def PCA_fromfile(fname, toFloat=False):
pca = ndict.loadz(fname)
return PCA_encdec(pca['eigvec'],pca['eigval'],pca['x_center'],pca['x_sd'], toFloat)
def main(n_z, n_hidden, dataset, seed, comment, gfx=True):
# Initialize logdir
import time
pre_dir = 'models/gpulearn_z_x_mnist_96-(500, 500)'
if os.environ.has_key('pretrain') and bool(int(os.environ['pretrain'])) == True:
comment+='_pre-train'
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
comment+='_prior'
pre_dir+='_prior'
if os.environ.has_key('cutoff'):
comment+=('_'+str(int(os.environ['cutoff'])))
if os.environ.has_key('train_residual') and bool(int(os.environ['train_residual'])) == True:
comment+='_train-residual'
pre_dir+='_train-residual'
if os.environ.has_key('sigma_square'):
comment+=('_'+str(float(os.environ['sigma_square'])))
pre_dir+=('_'+str(float(os.environ['sigma_square'])))
pre_dir+='/'
logdir = 'results/gpulearn_z_x_'+dataset+'_'+str(n_z)+'-'+str(n_hidden)+comment+'_'+str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
print 'gpulearn_z_x', n_z, n_hidden, dataset, seed
with open(logdir+'hook.txt', 'a') as f:
print >>f, 'learn_z_x', n_z, n_hidden, dataset, seed
np.random.seed(seed)
gfx_freq = 1
weight_decay = 0
# Init data
if dataset == 'mnist':
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size)
f_enc, f_dec = pp.Identity()
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
color.printBlue('Loading prior')
mnist_prior = sio.loadmat('data/mnist_prior/mnist_prior.mat')
train_mean_prior = mnist_prior['z_train']
test_mean_prior = mnist_prior['z_test']
valid_mean_prior = mnist_prior['z_valid']
else:
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
print '---------------------', type(train_x)
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
print '---------------------', type(x_train)
L_valid = 1
dim_input = (size,size)
n_x = size*size
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 50000
n_test = 10000
n_valid = 10000
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'higgs':
size = 28
f_enc, f_dec = pp.Identity()
inputfile = 'data/higgs/HIGGS.csv'
print 'loading file.'
x = np.loadtxt(inputfile, dtype='f4', delimiter=',')
print 'done.'
y = x[:,0].reshape((-1,1))
x = x[:,1:]
x = np.array(x, dtype='float32')
y = np.array(y, dtype='float32')
n_train = 10000000
n_valid = 500000
n_test = 500000
n_batch = 1000
derived_feat = 'all'
if os.environ.has_key('derived_feat'):
derived_feat = os.environ['derived_feat']
color.printBlue(derived_feat)
if derived_feat == 'high':
# Only the 7 high level features.
x = x[:, 21:28]
elif derived_feat == 'low':
# Only the 21 raw features.
x = x[:, 0:21]
else:
pass
train_x = x[0:n_train, :].T
y_train = y[0:n_train, :]
valid_x = x[n_train:n_train+n_valid, :].T
y_valid = y[n_train:n_train+n_valid, :]
test_x = x[n_train+n_valid:n_train+n_valid+n_test, :].T
y_test = y[n_train+n_valid:n_train+n_valid+n_test, :]
n_y = 2
n_x = train_x.shape[0]
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'tanh'
if os.environ.has_key('nonlinear'):
nonlinear = os.environ['nonlinear']
color.printBlue(nonlinear)
L_valid = 1
dim_input = (1,size)
type_px = 'gaussian'
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'cifar10':
import anglepy.data.cifar10 as cifar10
size = 32
train_x, train_y, test_x, test_y = cifar10.load_numpy()
train_x = train_x.astype(np.float32).T
test_x = test_x.astype(np.float32).T
##
f_enc, f_dec = pp.Identity()
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
color.printBlue('Loading prior')
cifar_prior = sio.loadmat('data/cifar10_prior/cifar10_prior.mat')
train_mean_prior = cifar_prior['z_train']
test_mean_prior = cifar_prior['z_test']
else:
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
x_valid = x_test
L_valid = 1
n_y = 10
dim_input = (size,size)
n_x = x['x'].shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'gaussian'
if os.environ.has_key('type_px'):
type_px = os.environ['type_px']
color.printBlue('Generative type: '+type_px)
n_train = 50000
n_test = 10000
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
#weight_decay = float(n_batch)/n_train
elif dataset == 'cifar10_zca':
import anglepy.data.cifar10 as cifar10
size = 32
train_x, train_y, test_x, test_y = cifar10.load_numpy()
train_x = train_x.astype(np.float32).T
test_x = test_x.astype(np.float32).T
##
f_enc, f_dec = pp.Identity()
zca_mean, zca_w, zca_winv = cifar10.zca(train_x)
train_x = zca_w.dot(train_x-zca_mean)
test_x = zca_w.dot(test_x-zca_mean)
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
color.printBlue('Loading prior')
cifar_prior = sio.loadmat('data/cifar10_prior/cifar10_prior.mat')
train_mean_prior = cifar_prior['z_train']
test_mean_prior = cifar_prior['z_test']
else:
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
x_valid = x_test
L_valid = 1
dim_input = (size,size)
n_y = 10
n_x = x['x'].shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'gaussian'
n_train = 50000
n_test = 10000
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
if os.environ.has_key('type_px'):
type_px = os.environ['type_px']
color.printBlue('Generative type: '+type_px)
nonlinear = 'softplus'
elif dataset == 'mnist_basic':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_'
tmp = sio.loadmat(data_dir+'train.mat')
#color.printRed(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'rectangle':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'rectangles_'
tmp = sio.loadmat(data_dir+'train.mat')
color.printRed(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,1000:]
valid_y = train_y[1000:]
train_x = train_x[:,:1000]
train_y = train_y[:1000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 1000
n_valid = 200
n_test = 50000
n_batch = 500
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
#print '3', n_x
elif dataset == 'convex':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'convex_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,6000:]
valid_y = train_y[6000:]
train_x = train_x[:,:6000]
train_y = train_y[:6000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 6000
n_valid = 2000
n_test = 50000
n_batch = 120
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'rectangle_image':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'rectangles_im_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_rot':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_all_rotation_normalized_float_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
f_enc, f_dec = pp.Identity()
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_rand':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_background_random_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
f_enc, f_dec = pp.Identity()
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_image':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_background_images_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
f_enc, f_dec = pp.Identity()
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_image_rot':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_all_background_images_rotation_normalized_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
f_enc, f_dec = pp.Identity()
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_binarized':
#import anglepy.data.mnist_binarized as mnist_binarized
# MNIST
import anglepy.data.mnist as mnist
size = 28
data_dir = '/home/lichongxuan/regbayes2/data/mat_data/'+'binarized_mnist_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
#train_y = tmp['t_train'].T.astype(np.int32)
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
tmp = sio.loadmat(data_dir+'valid.mat')
#print tmp.keys()
valid_x = tmp['x_valid'].T
#test_y = tmp['t_test'].T.astype(np.int32)
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
train_x = np.hstack((train_x, valid_x)).astype(np.float32)
train_mean_prior = np.hstack((train_mean_prior,valid_mean_prior)).astype(np.float32)
print train_mean_prior.shape
print train_x.shape
x = {'x': train_x.astype(np.float32), 'mean_prior':train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': test_x.astype(np.float32),'mean_prior':test_mean_prior.astype(np.float32)}
x_test = x_valid
L_valid = 1
dim_input = (28,28)
n_x = 28*28
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 60000
n_valid = 10000
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_binarized_own':
#import anglepy.data.mnist_binarized as mnist_binarized
# MNIST
import anglepy.data.mnist as mnist
size = 28
data_dir = 'data/mnist_binarized_own/'+'binarized_mnist_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['train_x'].T
#train_y = tmp['t_train'].T.astype(np.int32)
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['test_x'].T
tmp = sio.loadmat(data_dir+'valid.mat')
#print tmp.keys()
valid_x = tmp['valid_x'].T
#test_y = tmp['t_test'].T.astype(np.int32)
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
train_x = np.hstack((train_x, valid_x)).astype(np.float32)
train_mean_prior = np.hstack((train_mean_prior,valid_mean_prior)).astype(np.float32)
print train_mean_prior.shape
print train_x.shape
x = {'x': train_x.astype(np.float32), 'mean_prior':train_mean_prior.astype(np.float32)}
x_train = x
x_valid = {'x': test_x.astype(np.float32),'mean_prior':test_mean_prior.astype(np.float32)}
x_test = x_valid
L_valid = 1
dim_input = (28,28)
n_x = 28*28
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 60000
n_valid = 10000
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'freyface':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy()
np.random.shuffle(train_x)
x = {'x': train_x.T[:,0:n_train]}
x_valid = {'x': train_x.T[:,n_train:]}
L_valid = 1
dim_input = (28,20)
n_x = 20*28
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'bounded01'
nonlinear = 'tanh' #tanh works better with freyface #'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'freyface_pca':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
train_x = f_enc(train_x)
x = {'x': train_x[:,0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:,n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28,20)
n_x = train_x.shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'freyface_bernoulli':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
x = {'x': train_x[:,0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:,n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28,20)
n_x = train_x.shape[0]
type_pz = 'gaussianmarg'
type_px = 'bernoulli'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'norb_48_24300_pca':
size = 48
train_x, train_y, test_x, test_y = np.load('data/norb/norb_48_24300.npy')
_x = {'x': train_x, 'y': train_y}
#ndict.shuffleCols(_x)
#train_x = _x['x']
#train_y = _x['y']
#print _x['x'][:,:10000].shape
# Do PCA
print 'pca'
f_enc, f_dec, pca_params = pp.PCA(_x['x'][:,:10000], cutoff=500, toFloat=False)
ndict.savez(pca_params, logdir+'pca_params')
print 'done'
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
x = {'x': f_enc(train_x).astype(np.float32), 'mean_prior' : train_mean_prior.astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32), 'mean_prior' : test_mean_prior.astype(np.float32)}
x_test = {'x': f_enc(test_x).astype(np.float32), 'mean_prior' : test_mean_prior.astype(np.float32)}
x_train = x
print x['x'].shape
print x['mean_prior'].shape
L_valid = 1
n_y = 5
n_x = x['x'].shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'norb':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
byteToFloat = False
bernoulli_x = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'norb_pca':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
f_enc, f_dec, _ = pp.PCA(train_x, 0.999)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'norb_normalized':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
#f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
f_enc, f_dec, _ = pp.normalize(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'svhn':
# SVHN dataset
#import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = np.load('data/svhn/svhn.npy')
#extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
#x = {'x': np.hstack((train_x, extra_x)), 'y':np.hstack((train_y, extra_y))}
#ndict.shuffleCols(x)
x = {'x' : train_x, 'y': train_y}
print 'Performing PCA, can take a few minutes... '
cutoff = 300
if os.environ.has_key('cutoff'):
cutoff = int(os.environ['cutoff'])
color.printBlue('cutoff: '+str(cutoff))
f_enc, f_dec, pca_params = pp.PCA(x['x'][:,:10000], cutoff=cutoff, toFloat=True)
ndict.savez(pca_params, logdir+'pca_params')
print 'Done.'
