)
'''
print('mu_s', np.abs(mu_s[0]).mean())
print('sigma_s', np.abs(sigma_s[0]).mean())
print('z_s0', np.abs(z_s[0]).mean())
print('z_s1', np.abs(z_s[1]).mean(0)[:,0])
'''
#========================================================================
# Draw from f(z^{l+1} | z^{l}, s, Theta) for l >= 1
#========================================================================
chsi = compute_chsi(H, psi, mu_s, sigma_s)
chsi = ensure_psd(chsi)
rho = compute_rho(eta, H, psi, mu_s, sigma_s, zc_s, chsi)
# In the following z2 and z1 will denote z^{l+1} and z^{l} respectively
z2_z1s = draw_z2_z1s(chsi, rho, M, r)
#=======================================================================
# Compute the p(y| z1) for all variable categories
#=======================================================================
py_zl1 = fy_zl1(lambda_bin, y_bin, nj_bin, lambda_ord, y_ord, nj_ord,
lambda_categ, y_categ, nj_categ, z_s[0])
#========================================================================
# Draw from p(z1 | y, s) proportional to p(y | z1) * p(z1 | s) for all s
#========================================================================
zl1_ys = draw_zl1_ys(z_s, py_zl1, M)
#####################################################################################
################################# E step ############################################
#####################################################################################
#=====================================================================
# Compute conditional probabilities used in the appendix of asta paper
#=====================================================================
pzl1_ys, ps_y, p_y = E_step_GLLVM(z_s[0], mu_s[0], sigma_s[0], w_s,
py_zl1)
#del(py_zl1)
#=====================================================================
# Compute p(z^{(l)}| s, y). Equation (5) of the paper
#=====================================================================
pz2_z1s = fz2_z1s(t(pzl1_ys, (1, 0, 2)), z2_z1s, chsi, rho, S)
pz_ys = fz_ys(t(pzl1_ys, (1, 0, 2)), pz2_z1s)
#=====================================================================
# Compute MFA expectations
#=====================================================================
Ez_ys, E_z1z2T_ys, E_z2z2T_ys, EeeT_ys = \
E_step_DGMM(zl1_ys, H, z_s, zc_s, z2_z1s, pz_ys, pz2_z1s, S)
###########################################################################
############################ M step #######################################
###########################################################################
#=======================================================
# Compute MFA Parameters
#=======================================================
w_s = np.mean(ps_y, axis=0)
eta, H, psi = M_step_DGMM(Ez_ys, E_z1z2T_ys, E_z2z2T_ys, EeeT_ys, ps_y,
H, k)
#=======================================================
# Identifiability conditions
#=======================================================
# Update eta, H and Psi values
H = diagonal_cond(H, psi)
Ez, AT = compute_z_moments(w_s, eta, H, psi)
eta, H, psi = identifiable_estim_DGMM(eta, H, psi, Ez, AT)
del (Ez)
#=======================================================
# Compute GLLVM Parameters
#=======================================================
# We optimize each column separately as it is faster than all column jointly
# (and more relevant with the independence hypothesis)
lambda_bin = bin_params_GLLVM(y_bin, nj_bin, lambda_bin, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
lambda_ord = ord_params_GLLVM(y_ord, nj_ord, lambda_ord, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
lambda_categ = categ_params_GLLVM(y_categ, nj_categ, lambda_categ, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
###########################################################################
################## Clustering parameters updating #########################
###########################################################################
new_lik = np.sum(np.log(p_y))
likelihood.append(new_lik)
ratio = (new_lik - prev_lik) / abs(prev_lik)
print(likelihood)
idx_to_sum = tuple(set(range(1, L + 1)) - set([clustering_layer + 1]))
psl_y = ps_y.reshape(numobs, *k, order='C').sum(idx_to_sum)
temp_class = np.argmax(psl_y, axis=1)
try:
new_sil = silhouette_score(dm, temp_class, metric='precomputed')
except ValueError:
new_sil = -1
print('Silhouette score:', new_sil)
if best_sil < new_sil:
z = (ps_y[..., n_axis] * Ez_ys[clustering_layer]).sum(1)
best_sil = deepcopy(new_sil)
classes = deepcopy(temp_class)
fig = plt.figure(figsize=(8, 8))
plt.scatter(z[:, 0], z[:, 1])
plt.show()
# Refresh the classes only if they provide a better explanation of the data
if best_lik < new_lik:
best_lik = deepcopy(prev_lik)
if prev_lik < new_lik:
patience = 0
M = M_growth(it_num + 2, r, numobs)
else:
patience += 1
###########################################################################
######################## Parameter selection #############################
###########################################################################
is_not_min_specif = not (np.all(np.array(k) == n_clusters)
& np.array_equal(r, [2, 1]))
if look_for_simpler_network(
it_num) & perform_selec & is_not_min_specif:
r_to_keep = r_select(y_bin, y_ord, y_categ, zl1_ys, z2_z1s, w_s)
# If r_l == 0, delete the last l + 1: layers
new_L = np.sum([len(rl) != 0 for rl in r_to_keep]) - 1
k_to_keep = k_select(w_s, k, new_L, clustering_layer)
is_L_unchanged = L == new_L
is_r_unchanged = np.all(
[len(r_to_keep[l]) == r[l] for l in range(new_L + 1)])
is_k_unchanged = np.all(
[len(k_to_keep[l]) == k[l] for l in range(new_L)])
is_selection = not (is_r_unchanged & is_k_unchanged
& is_L_unchanged)
assert new_L > 0
if is_selection:
eta = [eta[l][k_to_keep[l]] for l in range(new_L)]
eta = [eta[l][:, r_to_keep[l]] for l in range(new_L)]
H = [H[l][k_to_keep[l]] for l in range(new_L)]
H = [H[l][:, r_to_keep[l]] for l in range(new_L)]
H = [H[l][:, :, r_to_keep[l + 1]] for l in range(new_L)]
psi = [psi[l][k_to_keep[l]] for l in range(new_L)]
psi = [psi[l][:, r_to_keep[l]] for l in range(new_L)]
psi = [psi[l][:, :, r_to_keep[l]] for l in range(new_L)]
if nb_bin > 0:
# Add the intercept:
bin_r_to_keep = np.concatenate([[0],
np.array(r_to_keep[0]) + 1
])
lambda_bin = lambda_bin[:, bin_r_to_keep]
if nb_ord > 0:
# Intercept coefficients handling is a little more complicated here
lambda_ord_intercept = [
lambda_ord_j[:-r[0]] for lambda_ord_j in lambda_ord
]
Lambda_ord_var = np.stack(
[lambda_ord_j[-r[0]:] for lambda_ord_j in lambda_ord])
Lambda_ord_var = Lambda_ord_var[:, r_to_keep[0]]
lambda_ord = [np.concatenate([lambda_ord_intercept[j], Lambda_ord_var[j]])\
for j in range(nb_ord)]
if nb_categ > 0:
lambda_categ_intercept = [
lambda_categ[j][:, 0] for j in range(nb_categ)
]
Lambda_categ_var = [
lambda_categ_j[:, -r[0]:]
for lambda_categ_j in lambda_categ
]
Lambda_categ_var = [
lambda_categ_j[:, r_to_keep[0]]
for lambda_categ_j in lambda_categ
]
lambda_categ = [np.hstack([lambda_categ_intercept[j][..., n_axis], Lambda_categ_var[j]])\
for j in range(nb_categ)]
w = w_s.reshape(*k, order='C')
new_k_idx_grid = np.ix_(*k_to_keep[:new_L])
# If layer deletion, sum the last components of the paths
if L > new_L:
deleted_dims = tuple(range(L)[new_L:])
w_s = w[new_k_idx_grid].sum(deleted_dims).flatten(