n_y = 10
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
color.printBlue('Loading prior')
train_mean_prior, train_y1, test_mean_prior, test_y1 = np.load('data/svhn/svhn_prior.npy')
print np.sum((train_y1 == train_y).astype(np.int32))
print np.sum((test_y1 == test_y).astype(np.int32))
else:
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
x = {'x': f_enc(x['x']).astype(np.float32), 'mean_prior':train_mean_prior.astype(np.float32)}
x_train = x
x_test = {'x': f_enc(test_x).astype(np.float32), 'mean_prior':test_mean_prior.astype(np.float32)}
x_valid = x_test
print x_train['x'].shape
print x_test['x'].shape
print train_y.shape
print test_y.shape
print x_train['mean_prior'].shape
print x_test['mean_prior'].shape
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size,size)
n_batch = 5000
n_train = 604388
n_valid = 26032
n_test = 26032
colorImg = True
bernoulli_x = False
byteToFloat = False
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
else:
print 'invalid data set'
exit()
#print '2', n_x
# Construct model
from anglepy.models import GPUVAE_Z_X
learning_rate1 = 3e-4
if os.environ.has_key('stepsize'):
learning_rate1 = float(os.environ['stepsize'])
color.printBlue(str(learning_rate1))
if os.environ.has_key('preoption'):
pre = int(os.environ['preoption'])
if pre == 1:
updates = get_adam_optimizer(learning_rate=3e-4, decay1=0.9, decay2=0.999, weight_decay=0)
elif pre ==2:
updates = get_adam_optimizer(learning_rate=3e-4, decay1=0.9, decay2=0.999, weight_decay=weight_decay)
else:
raise Exception('Prepotion unknown')
with open(logdir+'hook.txt', 'a') as f:
print >>f, 'preoption ' + str(pre)
else:
updates = get_adam_optimizer(learning_rate=learning_rate1, weight_decay=weight_decay)
#print '1', n_x
model = GPUVAE_Z_X(updates, n_x, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-3)
if os.environ.has_key('pretrain') and bool(int(os.environ['pretrain'])) == True:
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412689061/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412676966/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412695481/'
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412695455/'
#dir = '/Users/dpkingma/results/gpulearn_z_x_svhn_pca_300-(500, 500)__1413904756/'
if len(n_hidden) == 1:
color.printBlue('pre-training-1-layer')
layer_str = '-500'
elif len(n_hidden) == 2:
color.printBlue('pre-training-2-layers')
layer_str = '-(500, 500)'
else:
raise Exception()
pre_str = 'models/gpulearn_z_x_'
if dataset == 'mnist':
#dir = pre_str + 'mnist_'+str(n_z)+layer_str+'_longrun/'
dir = 'models/mnist_z_x_50-500-500_longrun/'
elif dataset == 'mnist_rot':
dir = pre_str + 'mnist_rot_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'mnist_back_rand':
dir = pre_str + 'mnist_back_rand_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'mnist_back_image':
dir = pre_str + 'mnist_back_image_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'mnist_back_image_rot':
dir = pre_str + 'mnist_back_image_rot_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'rectangle':
dir = pre_str + 'rectangle_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'rectangle_image':
dir = pre_str + 'rectangle_image_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'convex':
dir = pre_str + 'convex_'+str(n_z)+layer_str+'_longrun/'
elif dataset == 'mnist_basic':
dir = pre_str + 'mnist_basic_'+str(n_z)+layer_str+'_longrun/'
if dataset == 'svhn':
if (os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True):
print 'prior-------------------'
pre_dir = 'results/gpulearn_z_x_svhn_'+str(n_z)+'-500-500_prior_'+str(cutoff)+'_longrun/'
else:
pre_dir = 'results/gpulearn_z_x_svhn_'+str(n_z)+'-500-500_'+str(cutoff)+'_longrun/'
color.printBlue(pre_dir)
w = ndict.loadz(pre_dir+'w_best.ndict.tar.gz')
v = ndict.loadz(pre_dir+'v_best.ndict.tar.gz')
elif n_z == 50:
print 'n_z = 50', dir
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
else:
print 'n_z != 50'
w = ndict.loadz(pre_dir+'w_best.ndict.tar.gz')
v = ndict.loadz(pre_dir+'v_best.ndict.tar.gz')
ndict.set_value2(model.w, w)
ndict.set_value2(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Progress hook
def hook(epoch, t, ll):
if epoch%10 != 0: return
n_batch_n = n_batch
if n_batch_n > n_valid:
n_batch_n = n_valid
ll_valid, _ = model.est_loglik(x_valid, n_samples=L_valid, n_batch=n_batch_n, byteToFloat=byteToFloat)
ll_test = ll_valid
#if not dataset == 'mnist_binarized':
if not dataset == 'svhn':
ll_test, _ = model.est_loglik(x_test, n_samples=L_valid, n_batch=n_batch, byteToFloat=byteToFloat)
# Log
ndict.savez(ndict.get_value(model.v), logdir+'v')
ndict.savez(ndict.get_value(model.w), logdir+'w')
def infer(data, n_batch=1000):
#print '--', n_batch
size = data['x'].shape[1]
res = np.zeros((sum(n_hidden), size))
res1 = np.zeros((n_z,size))
res2 = np.zeros((n_hidden[-1],size))
res3 = np.zeros((n_z,size))
for i in range(0, size, n_batch):
idx_to = min(size, i+n_batch)
x_batch = ndict.getCols(data, i, idx_to)
# may have bugs
nn_batch = idx_to - i
_x, _z, _z_confab = model.gen_xz(x_batch, {}, nn_batch)
x_samples = _z_confab['x']
for (hi, hidden) in enumerate(_z_confab['hidden']):
res[sum(n_hidden[:hi]):sum(n_hidden[:hi+1]),i:i+nn_batch] = hidden
res1[:,i:i+nn_batch] = _z_confab['mean']
res2[:,i:i+nn_batch] = _z_confab['hidden'][-1]
res3[:,i:i+nn_batch] = _z_confab['logvar']
#print '--'
return res, res1, res2, res3
#print '..', n_batch
#if not dataset == 'mnist_binarized':
if not dataset == 'svhn':
z_test, z_test1, z_test2, vv_test = infer(x_test)
z_train, z_train1, z_train2, vv_train = infer(x_train)
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir+'v_best')
ndict.savez(ndict.get_value(model.w), logdir+'w_best')
#if not dataset == 'mnist_binarized':
if dataset == 'svhn':
pass
#np.save(logdir+'full_latent', ('z_test': z_test, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train))
#np.save(logdir+'last_latent', ('z_test': z_test2, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train2))
else:
sio.savemat(logdir+'full_latent.mat', {'z_test': z_test, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train})
sio.savemat(logdir+'mean_latent.mat', {'z_test': z_test1, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train1})
sio.savemat(logdir+'last_latent.mat', {'z_test': z_test2, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train2})
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir+'hook.txt', 'a') as f:
print >>f, "Finished"
exit()
print epoch, t, ll, ll_valid, ll_test, ll_valid_stats
with open(logdir+'hook.txt', 'a') as f:
print >>f, epoch, t, ll, ll_valid, ll_test, ll_valid_stats
'''
if dataset != 'svhn':
l_t, px_t, pz_t, qz_t = model.test(x_train, n_samples=1, n_batch=n_batch, byteToFloat=byteToFloat)
print 'Elogpx', px_t, 'Elogpz', pz_t, '-Elogqz', qz_t
#sigma_square = float(os.environ['sigma_square'])
print 'var', np.mean(np.exp(vv_train)), 'q', np.mean(np.abs(z_train1)), 'p', np.mean(np.abs(train_mean_prior)), 'd', np.mean(np.abs(z_train1-train_mean_prior))
with open(logdir+'hook.txt', 'a') as f:
print >>f, 'Elogpx', px_t, 'Elogpz', pz_t, '-Elogqz', qz_t
print >>f, 'var', np.mean(np.exp(vv_train)), 'q', np.mean(np.abs(z_train1)), 'p', np.mean(np.abs(train_mean_prior)), 'd', np.mean(np.abs(z_train1-train_mean_prior))
'''
# Graphics
if gfx and epoch%gfx_freq == 0:
#tail = '.png'
tail = '-'+str(epoch)+'.png'
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
if 'pca' not in dataset and 'random' not in dataset and 'normalized' not in dataset and 'zca' not in dataset:
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
if 'out_unif' in w:
image = paramgraphics.mat_to_img(f_dec(w['out_unif'].reshape((-1,1))), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_unif'+tail, 'PNG')
if n_z == 2:
n_width = 10
import scipy.stats
z = {'z':np.zeros((2,n_width**2))}
for i in range(0,n_width):
for j in range(0,n_width):
z['z'][0,n_width*i+j] = scipy.stats.norm.ppf(float(i)/n_width+0.5/n_width)
z['z'][1,n_width*i+j] = scipy.stats.norm.ppf(float(j)/n_width+0.5/n_width)
x, _, _z = model.gen_xz({}, z, n_width**2)
if dataset == 'mnist':
x = 1 - _z['x']
image = paramgraphics.mat_to_img(f_dec(_z['x']), dim_input)
image.save(logdir+'2dmanifold'+tail, 'PNG')
else:
if 'norb' in dataset or dataset=='svhn':
nn_batch_nn = 64
else:
nn_batch_nn = 144
if not(os.environ.has_key('train_residual') and bool(int(os.environ['train_residual'])) == True) and (os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True):
mp_in = np.random.randint(0,x_train['mean_prior'].shape[1],nn_batch_nn)
m_p = x_train['mean_prior'][:,mp_in]
s_s = 1
if os.environ.has_key('sigma_square'):
s_s = float(os.environ['sigma_square'])
x_samples = model.gen_xz_prior({}, {}, m_p, s_s, n_batch=nn_batch_nn)
x_samples = x_samples['x']
m_p1 = (np.ones((n_z, nn_batch_nn)).T * np.mean(x_train['mean_prior'], axis = 1)).T
x_samples1 = model.gen_xz_prior({}, {}, m_p1.astype(np.float32), s_s, n_batch=nn_batch_nn)
image = paramgraphics.mat_to_img(f_dec(x_samples1['x']), dim_input, colorImg=colorImg)
image.save(logdir+'mean_samples-prior'+tail, 'PNG')
x_samples11 = model.gen_xz_prior11({}, {}, m_p, s_s, n_batch=nn_batch_nn)
image = paramgraphics.mat_to_img(f_dec(x_samples11['x']), dim_input, colorImg=colorImg)
image.save(logdir+'prior-image'+tail, 'PNG')
else:
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=nn_batch_nn)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg)
image.save(logdir+'samples-prior'+tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
else:
# Model with preprocessing
if 'w0' in v:
tmp = f_dec(v['w0'][:].T)
#print dim_input
#print tmp.shape
if 'zca' in dataset or dataset=='svhn':
tmp = zca_dec(zca_mean, zca_winv, tmp)
image = paramgraphics.mat_to_img(tmp, dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0'+tail, 'PNG')
tmp = f_dec(w['out_w'][:])
if 'zca' in dataset:
tmp = zca_dec(zca_mean, zca_winv, tmp)
image = paramgraphics.mat_to_img(tmp, dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
if dataset == 'svhn':
nn_batch_nn = 64
else:
nn_batch_nn = 144
if not(os.environ.has_key('train_residual') and bool(int(os.environ['train_residual'])) == True) and (os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True):
mp_in = np.random.randint(0,x_train['mean_prior'].shape[1],nn_batch_nn)
m_p = x_train['mean_prior'][:,mp_in]
s_s = 1
if os.environ.has_key('sigma_square'):
s_s = float(os.environ['sigma_square'])
x_samples = model.gen_xz_prior({}, {}, m_p, s_s, n_batch=nn_batch_nn)