order='C')
else:
w_s = w[new_k_idx_grid].flatten(order='C')
w_s /= w_s.sum()
k = [len(k_to_keep[l]) for l in range(new_L)]
r = [len(r_to_keep[l]) for l in range(new_L + 1)]
k_aug = k + [1]
S = np.array([np.prod(k_aug[l:]) for l in range(new_L + 1)])
L = new_L
patience = 0
best_r = deepcopy(r)
best_k = deepcopy(k)
# Identifiability conditions
H = diagonal_cond(H, psi)
Ez, AT = compute_z_moments(w_s, eta, H, psi)
eta, H, psi = identifiable_estim_DGMM(eta, H, psi, Ez, AT)
print('New architecture:')
print('k', k)
print('r', r)
print('L', L)
print('S', S)
print("w_s", len(w_s))
prev_lik = deepcopy(new_lik)
it_num = it_num + 1
out = dict(likelihood = likelihood, classes = classes, z = z, \
best_r = best_r, best_k = best_k)
return (out)
def M1DGMM(y, n_clusters, r, k, init, var_distrib, nj, it = 50, \
eps = 1E-05, maxstep = 100, seed = None, perform_selec = True,\
dm = [], max_patience = 1, use_silhouette = True):# dm small hack to remove
''' Fit a Generalized Linear Mixture of Latent Variables Model (GLMLVM)
y (numobs x p ndarray): The observations containing mixed variables
n_clusters (int): The number of clusters to look for in the data
r (list): The dimension of latent variables through the first 2 layers
k (list): The number of components of the latent Gaussian mixture layers
init (dict): The initialisation parameters for the algorithm
var_distrib (p 1darray): An array containing the types of the variables in y
nj (p 1darray): For binary/count data: The maximum values that the variable can take.
For ordinal data: the number of different existing categories for each variable
it (int): The maximum number of MCEM iterations of the algorithm
eps (float): If the likelihood increase by less than eps then the algorithm stops
maxstep (int): The maximum number of optimisation step for each variable
seed (int): The random state seed to set (Only for numpy generated data for the moment)
perform_selec (Bool): Whether to perform architecture selection or not
use_silhouette (Bool): If True use the silhouette as quality criterion (best for clustering) else use
the likelihood (best for data augmentation).
------------------------------------------------------------------------------------------------
returns (dict): The predicted classes, the likelihood through the EM steps
and a continuous representation of the data
'''
prev_lik = - 1E16
best_lik = -1E16
best_sil = -1
new_sil = -1
tol = 0.01
patience = 0
is_looking_for_better_arch = False
# Initialize the parameters
eta = deepcopy(init['eta'])
psi = deepcopy(init['psi'])
lambda_bin = deepcopy(init['lambda_bin'])
lambda_ord = deepcopy(init['lambda_ord'])
lambda_cont = deepcopy(init['lambda_cont'])
lambda_categ = deepcopy(init['lambda_categ'])
H = deepcopy(init['H'])
w_s = deepcopy(init['w_s']) # Probability of path s' through the network for all s' in Omega
numobs = len(y)
likelihood = []
silhouette = []
it_num = 0
ratio = 1000
np.random.seed = seed
out = {} # Store the full output
# Dispatch variables between categories
y_bin = y[:, np.logical_or(var_distrib == 'bernoulli',var_distrib == 'binomial')]
nj_bin = nj[np.logical_or(var_distrib == 'bernoulli',var_distrib == 'binomial')].astype(int)
nb_bin = len(nj_bin)
y_ord = y[:, var_distrib == 'ordinal']
nj_ord = nj[var_distrib == 'ordinal'].astype(int)
nb_ord = len(nj_ord)
y_categ = y[:, var_distrib == 'categorical']
nj_categ = nj[var_distrib == 'categorical'].astype(int)
nb_categ = len(nj_categ)
y_cont = y[:, var_distrib == 'continuous'].astype(float)
nb_cont = y_cont.shape[1]
# Set y_count standard error to 1
y_cont = y_cont / y_cont.std(axis = 0, keepdims = True)