x_samples = zca_dec(zca_mean, zca_winv,x_samples['x'])
x_samples = np.minimum(np.maximum(x_samples, 0), 1)
x_samples11 = model.gen_xz_prior11({}, {}, m_p, s_s, n_batch=nn_batch_nn)
x_samples11 = zca_dec(zca_mean,zca_winv,x_samples11['x'])
x_samples11 = np.minimum(np.maximum(x_samples11, 0), 1)
image = paramgraphics.mat_to_img(x_samples11, dim_input, colorImg=colorImg)
image.save(logdir+'prior-image'+tail, 'PNG')
else:
_x, _z, _z_confab = model.gen_xz({}, {}, n_batch=nn_batch_nn)
x_samples = f_dec(_z_confab['x'])
x_samples = np.minimum(np.maximum(x_samples, 0), 1)
image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
'''
def infer(data, n_batch=1000):
#print '--', n_batch
size = data['x'].shape[1]
res = np.zeros((sum(n_hidden), size))
res1 = np.zeros((n_z,size))
res2 = np.zeros((n_hidden[-1],size))
res3 = np.zeros((n_z,size))
for i in range(0, size, n_batch):
idx_to = min(size, i+n_batch)
x_batch = ndict.getCols(data, i, idx_to)
# may have bugs
nn_batch = idx_to - i
_x, _z, _z_confab = model.gen_xz(x_batch, {}, nn_batch)
x_samples = _z_confab['x']
for (hi, hidden) in enumerate(_z_confab['hidden']):
res[sum(n_hidden[:hi]):sum(n_hidden[:hi+1]),i:i+nn_batch] = hidden
res1[:,i:i+nn_batch] = _z_confab['mean']
res2[:,i:i+nn_batch] = _z_confab['hidden'][-1]
res3[:,i:i+nn_batch] = _z_confab['logvar']
#
return res, res1, res2, res3
#print n_batch
#if not dataset == 'mnist_binarized':
z_test, z_test1, z_test2, vv_test = infer(x_test)
z_train, z_train1, z_train2, vv_train = infer(x_train)
l_t, px_t, pz_t, qz_t = model.test(x_train, n_samples=1, n_batch=n_batch, byteToFloat=byteToFloat)
print 'Elogpx', px_t, 'Elogpz', pz_t, '-Elogqz', qz_t
#sigma_square = float(os.environ['sigma_square'])
print 'var', np.mean(np.exp(vv_train)), 'q', np.mean(np.abs(z_train1)), 'p', np.mean(np.abs(train_mean_prior)), 'd', np.mean(np.abs(z_train1-train_mean_prior))
with open(logdir+'hook.txt', 'a') as f:
print >>f, 'Elogpx', px_t, 'Elogpz', pz_t, '-Elogqz', qz_t
print >>f, 'var', np.mean(np.exp(vv_train)), 'q', np.mean(np.abs(z_train1)), 'p', np.mean(np.abs(train_mean_prior)), 'd', np.mean(np.abs(z_train1-train_mean_prior))
#if not dataset == 'mnist_binarized':
sio.savemat(logdir+'full_latent.mat', {'z_test': z_test, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train})
sio.savemat(logdir+'mean_latent.mat', {'z_test': z_test1, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train1})
sio.savemat(logdir+'last_latent.mat', {'z_test': z_test2, 'train_y':train_y, 'test_y':test_y, 'z_train': z_train2})
'''
# Optimize
#SFO
dostep = epoch_vae_adam(model, x, n_batch=n_batch, bernoulli_x=bernoulli_x, byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
def main(n_passes, n_hidden, seed, alpha, n_minibatches, n_unlabeled,
n_classes):
"""
Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z)
And where 'x' is always observed and 'y' is _sometimes_ observed (hence semi-supervised).
We're going to use q(y|x) as a classification model.
"""
# Create the directory for the log and outputs.
logdir = 'results/learn_yz_x_hyp' + '-' + str(int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print("---------------")
print('Logdir:', logdir)
# Feed with the seed:
np.random.seed(seed)
# Load model for feature extraction
path = 'results/hyper_50-(500, 500)_longrun/'
# Load the parameters of the model that has been trained previously:
l1_v = ndict.loadz(path + 'v_best.ndict.tar.gz')
l1_w = ndict.loadz(path + 'w_best.ndict.tar.gz')
# Same hyperparameters that we use for training M1:
# Number of hidden nodes in the model:
n_h = (500, 500)
# Size of our feature vector:
n_x = 67 * 4
# Number of latent variables:
n_z = 50
nonlinear = 'softplus'
type_px = 'bernoulli'
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
# Create the M1:
from anglepy.models.VAE_Z_X import VAE_Z_X
l1_model = VAE_Z_X(n_x=n_x,
n_hidden_q=n_h,
n_z=n_z,
n_hidden_p=n_h,
nonlinear_q=nonlinear,
nonlinear_p=nonlinear,
type_px=type_px,
type_qz=type_qz,
type_pz=type_pz,
prior_sd=1)
# Load dataset:
from hyperspectralData import HyperspectralData
x_l, y_l, x_u, y_u, valid_x, valid_y, test_x, test_y = HyperspectralData(
).load_dataset_m2(n_unlabeled=n_unlabeled, n_classes=n_classes)
n_labeled = x_l.shape[1]
if n_labeled % n_minibatches != 0:
# We need to delete some samples
indexes_to_delete = np.random.choice(range(n_labeled),
size=(n_labeled % n_minibatches),
replace=False)
x_l = np.delete(x_l, indexes_to_delete, axis=1)
y_l = np.delete(y_l, indexes_to_delete, axis=1)
# Extract features
def transform(v, _x):
# Get the mean and the variance of the distribution learned to generate the z of the dataset.
return l1_model.dist_qz['z'](*([_x] + list(v.values()) +
[np.ones((1, _x.shape[1]))]))
# 3. Extract features
x_mean_u, x_logvar_u = transform(l1_v, x_u)
x_mean_l, x_logvar_l = transform(l1_v, x_l)
x_unlabeled = {'mean': x_mean_u, 'logvar': x_logvar_u, 'y': y_u}
x_labeled = {'mean': x_mean_l, 'logvar': x_logvar_l, 'y': y_l}
valid_x, _ = transform(l1_v, valid_x)
test_x, _ = transform(l1_v, test_x)
# Copied from learn_yz_x_ss:
n_x = l1_w[b'w0'].shape[1]
n_y = n_classes
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
# Init VAE model p(x,y,z)
from anglepy.models.VAE_YZ_X import VAE_YZ_X
uniform_y = True
model = VAE_YZ_X(n_x,
n_y,
n_hidden,
n_z,
n_hidden,
nonlinear,
nonlinear,
type_px,
type_qz=type_qz,
type_pz=type_pz,
prior_sd=1,
uniform_y=uniform_y)
v, w = model.init_w(1e-3)
# Init q(y|x) model
from anglepy.models.MLP_Categorical import MLP_Categorical
n_units = [n_x] + list(n_hidden) + [n_y]
model_qy = MLP_Categorical(n_units=n_units,
prior_sd=1,
nonlinearity=nonlinear)
u = model_qy.init_w(1e-3)
write_headers(logdir)
# Progress hook
t0 = time.time()
def hook(step, u, v, w, ll):
print("---------------")
print("Current results:")
print("Step:", step)
print(" ")
# Get classification error of validation and test sets
def error(dataset_x, dataset_y):
_, _, _z = model_qy.gen_xz(u, {'x': dataset_x}, {})
n_examples = 20
max_row = dataset_y.shape[1]
example_rows = np.random.choice(max_row,
size=n_examples,
replace=False)
print(" Predictions:", np.argmax(_z['py'], axis=0)[example_rows])
print(" Real: ", np.argmax(dataset_y, axis=0)[example_rows])
return np.sum(
np.argmax(_z['py'], axis=0) != np.argmax(dataset_y, axis=0)
) / (0.0 + dataset_y.shape[1])
print("Validset:")
valid_error = error(valid_x, valid_y)
print("Testset:")
test_error = error(test_x, test_y)
# Save variables
ndict.savez(u, logdir + 'u')
ndict.savez(v, logdir + 'v')
ndict.savez(w, logdir + 'w')
time_elapsed = time.time() - t0
# This will be showing the current results and write them in a file:
with open(logdir + 'AA_results.txt', 'a') as file:
file.write(
str(step) + ',' + str(time_elapsed) + ',' + str(valid_error) +
',' + str(test_error) + '\n')
print("Time elapsed:", time_elapsed)
print("Validset error:", valid_error)
print("Testset error:", test_error)
print("LogLikelihood:", ll)
return valid_error
# Optimize
result = optim_vae_ss_adam(alpha,
model_qy,
model,
x_labeled,
x_unlabeled,
n_y,
u,
v,
w,
n_minibatches=n_minibatches,
n_passes=n_passes,
hook=hook)
return result
def main(n_z, n_hidden, dataset, seed, comment, gfx=True):
# Initialize logdir
import time
logdir = 'results/gpulearn_z_x_' + dataset + '_' + str(n_z) + '-' + str(
n_hidden) + '_' + comment + '_' + str(int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
print 'gpulearn_z_x', n_z, n_hidden, dataset, seed
with open(logdir + 'hook.txt', 'a') as f:
print >> f, 'learn_z_x', n_z, n_hidden, dataset, seed
np.random.seed(seed)
gfx_freq = 1
weight_decay = 0
f_enc, f_dec = lambda x: x, lambda x: x
# Init data
if dataset == 'mnist':
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(
size)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (size, size)
n_x = size * size
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 50000
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch) / n_train
if dataset == 'mnist_binarized':
import anglepy.data.mnist_binarized as mnist_binarized
# MNIST
train_x, valid_x, test_x = mnist_binarized.load_numpy(28)
x = {'x': np.hstack((train_x, valid_x)).astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (28, 28)
n_x = 28 * 28
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'mog'
nonlinear = 'rectlin'
type_px = 'bernoulli'
n_train = 60000
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / n_train
elif dataset == 'freyface':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy()
np.random.shuffle(train_x)
x = {'x': train_x.T[:, 0:n_train]}
x_valid = {'x': train_x.T[:, n_train:]}
L_valid = 1
dim_input = (28, 20)
n_x = 20 * 28
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'bounded01'
nonlinear = 'tanh' #tanh works better with freyface #'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / n_train
elif dataset == 'freyface_pca':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
train_x = f_enc(train_x)
x = {'x': train_x[:, 0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:, n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28, 20)
n_x = train_x.shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'freyface_bernoulli':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
x = {'x': train_x[:, 0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:, n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28, 20)
n_x = train_x.shape[0]
type_pz = 'gaussianmarg'
type_px = 'bernoulli'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'norb':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
byteToFloat = False
bernoulli_x = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'norb_pca':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
f_enc, f_dec, _ = pp.PCA(train_x, 0.999)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'norb_normalized':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
#f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
f_enc, f_dec, _ = pp.normalize(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'svhn':
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = svhn.load_numpy(
False, binarize_y=True) #norb.load_resized(size, binarize_y=True)
extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
x = {
'x': np.hstack((train_x, extra_x)),
'y': np.hstack((train_y, extra_y))
}
ndict.shuffleCols(x)
print 'Performing PCA, can take a few minutes... ',
f_enc, f_dec, pca_params = pp.PCA(x['x'][:, :10000],
cutoff=600,
toFloat=True)
ndict.savez(pca_params, logdir + 'pca_params')
print 'Done.'
n_y = 10
x = {'x': f_enc(x['x']).astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size, size)
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
# Construct model
from anglepy.models import GPUVAE_Z_X
updates = get_adam_optimizer(learning_rate=3e-4, weight_decay=weight_decay)
model = GPUVAE_Z_X(updates,
n_x,
n_hidden,
n_z,
n_hidden[::-1],
nonlinear,
nonlinear,
type_px,
type_qz=type_qz,
type_pz=type_pz,
prior_sd=100,
init_sd=1e-3)
if False:
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412689061/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412676966/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412695481/'
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412695455/'
#dir = '/Users/dpkingma/results/gpulearn_z_x_svhn_pca_300-(500, 500)__1413904756/'
dir = '/home/ubuntu/results/gpulearn_z_x_mnist_50-[500, 500]__1414259423/'
w = ndict.loadz(dir + 'w_best.ndict.tar.gz')
v = ndict.loadz(dir + 'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Progress hook
def hook(epoch, t, ll):
if epoch % 10 != 0: return
ll_valid, _ = model.est_loglik(x_valid,
n_samples=L_valid,
n_batch=n_batch,
byteToFloat=byteToFloat)
# Log
ndict.savez(ndict.get_value(model.v), logdir + 'v')
ndict.savez(ndict.get_value(model.w), logdir + 'w')
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir + 'v_best')
ndict.savez(ndict.get_value(model.w), logdir + 'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir + 'hook.txt', 'a') as f:
print >> f, "Finished"
exit()
print epoch, t, ll, ll_valid, ll_valid_stats
with open(logdir + 'hook.txt', 'a') as f:
print >> f, epoch, t, ll, ll_valid, ll_valid_stats
# Graphics
if gfx and epoch % gfx_freq == 0:
#tail = '.png'
tail = '-' + str(epoch) + '.png'
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
if 'pca' not in dataset and 'random' not in dataset and 'normalized' not in dataset:
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'q_w0' + tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_w' + tail, 'PNG')
if 'out_unif' in w:
image = paramgraphics.mat_to_img(f_dec(
w['out_unif'].reshape((-1, 1))),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_unif' + tail, 'PNG')
if n_z == 2:
n_width = 10
import scipy.stats
z = {'z': np.zeros((2, n_width**2))}
for i in range(0, n_width):
for j in range(0, n_width):
z['z'][0, n_width * i + j] = scipy.stats.norm.ppf(
float(i) / n_width + 0.5 / n_width)
z['z'][1, n_width * i + j] = scipy.stats.norm.ppf(
float(j) / n_width + 0.5 / n_width)
x, _, _z = model.gen_xz({}, z, n_width**2)
if dataset == 'mnist':
x = 1 - _z['x']
image = paramgraphics.mat_to_img(f_dec(_z['x']), dim_input)
image.save(logdir + '2dmanifold' + tail, 'PNG')
else:
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples),
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples' + tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
else:
# Model with preprocessing
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'q_w0' + tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_w' + tail, 'PNG')
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = f_dec(_z_confab['x'])
x_samples = np.minimum(np.maximum(x_samples, 0), 1)
image = paramgraphics.mat_to_img(x_samples,
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples' + tail, 'PNG')
# Optimize
#SFO
dostep = epoch_vae_adam(model,
x,
n_batch=n_batch,
bernoulli_x=bernoulli_x,
byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
def main(n_z, n_hidden, dataset, seed, gfx=True, _size=None):
'''Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z).
x and y are (always) observed.
I.e. this cannot be used for semi-supervised learning
'''
assert (type(n_hidden) == tuple or type(n_hidden) == list)
assert type(n_z) == int
assert isinstance(dataset, basestring)
print 'gpulearn_yz_x', n_z, n_hidden, dataset, seed
comment = ''
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
comment += 'prior-'
if os.environ.has_key('default') and bool(int(os.environ['default'])) == True:
comment += 'default-'
else:
comment += 'not_default-'
import time
logdir = 'results/gpulearn_yz_x_'+dataset+'_'+str(n_z)+'-'+str(n_hidden)+comment+'-'+str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
np.random.seed(seed)
# Init data
if dataset == 'mnist':
'''
What works well:
100-2-100 (Generated digits stay bit shady)
1000-2-1000 (Needs pretty long training)
'''
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size, binarize_y=True)
f_enc, f_dec = lambda x:x, lambda x:x
if os.environ.has_key('prior') and bool(int(os.environ['prior'])) == True:
color.printBlue('Loading prior')
mnist_prior = sio.loadmat('data/mnist_prior/mnist_prior.mat')
train_mean_prior = mnist_prior['z_train']
valid_mean_prior = mnist_prior['z_valid']
else:
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
x = {'x': train_x[:,:].astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': train_y[:,:].astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32),'y': valid_y.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
mosaic_w = 5
mosaic_h = 2
type_px = 'bernoulli'
#print 'Network Structure:', n_z,
elif dataset == 'mnist_basic':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_'
tmp = sio.loadmat(data_dir+'train.mat')
#color.printRed(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'rectangle':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'rectangles_'
tmp = sio.loadmat(data_dir+'train.mat')
color.printRed(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,1000:]
valid_y = train_y[1000:]
train_x = train_x[:,:1000]
train_y = train_y[:1000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 1000
n_valid = 200
n_test = 50000
n_batch = 500
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'convex':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'convex_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,6000:]
valid_y = train_y[6000:]
train_x = train_x[:,:6000]
train_y = train_y[:6000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 6000
n_valid = 2000
n_test = 50000
n_batch = 120
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'rectangle_image':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'rectangles_im_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 2
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_rot':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_all_rotation_normalized_float_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_rand':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_background_random_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_image':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_background_images_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'mnist_back_image_rot':
# MNIST
size = 28
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_all_background_images_rotation_normalized_'
tmp = sio.loadmat(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
test_x = tmp['x_test'].T
test_y = tmp['t_test'].T.astype(np.int32)
print train_x.shape
print train_y.shape
print test_x.shape
print test_y.shape
f_enc, f_dec = pp.Identity()
train_mean_prior = np.zeros((n_z,train_x.shape[1]))
test_mean_prior = np.zeros((n_z,test_x.shape[1]))
valid_mean_prior = np.zeros((n_z,valid_x.shape[1]))
'''
x = {'x': train_x.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
'''
x = {'x': train_x.astype(np.float32), 'mean_prior': train_mean_prior.astype(np.float32), 'y': labelToMat(train_y).astype(np.float32)}
x_train = x
x_valid = {'x': valid_x.astype(np.float32), 'mean_prior': valid_mean_prior.astype(np.float32), 'y': labelToMat(valid_y).astype(np.float32)}
x_test = {'x': test_x.astype(np.float32), 'mean_prior': test_mean_prior.astype(np.float32), 'y': labelToMat(test_y).astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 10000
n_valid = 2000
n_test = 50000
n_batch = 200
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
else:
raise Exception('Unknown dataset.')