L = len(k)
k_aug = k + [1]
S = np.array([np.prod(k_aug[l:]) for l in range(L + 1)])
M = M_growth(1, r, numobs)
assert nb_bin + nb_ord + nb_cont + nb_categ > 0
if nb_bin + nb_ord + nb_cont + nb_categ != len(var_distrib):
raise ValueError('Some variable types were not understood,\
existing types are: continuous, categorical,\
ordinal, binomial and bernoulli')
# Compute the Gower matrix
if len(dm) == 0:
cat_features = np.logical_or(var_distrib == 'categorical', var_distrib == 'bernoulli')
dm = gower_matrix(y, cat_features = cat_features)
# Do not stop the iterations if there are some iterations left or if the likelihood is increasing
# or if we have not reached the maximum patience and if a new architecture was looked for
# in the previous iteration
while ((it_num < it) & (ratio > eps) & (patience <= max_patience)) | is_looking_for_better_arch:
print(it_num)
# The clustering layer is the one used to perform the clustering
# i.e. the layer l such that k[l] == n_clusters
if not(isnumeric(n_clusters)):
if n_clusters == 'auto':
clustering_layer = 0
else:
raise ValueError('Please enter an int or "auto" for n_clusters')
else:
assert (np.array(k) == n_clusters).any()
clustering_layer = np.argmax(np.array(k) == n_clusters)
#####################################################################################
################################# S step ############################################
#####################################################################################
#=====================================================================
# Draw from f(z^{l} | s, Theta) for all s in Omega
#=====================================================================
mu_s, sigma_s = compute_path_params(eta, H, psi)
sigma_s = ensure_psd(sigma_s)
z_s, zc_s = draw_z_s(mu_s, sigma_s, eta, M)
#========================================================================
# Draw from f(z^{l+1} | z^{l}, s, Theta) for l >= 1
#========================================================================
chsi = compute_chsi(H, psi, mu_s, sigma_s)
chsi = ensure_psd(chsi)
rho = compute_rho(eta, H, psi, mu_s, sigma_s, zc_s, chsi)
# In the following z2 and z1 will denote z^{l+1} and z^{l} respectively
z2_z1s = draw_z2_z1s(chsi, rho, M, r)
#=======================================================================
# Compute the p(y| z1) for all variable categories
#=======================================================================
py_zl1 = fy_zl1(lambda_bin, y_bin, nj_bin, lambda_ord, y_ord, nj_ord, \
lambda_categ, y_categ, nj_categ, y_cont, lambda_cont, z_s[0])
#========================================================================
# Draw from p(z1 | y, s) proportional to p(y | z1) * p(z1 | s) for all s
#========================================================================
zl1_ys = draw_zl1_ys(z_s, py_zl1, M)
#####################################################################################
################################# E step ############################################
#####################################################################################
#=====================================================================
# Compute conditional probabilities used in the appendix of asta paper
#=====================================================================
pzl1_ys, ps_y, p_y = E_step_GLLVM(z_s[0], mu_s[0], sigma_s[0], w_s, py_zl1)
#=====================================================================
# Compute p(z^{(l)}| s, y). Equation (5) of the paper
#=====================================================================
pz2_z1s = fz2_z1s(t(pzl1_ys, (1, 0, 2)), z2_z1s, chsi, rho, S)