# Init model
n_hidden_q = n_hidden
n_hidden_p = n_hidden
from anglepy.models import GPUVAE_YZ_X
if os.environ.has_key('default') and bool(int(os.environ['default'])) == True:
updates = get_adam_optimizer(alpha=3e-4, beta1=0.9, beta2=0.999, weight_decay=0)
else:
updates = get_adam_optimizer(alpha=3e-4, beta1=0.1, beta2=0.001, weight_decay=1000.0/50000.0)
model = GPUVAE_YZ_X(updates, n_x, n_y, n_hidden_q, n_z, n_hidden_p[::-1], 'softplus', 'softplus', type_px=type_px, type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1, uniform_y=True)
if False:
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414094291/'
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414163488/'
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Fixed sample for visualisation
z_sample = {'z': np.repeat(np.random.standard_normal(size=(n_z, 12)), 12, axis=1).astype(np.float32)}
y_sample = {'y': np.tile(np.random.multinomial(1, [1./n_y]*n_y, size=12).T, (1, 12))}
# Progress hook
def hook(epoch, t, ll):
if epoch%10 != 0:
return
ll_valid, _ = model.est_loglik(x_valid, n_samples=L_valid, n_batch=n_batch, byteToFloat=byteToFloat)
if math.isnan(ll_valid):
print "NaN detected. Reverting to saved best parameters"
ndict.set_value(model.v, ndict.loadz(logdir+'v.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(logdir+'w.ndict.tar.gz'))
return
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir+'v_best')
ndict.savez(ndict.get_value(model.w), logdir+'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if False and ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir+'hook.txt', 'a') as f:
print >>f, "Finished"
exit()
# Log
ndict.savez(ndict.get_value(model.v), logdir+'v')
ndict.savez(ndict.get_value(model.w), logdir+'w')
print epoch, t, ll, ll_valid
with open(logdir+'hook.txt', 'a') as f:
print >>f, t, ll, ll_valid
if gfx:
# Graphics
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
tail = '-'+str(epoch)+'.png'
image = paramgraphics.mat_to_img(f_dec(v['w0x'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0x'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
_x = {'y': np.random.multinomial(1, [1./n_y]*n_y, size=144).T}
_, _, _z_confab = model.gen_xz(_x, {}, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
_, _, _z_confab = model.gen_xz(y_sample, z_sample, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples_fixed'+tail, 'PNG')
if n_z == 2:
import ImageFont
import ImageDraw
n_width = 10
submosaic_offset = 15
submosaic_width = (dim_input[1]*n_width)
submosaic_height = (dim_input[0]*n_width)
mosaic = Image.new("RGB", (submosaic_width*mosaic_w, submosaic_offset+submosaic_height*mosaic_h))
for digit in range(0,n_y):
if digit >= mosaic_h*mosaic_w: continue
_x = {}
n_batch_plot = n_width*n_width
_x['y'] = np.zeros((n_y,n_batch_plot))
_x['y'][digit,:] = 1
_z = {'z':np.zeros((2,n_width**2))}
for i in range(0,n_width):
for j in range(0,n_width):
_z['z'][0,n_width*i+j] = scipy.stats.norm.ppf(float(i)/n_width+0.5/n_width)
_z['z'][1,n_width*i+j] = scipy.stats.norm.ppf(float(j)/n_width+0.5/n_width)
_x, _, _z_confab = model.gen_xz(_x, _z, n_batch=n_batch_plot)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg, tile_spacing=(0,0))
#image.save(logdir+'samples_digit_'+str(digit)+'_'+tail, 'PNG')
mosaic_x = (digit%mosaic_w)*submosaic_width
mosaic_y = submosaic_offset+int(digit/mosaic_w)*submosaic_height
mosaic.paste(image, (mosaic_x, mosaic_y))
draw = ImageDraw.Draw(mosaic)
draw.text((1,1),"Epoch #"+str(epoch)+" Loss="+str(int(ll)))
#plt.savefig(logdir+'mosaic'+tail, format='PNG')
mosaic.save(logdir+'mosaic'+tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
# Optimize
dostep = epoch_vae_adam(model, x, n_batch=n_batch, bernoulli_x=bernoulli_x, byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
# Compute prior probabilities per class
train_y = mnist.binarize_labels(train_y)
prior_y = train_y.mean(axis=1).reshape((10,1))
# Create model
n_x = 28*28
n_y = 10
n_z = 50
n_hidden = 500,500
updates = None
model = GPUVAE_YZ_X(updates, n_x, n_y, n_hidden, n_z, n_hidden, 'softplus', 'softplus', type_px='bernoulli', type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1, uniform_y=True)
# Load parameters
dir = 'models/mnist_yz_x_50-500-500/'
ndict.set_value(model.v, ndict.loadz(dir+'v_best.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(dir+'w_best.ndict.tar.gz'))
else:
raise Exception("Unknown dataset")
# Make predictions on test set
def get_lowerbound():
lb = np.zeros((n_y,test_x.shape[1]))
for _class in range(n_y):
y = np.zeros((n_y,test_x.shape[1]))
y[_class,:] = 1
_lb = model.eval({'x': test_x.astype(np.float32), 'y':y.astype(np.float32)}, {})
lb[_class,:] = _lb
return lb
colorImg = True
binarize = False
if True:
if False:
n_hidden = (500,500)
n_z = 300
dir = 'models/svhn_yz_x_300-500-500/'
else:
n_hidden = (1000,1000)
n_z = 300
dir = 'models/svhn_yz_x_300-1000-1000/'
from anglepy.models import GPUVAE_YZ_X
model = GPUVAE_YZ_X(None, n_x, n_y, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-2)
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# PCA
pca = ndict.loadz(dir+'pca_params.ndict.tar.gz')
def f_dec(x):
result = pca['eigvec'].dot(x * np.sqrt(pca['eigval'])) * pca['x_sd'] + pca['x_center']
result = np.maximum(0, np.minimum(1, result))
return result
if dataset == 'mnist':
n_x = 28*28
dim_input = (28,28)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
# Compute prior probabilities per class
train_y = mnist.binarize_labels(train_y)
prior_y = train_y.mean(axis=1).reshape((10,1))
# Create model
n_x = 28*28
n_y = 10
n_hidden = 500,500
updates = None
print 'n_z:', n_z
model = GPUVAE_YZ_X(updates, n_x, n_y, n_hidden, n_z, n_hidden, 'softplus', 'softplus', type_px='bernoulli', type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1, uniform_y=True)
# Load parameters
ndict.set_value(model.v, ndict.loadz(dir+'v_best.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(dir+'w_best.ndict.tar.gz'))
elif dataset == 'mnist_basic':
data_dir = os.environ['ML_DATA_PATH']+'/mnist_variations/'+'mnist_'
tmp = sio.loadmat(data_dir+'train.mat')
#color.printRed(data_dir+'train.mat')
train_x = tmp['x_train'].T
train_y = tmp['t_train'].T.astype(np.int32)
# validation 2000
valid_x = train_x[:,10000:]
valid_y = train_y[10000:]
train_x = train_x[:,:10000]
train_y = train_y[:10000]
tmp = sio.loadmat(data_dir+'test.mat')
import numpy as np
from anglepy import ndict
import scipy.io as sio
import cPickle, gzip
import math
import os, sys
# load data, recognition model and generative model
print 'Loading data...'
dir = sys.argv[1]
p_type = sys.argv[5]
if p_type == 'null':
p_type = ''
v = ndict.loadz(dir+'v'+p_type+'.ndict.tar.gz')
w = ndict.loadz(dir+'w'+p_type+'.ndict.tar.gz')
# perturb data
print 'Loading perturbed data...'
width = 28
height = 28
denoise_tpye = 1 # sample or mean
pertub_type = int(sys.argv[2])
pertub_prob = float(sys.argv[3])
denoise_times = int(sys.argv[4]) # denoising epoch
print pertub_type, pertub_prob, denoise_times
if pertub_type == 4:
type_px = 'gaussian'
nonlinear = 'softplus'
n_y = 10
n_batch_w = 10
colorImg = True
binarize = False
if True:
n_hidden = (500,500)
n_z = 300
dir = 'models/svhn_yz_x_300-500-500/'
from anglepy.models import GPUVAE_YZ_X
model = GPUVAE_YZ_X(None, n_x, n_y, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-2)
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# PCA
f_enc, f_dec = pp.PCA_fromfile(dir+'pca_params.ndict.tar.gz')
if dataset == 'mnist':
# MNIST
import anglepy.data.mnist as mnist
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size=28, binarize_y=True)
f_enc, f_dec = lambda x:x, lambda x:x
n_x = 28*28
dim_input = (28,28)
def main(n_z, n_hidden, dataset, seed, comment, gfx=True):
# Initialize logdir
#---------------------
# Setasouto:
# Create the directory to save the outputs files and log.
#---------------------
import time
logdir = 'results/gpulearn_z_x_' + dataset + '_' + str(n_z) + '-' + str(
n_hidden) + '_' + comment + '_' + str(int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print('logdir:', logdir)
print('gpulearn_z_x', n_z, n_hidden, dataset, seed)
with open(logdir + 'hook.txt', 'a') as f:
print(f, 'learn_z_x', n_z, n_hidden, dataset, seed)
np.random.seed(seed)
gfx_freq = 1
weight_decay = 0
f_enc, f_dec = lambda x: x, lambda x: x
# Init data
if dataset == 'mnist':
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(
size)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (size, size)
n_x = size * size
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 50000
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch) / n_train
if dataset == 'mnist_binarized':
import anglepy.data.mnist_binarized as mnist_binarized
# MNIST
train_x, valid_x, test_x = mnist_binarized.load_numpy(28)
x = {'x': np.hstack((train_x, valid_x)).astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (28, 28)
n_x = 28 * 28
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'mog'
nonlinear = 'rectlin'
type_px = 'bernoulli'
n_train = 60000
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / n_train
elif dataset == 'freyface':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy()
np.random.shuffle(train_x)
x = {'x': train_x.T[:, 0:n_train]}
x_valid = {'x': train_x.T[:, n_train:]}
L_valid = 1
dim_input = (28, 20)
n_x = 20 * 28
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'bounded01'
nonlinear = 'tanh' #tanh works better with freyface #'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / n_train
elif dataset == 'freyface_pca':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
train_x = f_enc(train_x)
x = {'x': train_x[:, 0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:, n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28, 20)
n_x = train_x.shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'freyface_bernoulli':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
x = {'x': train_x[:, 0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:, n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28, 20)
n_x = train_x.shape[0]
type_pz = 'gaussianmarg'
type_px = 'bernoulli'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'norb':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
byteToFloat = False
bernoulli_x = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'norb_pca':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
f_enc, f_dec, _ = pp.PCA(train_x, 0.999)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'norb_normalized':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
#f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
f_enc, f_dec, _ = pp.normalize(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size, size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / train_x.shape[1]
elif dataset == 'svhn':
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = svhn.load_numpy(
False, binarize_y=True) #norb.load_resized(size, binarize_y=True)
extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
x = {
'x': np.hstack((train_x, extra_x)),
'y': np.hstack((train_y, extra_y))
}
ndict.shuffleCols(x)
print('Performing PCA, can take a few minutes... ',
f_enc,
f_dec,
pca_params=pp.PCA(x['x'][:, :10000], cutoff=600, toFloat=True))
ndict.savez(pca_params, logdir + 'pca_params')
print('Done.')
n_y = 10
x = {'x': f_enc(x['x']).astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size, size)
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
elif dataset == 'hyper':
# Hyperspectral images:
# Import 1 file of the dataset
# TODO: import more files: Edit hyperspectralData.py
#I added the hyperspectralData file in the anglepy library
from hyperspectralData import HyperspectralData
train_x, train_y, valid_x, valid_y, test_x, test_y = HyperspectralData(
).load_numpy(100000)
#Dim input: How it has to be written like an image. We said that is:
dim_input = (67, 4)
n_x = train_x.shape[0] #Dimension of our data vector.
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32)}
L_valid = 1
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = train_x.shape[1]
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch) / n_train
#Write the hyperparameters used:
with open(logdir + 'AA_hyperparameters.txt', 'w') as file:
file.write("L_valid: " + str(L_valid) + '\n')
file.write("type_qz: " + type_qz + '\n')
file.write("type_pz: " + type_pz + '\n')
file.write("Nonlinear: " + nonlinear + '\n')
file.write("type_px: " + type_px + '\n')
file.write("n_train: " + str(n_train) + '\n')
file.write("n_batch: " + str(n_batch) + '\n')
file.write("colorImg: " + str(colorImg) + '\n')
file.write("bernoulli_x: " + str(bernoulli_x) + '\n')
file.write("byteToFloat: " + str(byteToFloat) + '\n')
file.close()
# Write the headers for the csv file output:
with open(logdir + 'AA_results.txt', 'w') as file:
# Like a csv file:
file.write("Step" + ',' + "TimeElapsed" + ',' +
"LowerboundMinibatch" + ',' + "LowerboundValid" + ',' +
"NumStepNotImproving" + '\n')
file.close()
# Construct model
from anglepy.models import GPUVAE_Z_X
updates = get_adam_optimizer(learning_rate=3e-4, weight_decay=weight_decay)
model = GPUVAE_Z_X(updates,
n_x,
n_hidden,
n_z,
n_hidden[::-1],
nonlinear,
nonlinear,
type_px,
type_qz=type_qz,
type_pz=type_pz,
prior_sd=100,
init_sd=1e-3)
#---------------
# SetaSouto:
# The [::-1] is to reverse the list.
#---------------
if False:
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412689061/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412676966/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412695481/'
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412695455/'
#dir = '/Users/dpkingma/results/gpulearn_z_x_svhn_pca_300-(500, 500)__1413904756/'
dir = '/home/ubuntu/results/gpulearn_z_x_mnist_50-[500, 500]__1414259423/'
w = ndict.loadz(dir + 'w_best.ndict.tar.gz')
v = ndict.loadz(dir + 'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Progress hook
def hook(epoch, t, ll):
'''
Documented by SetaSouto, may contains errors.
:epoch: Number of the current step.
:t: Time elapsed from the beginning.
:ll: Loglikelihood (?).
'''
if epoch % 10 != 0: return
ll_valid, _ = model.est_loglik(x_valid,
n_samples=L_valid,
n_batch=n_batch,
byteToFloat=byteToFloat)
# Log
ndict.savez(ndict.get_value(model.v), logdir + 'v')
ndict.savez(ndict.get_value(model.w), logdir + 'w')
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir + 'v_best')
ndict.savez(ndict.get_value(model.w), logdir + 'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if ll_valid_stats[1] > 100:
print("Finished")
with open(logdir + 'hook.txt', 'a') as f:
print(f, "Finished")
exit()
# This will be showing the current results and write them in a file:
with open(logdir + 'AA_results.txt', 'a') as file:
# Like a csv file:
file.write(
str(epoch) + ',' + str(t) + ',' + str(ll) + ',' +
str(ll_valid) + ',' + str(ll_valid_stats[1]) + '\n')
file.close()
print("-------------------------")
print("Current results:")
print(" ")
print("Step:", epoch)
print("Time elapsed:", t)
print("Loglikelihood minibatch:", ll)
print("Loglikelihood validSet:", ll_valid)
print("N not improving:", ll_valid_stats[1])
#print(epoch, t, ll, ll_valid, ll_valid_stats)
#This print the file where are written the stats.
#with open(logdir+'hook.txt', 'a') as f:
#print(f, epoch, t, ll, ll_valid, ll_valid_stats)
# Graphics
if gfx and epoch % gfx_freq == 0:
#tail = '.png'
tail = '-' + str(epoch) + '.png'
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
if 'pca' not in dataset and 'random' not in dataset and 'normalized' not in dataset:
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'q_w0' + tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_w' + tail, 'PNG')
if 'out_unif' in w:
image = paramgraphics.mat_to_img(f_dec(
w['out_unif'].reshape((-1, 1))),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_unif' + tail, 'PNG')
if n_z == 2:
n_width = 10
import scipy.stats
z = {'z': np.zeros((2, n_width**2))}
for i in range(0, n_width):
for j in range(0, n_width):
z['z'][0, n_width * i + j] = scipy.stats.norm.ppf(
float(i) / n_width + 0.5 / n_width)
z['z'][1, n_width * i + j] = scipy.stats.norm.ppf(
float(j) / n_width + 0.5 / n_width)
x, _, _z = model.gen_xz({}, z, n_width**2)
if dataset == 'mnist':
x = 1 - _z['x']
image = paramgraphics.mat_to_img(f_dec(_z['x']), dim_input)
image.save(logdir + '2dmanifold' + tail, 'PNG')
else:
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples),
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples' + tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
else:
# Model with preprocessing
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'q_w0' + tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_w' + tail, 'PNG')
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = f_dec(_z_confab['x'])
x_samples = np.minimum(np.maximum(x_samples, 0), 1)
image = paramgraphics.mat_to_img(x_samples,
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples' + tail, 'PNG')
# Optimize
#SFO
dostep = epoch_vae_adam(model,
x,
n_batch=n_batch,
bernoulli_x=bernoulli_x,
byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
def main(n_z, n_hidden, dataset, seed, gfx=True, _size=None):
'''Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z).
x and y are (always) observed.
I.e. this cannot be used for semi-supervised learning
'''
assert (type(n_hidden) == tuple or type(n_hidden) == list)
assert type(n_z) == int
assert isinstance(dataset, str)
print('gpulearn_yz_x', n_z, n_hidden, dataset, seed)
import time
logdir = 'results/gpulearn_yz_x_' + dataset + '_' + str(n_z) + '-' + str(
n_hidden) + '-' + str(int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print('logdir:', logdir)
np.random.seed(seed)
# Init data
if dataset == 'mnist':
'''
What works well:
100-2-100 (Generated digits stay bit shady)
1000-2-1000 (Needs pretty long training)
'''
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(
size, binarize_y=True)
f_enc, f_dec = lambda x: x, lambda x: x
x = {
'x': train_x[:, :].astype(np.float32),
'y': train_y[:, :].astype(np.float32)
}
x_valid = {
'x': valid_x.astype(np.float32),
'y': valid_y.astype(np.float32)
}
L_valid = 1
dim_input = (size, size)
n_x = size * size
n_y = 10
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
mosaic_w = 5
mosaic_h = 2
type_px = 'bernoulli'
elif dataset == 'norb':
# resized NORB dataset, reshuffled
import anglepy.data.norb as norb
size = _size #48
train_x, train_y, test_x, test_y = norb.load_resized(size,
binarize_y=True)
_x = {'x': train_x, 'y': train_y}
ndict.shuffleCols(_x)
train_x = _x['x']
train_y = _x['y']
# Do PCA
f_enc, f_dec, pca_params = pp.PCA(_x['x'][:, :10000],
cutoff=2000,
toFloat=False)
ndict.savez(pca_params, logdir + 'pca_params')
x = {
'x': f_enc(train_x).astype(np.float32),
'y': train_y.astype(np.float32)
}
x_valid = {
'x': f_enc(test_x).astype(np.float32),
'y': test_y.astype(np.float32)
}
L_valid = 1
n_x = x['x'].shape[0]
n_y = 5
dim_input = (size, size)
n_batch = 1000 #23400/900 = 27
colorImg = False
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 1
type_px = 'gaussian'
elif dataset == 'norb_instances':
# resized NORB dataset with the instances as classes
import anglepy.data.norb2 as norb2
size = _size #48
x, y = norb2.load_numpy_subclasses(size, binarize_y=True)
_x = {'x': x, 'y': y}
ndict.shuffleCols(_x)
# Do pre=processing
if True:
# Works
f_enc, f_dec, pca_params = pp.PCA(_x['x'][:, :10000],
cutoff=600,
global_sd=True,
toFloat=True)
ndict.savez(pca_params, logdir + 'pca_params')
elif False:
# Doesn't work
f_enc, f_dec, pp_params = pp.normalize_noise(_x['x'][:, :50000],
noise_sd=0.01,
global_sd=True,
toFloat=True)
else:
# Doesn't work
f_enc, f_dec, params = pp.normalize_random(x=x[:, :10000],
global_sd=True,
toFloat=True)
ndict.savez(params, logdir + 'normalize_random_params')
n_valid = 5000
x = {
'x': f_enc(_x['x'][:, :-n_valid]).astype(np.float32),
'y': _x['y'][:, :-n_valid].astype(np.float32)
}
x_valid = {
'x': f_enc(_x['x'][:, :n_valid]).astype(np.float32),
'y': _x['y'][:, :n_valid].astype(np.float32)
}
L_valid = 1
n_x = x['x'].shape[0]
n_y = 50
dim_input = (size, size)
n_batch = 5000 #23400/900 = 27
colorImg = False
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 1
type_px = 'gaussian'
elif dataset == 'svhn':
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = svhn.load_numpy(
False, binarize_y=True) #norb.load_resized(size, binarize_y=True)
extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
x = {
'x': np.hstack((train_x, extra_x)),
'y': np.hstack((train_y, extra_y))
}
ndict.shuffleCols(x)
#f_enc, f_dec, (x_sd, x_mean) = pp.preprocess_normalize01(train_x, True)
f_enc, f_dec, pca_params = pp.PCA(x['x'][:, :10000],
cutoff=1000,
toFloat=True)
ndict.savez(pca_params, logdir + 'pca_params')
n_y = 10
x = {
'x': f_enc(x['x']).astype(np.float32),
'y': x['y'].astype(np.float32)
}
x_valid = {
'x': f_enc(test_x).astype(np.float32),
'y': test_y.astype(np.float32)
}
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size, size)
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 2
type_px = 'gaussian'
# Init model
n_hidden_q = n_hidden
n_hidden_p = n_hidden
from anglepy.models import GPUVAE_YZ_X
updates = get_adam_optimizer(alpha=3e-4,
beta1=0.9,
beta2=0.999,
weight_decay=0)
model = GPUVAE_YZ_X(updates,
n_x,
n_y,
n_hidden_q,
n_z,
n_hidden_p[::-1],
'softplus',
'softplus',
type_px=type_px,
type_qz='gaussianmarg',
type_pz='gaussianmarg',
prior_sd=1,
uniform_y=True)
if False:
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414094291/'
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414163488/'
w = ndict.loadz(dir + 'w_best.ndict.tar.gz')
v = ndict.loadz(dir + 'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Fixed sample for visualisation
z_sample = {
'z':
np.repeat(np.random.standard_normal(size=(n_z, 12)), 12,
axis=1).astype(np.float32)
}
y_sample = {
'y':
np.tile(
np.random.multinomial(1, [1. / n_y] * n_y, size=12).T, (1, 12))
}
# Progress hook
def hook(epoch, t, ll):
if epoch % 10 != 0:
return
ll_valid, _ = model.est_loglik(x_valid,
n_samples=L_valid,
n_batch=n_batch,
byteToFloat=byteToFloat)
if math.isnan(ll_valid):
print("NaN detected. Reverting to saved best parameters")
ndict.set_value(model.v, ndict.loadz(logdir + 'v.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(logdir + 'w.ndict.tar.gz'))
return
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir + 'v_best')
ndict.savez(ndict.get_value(model.w), logdir + 'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if False and ll_valid_stats[1] > 1000:
print("Finished")
with open(logdir + 'hook.txt', 'a') as f:
print("Finished", file=f)
exit()
# Log
ndict.savez(ndict.get_value(model.v), logdir + 'v')
ndict.savez(ndict.get_value(model.w), logdir + 'w')
print(epoch, t, ll, ll_valid)
with open(logdir + 'hook.txt', 'a') as f:
print(t, ll, ll_valid, file=f)
if gfx:
# Graphics
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
tail = '-' + str(epoch) + '.png'
image = paramgraphics.mat_to_img(f_dec(v['w0x'][:].T),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'q_w0x' + tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]),
dim_input,
True,
colorImg=colorImg)
image.save(logdir + 'out_w' + tail, 'PNG')
_x = {'y': np.random.multinomial(1, [1. / n_y] * n_y, size=144).T}
_, _, _z_confab = model.gen_xz(_x, {}, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']),
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples' + tail, 'PNG')
_, _, _z_confab = model.gen_xz(y_sample, z_sample, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']),
dim_input,
colorImg=colorImg)
image.save(logdir + 'samples_fixed' + tail, 'PNG')
if n_z == 2:
import Image
import ImageFont
import ImageDraw
n_width = 10
submosaic_offset = 15
submosaic_width = (dim_input[1] * n_width)
submosaic_height = (dim_input[0] * n_width)
mosaic = Image.new(
"RGB", (submosaic_width * mosaic_w,
submosaic_offset + submosaic_height * mosaic_h))
for digit in range(0, n_y):
if digit >= mosaic_h * mosaic_w: continue
_x = {}
n_batch_plot = n_width * n_width
_x['y'] = np.zeros((n_y, n_batch_plot))
_x['y'][digit, :] = 1
_z = {'z': np.zeros((2, n_width**2))}
for i in range(0, n_width):
for j in range(0, n_width):
_z['z'][0, n_width * i + j] = scipy.stats.norm.ppf(
float(i) / n_width + 0.5 / n_width)
_z['z'][1, n_width * i + j] = scipy.stats.norm.ppf(
float(j) / n_width + 0.5 / n_width)
_x, _, _z_confab = model.gen_xz(_x,
_z,
n_batch=n_batch_plot)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples),
dim_input,
colorImg=colorImg,
tile_spacing=(0, 0))
#image.save(logdir+'samples_digit_'+str(digit)+'_'+tail, 'PNG')
mosaic_x = (digit % mosaic_w) * submosaic_width
mosaic_y = submosaic_offset + int(
digit / mosaic_w) * submosaic_height
mosaic.paste(image, (mosaic_x, mosaic_y))
draw = ImageDraw.Draw(mosaic)
draw.text((1, 1),
"Epoch #" + str(epoch) + " Loss=" + str(int(ll)))
#plt.savefig(logdir+'mosaic'+tail, format='PNG')
mosaic.save(logdir + 'mosaic' + tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
# Optimize
dostep = epoch_vae_adam(model,
x,
n_batch=n_batch,
bernoulli_x=bernoulli_x,
byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
import numpy as np
import anglepy.ndict as ndict
# Path to the result's directory from the M1's training:
path = "results/hyper_50-(500, 500)_longrun/"
# Loads the parameters that has been training previously:
l1_v = ndict.loadz(path + 'v_best.ndict.tar.gz')
# Number of hidden nodes in the model:
n_h = (500, 500)
# Create the M1:
from anglepy.models.VAE_Z_X import VAE_Z_X
# We have to use the same hyperparameters from the training:
l1_model = VAE_Z_X(n_x=67 * 4,
n_hidden_q=n_h,
n_z=50,
n_hidden_p=n_h,
nonlinear_q='softplus',
nonlinear_p='softplus',
type_px='bernoulli',
type_qz='gaussianmarg',
type_pz='gaussianmarg',
prior_sd=1)