pz_ys = fz_ys(t(pzl1_ys, (1, 0, 2)), pz2_z1s)
#=====================================================================
# Compute MFA expectations
#=====================================================================
Ez_ys, E_z1z2T_ys, E_z2z2T_ys, EeeT_ys = \
E_step_DGMM(zl1_ys, H, z_s, zc_s, z2_z1s, pz_ys, pz2_z1s, S)
###########################################################################
############################ M step #######################################
###########################################################################
#=======================================================
# Compute MFA Parameters
#=======================================================
w_s = np.mean(ps_y, axis = 0)
eta, H, psi = M_step_DGMM(Ez_ys, E_z1z2T_ys, E_z2z2T_ys, EeeT_ys, ps_y, H, k)
#=======================================================
# Identifiability conditions
#=======================================================
# Update eta, H and Psi values
H = diagonal_cond(H, psi)
Ez, AT = compute_z_moments(w_s, eta, H, psi)
eta, H, psi = identifiable_estim_DGMM(eta, H, psi, Ez, AT)
del(Ez)
#=======================================================
# Compute GLLVM Parameters
#=======================================================
lambda_bin = bin_params_GLLVM(y_bin, nj_bin, lambda_bin, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
lambda_ord = ord_params_GLLVM(y_ord, nj_ord, lambda_ord, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
lambda_categ = categ_params_GLLVM(y_categ, nj_categ, lambda_categ, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
lambda_cont = cont_params_GLLVM(y_cont, lambda_cont, ps_y, pzl1_ys, z_s[0], AT[0],\
tol = tol, maxstep = maxstep)
###########################################################################
################## Clustering parameters updating #########################
###########################################################################
new_lik = np.sum(np.log(p_y))
likelihood.append(new_lik)
silhouette.append(new_sil)
ratio = abs((new_lik - prev_lik)/prev_lik)
idx_to_sum = tuple(set(range(1, L + 1)) - set([clustering_layer + 1]))
psl_y = ps_y.reshape(numobs, *k, order = 'C').sum(idx_to_sum)
temp_class = np.argmax(psl_y, axis = 1)
try:
new_sil = silhouette_score(dm, temp_class, metric = 'precomputed')
except ValueError:
new_sil = -1
# Store the params according to the silhouette or likelihood
is_better = (best_sil < new_sil) if use_silhouette else (best_lik < new_lik)
if is_better:
z = (ps_y[..., n_axis] * Ez_ys[clustering_layer]).sum(1)
best_sil = deepcopy(new_sil)
classes = deepcopy(temp_class)
'''
plt.figure(figsize=(8,8))
plt.scatter(z[:, 0], z[:, 1], c = classes)
plt.show()
'''
# Store the output
out['classes'] = deepcopy(classes)
out['best_z'] = deepcopy(z_s[0])
out['Ez.y'] = z
out['best_k'] = deepcopy(k)
out['best_r'] = deepcopy(r)
out['best_w_s'] = deepcopy(w_s)
out['lambda_bin'] = deepcopy(lambda_bin)
out['lambda_ord'] = deepcopy(lambda_ord)
out['lambda_categ'] = deepcopy(lambda_categ)
out['lambda_cont'] = deepcopy(lambda_cont)
out['eta'] = deepcopy(eta)
out['mu'] = deepcopy(mu_s)
out['sigma'] = deepcopy(sigma_s)
out['psl_y'] = deepcopy(psl_y)
out['ps_y'] = deepcopy(ps_y)
# Refresh the classes only if they provide a better explanation of the data
if best_lik < new_lik:
best_lik = deepcopy(prev_lik)
if prev_lik < new_lik:
patience = 0
M = M_growth(it_num + 2, r, numobs)
else:
patience += 1
###########################################################################
######################## Parameter selection #############################
###########################################################################
min_nb_clusters = 2
if isnumeric(n_clusters): # To change when add multi mode
is_not_min_specif = not(np.all(np.array(k) == n_clusters) & np.array_equal(r, [2,1]))
else:
is_not_min_specif = not(np.all(np.array(k) == min_nb_clusters) & np.array_equal(r, [2,1]))
is_looking_for_better_arch = look_for_simpler_network(it_num) & perform_selec & is_not_min_specif
if is_looking_for_better_arch:
r_to_keep = r_select(y_bin, y_ord, y_categ, y_cont, zl1_ys, z2_z1s, w_s)
# If r_l == 0, delete the last l + 1: layers
new_L = np.sum([len(rl) != 0 for rl in r_to_keep]) - 1
k_to_keep = k_select(w_s, k, new_L, clustering_layer, not(isnumeric(n_clusters)))
is_L_unchanged = (L == new_L)
is_r_unchanged = np.all([len(r_to_keep[l]) == r[l] for l in range(new_L + 1)])
is_k_unchanged = np.all([len(k_to_keep[l]) == k[l] for l in range(new_L)])
is_selection = not(is_r_unchanged & is_k_unchanged & is_L_unchanged)
assert new_L > 0
if is_selection:
eta = [eta[l][k_to_keep[l]] for l in range(new_L)]
eta = [eta[l][:, r_to_keep[l]] for l in range(new_L)]
H = [H[l][k_to_keep[l]] for l in range(new_L)]
H = [H[l][:, r_to_keep[l]] for l in range(new_L)]
H = [H[l][:, :, r_to_keep[l + 1]] for l in range(new_L)]
psi = [psi[l][k_to_keep[l]] for l in range(new_L)]
psi = [psi[l][:, r_to_keep[l]] for l in range(new_L)]
psi = [psi[l][:, :, r_to_keep[l]] for l in range(new_L)]
if nb_bin > 0:
# Add the intercept:
bin_r_to_keep = np.concatenate([[0], np.array(r_to_keep[0]) + 1])
lambda_bin = lambda_bin[:, bin_r_to_keep]
if nb_ord > 0:
# Intercept coefficients handling is a little more complicated here
lambda_ord_intercept = [lambda_ord_j[:-r[0]] for lambda_ord_j in lambda_ord]
Lambda_ord_var = np.stack([lambda_ord_j[-r[0]:] for lambda_ord_j in lambda_ord])
Lambda_ord_var = Lambda_ord_var[:, r_to_keep[0]]
lambda_ord = [np.concatenate([lambda_ord_intercept[j], Lambda_ord_var[j]])\
for j in range(nb_ord)]
# To recheck
if nb_cont > 0:
# Add the intercept:
cont_r_to_keep = np.concatenate([[0], np.array(r_to_keep[0]) + 1])
lambda_cont = lambda_cont[:, cont_r_to_keep]
if nb_categ > 0:
lambda_categ_intercept = [lambda_categ[j][:, 0] for j in range(nb_categ)]
Lambda_categ_var = [lambda_categ_j[:,-r[0]:] for lambda_categ_j in lambda_categ]
Lambda_categ_var = [lambda_categ_j[:, r_to_keep[0]] for lambda_categ_j in lambda_categ]
lambda_categ = [np.hstack([lambda_categ_intercept[j][..., n_axis], Lambda_categ_var[j]])\
for j in range(nb_categ)]
w = w_s.reshape(*k, order = 'C')
new_k_idx_grid = np.ix_(*k_to_keep[:new_L])
# If layer deletion, sum the last components of the paths
if L > new_L:
deleted_dims = tuple(range(L)[new_L:])
w_s = w[new_k_idx_grid].sum(deleted_dims).flatten(order = 'C')
else:
w_s = w[new_k_idx_grid].flatten(order = 'C')
w_s /= w_s.sum()
# Refresh the classes: TO RECHECK
#idx_to_sum = tuple(set(range(1, L + 1)) - set([clustering_layer + 1]))
#ps_y_tmp = ps_y.reshape(numobs, *k, order = 'C').sum(idx_to_sum)
#np.argmax(ps_y_tmp[:, k_to_keep[0]], axis = 1)
k = [len(k_to_keep[l]) for l in range(new_L)]
r = [len(r_to_keep[l]) for l in range(new_L + 1)]
k_aug = k + [1]
S = np.array([np.prod(k_aug[l:]) for l in range(new_L + 1)])
L = new_L
patience = 0
# Identifiability conditions
H = diagonal_cond(H, psi)
Ez, AT = compute_z_moments(w_s, eta, H, psi)
eta, H, psi = identifiable_estim_DGMM(eta, H, psi, Ez, AT)
del(Ez)
print('New architecture:')
print('k', k)
print('r', r)
print('L', L)
print('S',S)
print("w_s", len(w_s))
prev_lik = deepcopy(new_lik)
it_num = it_num + 1
print(likelihood)
print(silhouette)
out['likelihood'] = likelihood
out['silhouette'] = silhouette
return(out)