# Now we have to load the dataset that we wanna use.
from hyperspectralData import HyperspectralData
nsamples = 100
train_x, train_y, valid_x, valid_y, test_x, test_y = HyperspectralData(
).load_numpy(nsamples)
def PCA_fromfile(fname, toFloat=False):
pca = ndict.loadz(fname)
return PCA_encdec(pca['eigvec'], pca['eigval'], pca['x_center'],
pca['x_sd'], toFloat)
colorImg = True
binarize = False
if True:
if False:
n_hidden = (500,500)
n_z = 300
dir = 'models/svhn_yz_x_300-500-500/'
else:
n_hidden = (1000,1000)
n_z = 300
dir = 'models/svhn_yz_x_300-1000-1000/'
from anglepy.models import GPUVAE_YZ_X
model = GPUVAE_YZ_X(None, n_x, n_y, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-2)
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# PCA
pca = ndict.loadz(dir+'pca_params.ndict.tar.gz')
def f_dec(x):
result = pca['eigvec'].dot(x * np.sqrt(pca['eigval'])) * pca['x_sd'] + pca['x_center']
result = np.maximum(0, np.minimum(1, result))
return result
if dataset == 'mnist':
n_x = 28*28
dim_input = (28,28)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
def main(n_z, n_hidden, dataset, seed, gfx=True, _size=None):
'''Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z).
x and y are (always) observed.
I.e. this cannot be used for semi-supervised learning
'''
assert (type(n_hidden) == tuple or type(n_hidden) == list)
assert type(n_z) == int
assert isinstance(dataset, basestring)
print 'gpulearn_yz_x', n_z, n_hidden, dataset, seed
import time
logdir = 'results/gpulearn_yz_x_'+dataset+'_'+str(n_z)+'-'+str(n_hidden)+'-'+str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
np.random.seed(seed)
# Init data
if dataset == 'mnist':
'''
What works well:
100-2-100 (Generated digits stay bit shady)
1000-2-1000 (Needs pretty long training)
'''
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size, binarize_y=True)
f_enc, f_dec = lambda x:x, lambda x:x
x = {'x': train_x[:,:].astype(np.float32), 'y': train_y[:,:].astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32), 'y': valid_y.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
n_y = 10
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
mosaic_w = 5
mosaic_h = 2
type_px = 'bernoulli'
elif dataset == 'norb':
# resized NORB dataset, reshuffled
import anglepy.data.norb as norb
size = _size #48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
_x = {'x': train_x, 'y': train_y}
ndict.shuffleCols(_x)
train_x = _x['x']
train_y = _x['y']
# Do PCA
f_enc, f_dec, pca_params = pp.PCA(_x['x'][:,:10000], cutoff=2000, toFloat=False)
ndict.savez(pca_params, logdir+'pca_params')
x = {'x': f_enc(train_x).astype(np.float32), 'y':train_y.astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32), 'y':test_y.astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
n_y = 5
dim_input = (size,size)
n_batch = 1000 #23400/900 = 27
colorImg = False
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 1
type_px = 'gaussian'
elif dataset == 'norb_instances':
# resized NORB dataset with the instances as classes
import anglepy.data.norb2 as norb2
size = _size #48
x, y = norb2.load_numpy_subclasses(size, binarize_y=True)
_x = {'x': x, 'y': y}
ndict.shuffleCols(_x)
# Do pre=processing
if True:
# Works
f_enc, f_dec, pca_params = pp.PCA(_x['x'][:,:10000], cutoff=600, global_sd=True, toFloat=True)
ndict.savez(pca_params, logdir+'pca_params')
elif False:
# Doesn't work
f_enc, f_dec, pp_params = pp.normalize_noise(_x['x'][:,:50000], noise_sd=0.01, global_sd=True, toFloat=True)
else:
# Doesn't work
f_enc, f_dec, params = pp.normalize_random(x=x[:,:10000], global_sd=True, toFloat=True)
ndict.savez(params, logdir+'normalize_random_params')
n_valid = 5000
x = {'x': f_enc(_x['x'][:,:-n_valid]).astype(np.float32), 'y':_x['y'][:,:-n_valid].astype(np.float32)}
x_valid = {'x': f_enc(_x['x'][:,:n_valid]).astype(np.float32), 'y':_x['y'][:,:n_valid].astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
n_y = 50
dim_input = (size,size)
n_batch = 5000 #23400/900 = 27
colorImg = False
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 1
type_px = 'gaussian'
elif dataset == 'svhn':
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = svhn.load_numpy(False, binarize_y=True) #norb.load_resized(size, binarize_y=True)
extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
x = {'x': np.hstack((train_x, extra_x)), 'y':np.hstack((train_y, extra_y))}
ndict.shuffleCols(x)
#f_enc, f_dec, (x_sd, x_mean) = pp.preprocess_normalize01(train_x, True)
f_enc, f_dec, pca_params = pp.PCA(x['x'][:,:10000], cutoff=1000, toFloat=True)
ndict.savez(pca_params, logdir+'pca_params')
n_y = 10
x = {'x': f_enc(x['x']).astype(np.float32), 'y': x['y'].astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32), 'y': test_y.astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size,size)
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
mosaic_w = 5
mosaic_h = 2
type_px = 'gaussian'
# Init model
n_hidden_q = n_hidden
n_hidden_p = n_hidden
from anglepy.models import GPUVAE_YZ_X
updates = get_adam_optimizer(alpha=3e-4, beta1=0.9, beta2=0.999, weight_decay=0)
model = GPUVAE_YZ_X(updates, n_x, n_y, n_hidden_q, n_z, n_hidden_p[::-1], 'softplus', 'softplus', type_px=type_px, type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1, uniform_y=True)
if False:
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414094291/'
dir = '/home/ubuntu/results/gpulearn_yz_x_svhn_300-(500, 500)-1414163488/'
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Fixed sample for visualisation
z_sample = {'z': np.repeat(np.random.standard_normal(size=(n_z, 12)), 12, axis=1).astype(np.float32)}
y_sample = {'y': np.tile(np.random.multinomial(1, [1./n_y]*n_y, size=12).T, (1, 12))}
# Progress hook
def hook(epoch, t, ll):
if epoch%10 != 0:
return
ll_valid, _ = model.est_loglik(x_valid, n_samples=L_valid, n_batch=n_batch, byteToFloat=byteToFloat)
if math.isnan(ll_valid):
print "NaN detected. Reverting to saved best parameters"
ndict.set_value(model.v, ndict.loadz(logdir+'v.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(logdir+'w.ndict.tar.gz'))
return
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir+'v_best')
ndict.savez(ndict.get_value(model.w), logdir+'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if False and ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir+'hook.txt', 'a') as f:
print >>f, "Finished"
exit()
# Log
ndict.savez(ndict.get_value(model.v), logdir+'v')
ndict.savez(ndict.get_value(model.w), logdir+'w')
print epoch, t, ll, ll_valid
with open(logdir+'hook.txt', 'a') as f:
print >>f, t, ll, ll_valid
if gfx:
# Graphics
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
tail = '-'+str(epoch)+'.png'
image = paramgraphics.mat_to_img(f_dec(v['w0x'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0x'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
_x = {'y': np.random.multinomial(1, [1./n_y]*n_y, size=144).T}
_, _, _z_confab = model.gen_xz(_x, {}, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
_, _, _z_confab = model.gen_xz(y_sample, z_sample, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples_fixed'+tail, 'PNG')
if n_z == 2:
import ImageFont
import ImageDraw
n_width = 10
submosaic_offset = 15
submosaic_width = (dim_input[1]*n_width)
submosaic_height = (dim_input[0]*n_width)
mosaic = Image.new("RGB", (submosaic_width*mosaic_w, submosaic_offset+submosaic_height*mosaic_h))
for digit in range(0,n_y):
if digit >= mosaic_h*mosaic_w: continue
_x = {}
n_batch_plot = n_width*n_width
_x['y'] = np.zeros((n_y,n_batch_plot))
_x['y'][digit,:] = 1
_z = {'z':np.zeros((2,n_width**2))}
for i in range(0,n_width):
for j in range(0,n_width):
_z['z'][0,n_width*i+j] = scipy.stats.norm.ppf(float(i)/n_width+0.5/n_width)
_z['z'][1,n_width*i+j] = scipy.stats.norm.ppf(float(j)/n_width+0.5/n_width)
_x, _, _z_confab = model.gen_xz(_x, _z, n_batch=n_batch_plot)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg, tile_spacing=(0,0))
#image.save(logdir+'samples_digit_'+str(digit)+'_'+tail, 'PNG')
mosaic_x = (digit%mosaic_w)*submosaic_width
mosaic_y = submosaic_offset+int(digit/mosaic_w)*submosaic_height
mosaic.paste(image, (mosaic_x, mosaic_y))
draw = ImageDraw.Draw(mosaic)
draw.text((1,1),"Epoch #"+str(epoch)+" Loss="+str(int(ll)))
#plt.savefig(logdir+'mosaic'+tail, format='PNG')
mosaic.save(logdir+'mosaic'+tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
# Optimize
dostep = epoch_vae_adam(model, x, n_batch=n_batch, bernoulli_x=bernoulli_x, byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
def main(n_z, n_hidden, dataset, seed, comment, gfx=True):
# Initialize logdir
import time
logdir = 'results/gpulearn_z_x_'+dataset+'_'+str(n_z)+'-'+str(n_hidden)+'_'+comment+'_'+str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
print 'gpulearn_z_x', n_z, n_hidden, dataset, seed
with open(logdir+'hook.txt', 'a') as f:
print >>f, 'learn_z_x', n_z, n_hidden, dataset, seed
np.random.seed(seed)
gfx_freq = 1
weight_decay = 0
f_enc, f_dec = lambda x:x, lambda x:x
# Init data
if dataset == 'mnist':
import anglepy.data.mnist as mnist
# MNIST
size = 28
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': valid_x.astype(np.float32)}
x_test = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (size,size)
n_x = size*size
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
nonlinear = 'softplus'
type_px = 'bernoulli'
n_train = 50000
n_batch = 1000
colorImg = False
bernoulli_x = True
byteToFloat = False
weight_decay = float(n_batch)/n_train
if dataset == 'mnist_binarized':
import anglepy.data.mnist_binarized as mnist_binarized
# MNIST
train_x, valid_x, test_x = mnist_binarized.load_numpy(28)
x = {'x': np.hstack((train_x, valid_x)).astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
dim_input = (28,28)
n_x = 28*28
n_y = 10
type_qz = 'gaussianmarg'
type_pz = 'mog'
nonlinear = 'rectlin'
type_px = 'bernoulli'
n_train = 60000
n_batch = 1000
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'freyface':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy()
np.random.shuffle(train_x)
x = {'x': train_x.T[:,0:n_train]}
x_valid = {'x': train_x.T[:,n_train:]}
L_valid = 1
dim_input = (28,20)
n_x = 20*28
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'bounded01'
nonlinear = 'tanh' #tanh works better with freyface #'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
weight_decay = float(n_batch)/n_train
elif dataset == 'freyface_pca':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
train_x = f_enc(train_x)
x = {'x': train_x[:,0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:,n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28,20)
n_x = train_x.shape[0]
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'freyface_bernoulli':
# Frey's face
import anglepy.data.freyface as freyface
n_train = 1600
train_x = freyface.load_numpy().T
np.random.shuffle(train_x.T)
x = {'x': train_x[:,0:n_train].astype(np.float32)}
x_valid = {'x': train_x[:,n_train:].astype(np.float32)}
L_valid = 1
dim_input = (28,20)
n_x = train_x.shape[0]
type_pz = 'gaussianmarg'
type_px = 'bernoulli'
nonlinear = 'softplus'
n_batch = 100
colorImg = False
bernoulli_x = False
byteToFloat = False
elif dataset == 'norb':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
byteToFloat = False
bernoulli_x = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'norb_pca':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
f_enc, f_dec, _ = pp.PCA(train_x, 0.999)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'norb_normalized':
# small NORB dataset
import anglepy.data.norb as norb
size = 48
train_x, train_y, test_x, test_y = norb.load_resized(size, binarize_y=True)
#f_enc, f_dec, _ = pp.PCA(train_x, 0.99)
#f_enc, f_dec, _ = pp.normalize_random(train_x)
f_enc, f_dec, _ = pp.normalize(train_x)
train_x = f_enc(train_x)
test_x = f_enc(test_x)
x = {'x': train_x.astype(np.float32)}
x_valid = {'x': test_x.astype(np.float32)}
L_valid = 1
n_x = train_x.shape[0]
dim_input = (size,size)
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
n_batch = 900 #23400/900 = 27
colorImg = False
#binarize = False
bernoulli_x = False
byteToFloat = False
weight_decay= float(n_batch)/train_x.shape[1]
elif dataset == 'svhn':
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, test_x, test_y = svhn.load_numpy(False, binarize_y=True) #norb.load_resized(size, binarize_y=True)
extra_x, extra_y = svhn.load_numpy_extra(False, binarize_y=True)
x = {'x': np.hstack((train_x, extra_x)), 'y':np.hstack((train_y, extra_y))}
ndict.shuffleCols(x)
print 'Performing PCA, can take a few minutes... ',
f_enc, f_dec, pca_params = pp.PCA(x['x'][:,:10000], cutoff=600, toFloat=True)
ndict.savez(pca_params, logdir+'pca_params')
print 'Done.'
n_y = 10
x = {'x': f_enc(x['x']).astype(np.float32)}
x_valid = {'x': f_enc(test_x).astype(np.float32)}
L_valid = 1
n_x = x['x'].shape[0]
dim_input = (size,size)
n_batch = 5000
colorImg = True
bernoulli_x = False
byteToFloat = False
type_qz = 'gaussianmarg'
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
# Construct model
from anglepy.models import GPUVAE_Z_X
updates = get_adam_optimizer(learning_rate=3e-4, weight_decay=weight_decay)
model = GPUVAE_Z_X(updates, n_x, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-3)
if False:
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412689061/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412676966/'
#dir = '/Users/dpkingma/results/learn_z_x_svhn_bernoulli_300-(1000, 1000)_l1l2_sharing_and_1000HU_1412695481/'
#dir = '/Users/dpkingma/results/learn_z_x_mnist_binarized_50-(500, 500)_mog_1412695455/'
#dir = '/Users/dpkingma/results/gpulearn_z_x_svhn_pca_300-(500, 500)__1413904756/'
dir = '/home/ubuntu/results/gpulearn_z_x_mnist_50-[500, 500]__1414259423/'
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# Some statistics for optimization
ll_valid_stats = [-1e99, 0]
# Progress hook
def hook(epoch, t, ll):
if epoch%10 != 0: return
ll_valid, _ = model.est_loglik(x_valid, n_samples=L_valid, n_batch=n_batch, byteToFloat=byteToFloat)
# Log
ndict.savez(ndict.get_value(model.v), logdir+'v')
ndict.savez(ndict.get_value(model.w), logdir+'w')
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir+'v_best')
ndict.savez(ndict.get_value(model.w), logdir+'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir+'hook.txt', 'a') as f:
print >>f, "Finished"
exit()
print epoch, t, ll, ll_valid, ll_valid_stats
with open(logdir+'hook.txt', 'a') as f:
print >>f, epoch, t, ll, ll_valid, ll_valid_stats
# Graphics
if gfx and epoch%gfx_freq == 0:
#tail = '.png'
tail = '-'+str(epoch)+'.png'
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
if 'pca' not in dataset and 'random' not in dataset and 'normalized' not in dataset:
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
if 'out_unif' in w:
image = paramgraphics.mat_to_img(f_dec(w['out_unif'].reshape((-1,1))), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_unif'+tail, 'PNG')
if n_z == 2:
n_width = 10
import scipy.stats
z = {'z':np.zeros((2,n_width**2))}
for i in range(0,n_width):
for j in range(0,n_width):
z['z'][0,n_width*i+j] = scipy.stats.norm.ppf(float(i)/n_width+0.5/n_width)
z['z'][1,n_width*i+j] = scipy.stats.norm.ppf(float(j)/n_width+0.5/n_width)
x, _, _z = model.gen_xz({}, z, n_width**2)
if dataset == 'mnist':
x = 1 - _z['x']
image = paramgraphics.mat_to_img(f_dec(_z['x']), dim_input)
image.save(logdir+'2dmanifold'+tail, 'PNG')
else:
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
#x_samples = _x['x']
#image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
#image.save(logdir+'samples2'+tail, 'PNG')
else:
# Model with preprocessing
if 'w0' in v:
image = paramgraphics.mat_to_img(f_dec(v['w0'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
_x, _, _z_confab = model.gen_xz({}, {}, n_batch=144)
x_samples = f_dec(_z_confab['x'])
x_samples = np.minimum(np.maximum(x_samples, 0), 1)
image = paramgraphics.mat_to_img(x_samples, dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
# Optimize
#SFO
dostep = epoch_vae_adam(model, x, n_batch=n_batch, bernoulli_x=bernoulli_x, byteToFloat=byteToFloat)
loop_va(dostep, hook)
pass
def main(n_passes, n_labeled, n_z, n_hidden, dataset, seed, alpha, n_minibatches, comment):
'''
Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z)
And where 'x' is always observed and 'y' is _sometimes_ observed (hence semi-supervised).
We're going to use q(y|x) as a classification model.
'''
import time
logdir = 'results/learn_yz_x_ss_'+dataset+'_'+str(n_z)+'-'+str(n_hidden)+'_nlabeled'+str(n_labeled)+'_alpha'+str(alpha)+'_seed'+str(seed)+'_'+comment+'-'+str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print 'logdir:', logdir
print sys.argv[0], n_labeled, n_z, n_hidden, dataset, seed, comment
np.random.seed(seed)
# Init data
if dataset == 'mnist_2layer':
size = 28
dim_input = (size,size)
# Load model for feature extraction
path = 'models/mnist_z_x_50-500-500_longrun/' #'models/mnist_z_x_50-600-600/'
l1_v = ndict.loadz(path+'v.ndict.tar.gz')
l1_w = ndict.loadz(path+'w.ndict.tar.gz')
n_h = (500,500)
from anglepy.models.VAE_Z_X import VAE_Z_X
l1_model = VAE_Z_X(n_x=28*28, n_hidden_q=n_h, n_z=50, n_hidden_p=n_h, nonlinear_q='softplus', nonlinear_p='softplus', type_px='bernoulli', type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1)
# Load dataset
import anglepy.data.mnist as mnist
# load train and test sets
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy_split(size, binarize_y=True)
# create labeled/unlabeled split in training set
x_l, y_l, x_u, y_u = mnist.create_semisupervised(train_x, train_y, n_labeled)
# Extract features
# 1. Determine which dimensions to keep
def transform(v, _x):
return l1_model.dist_qz['z'](*([_x] + v.values() + [np.ones((1, _x.shape[1]))]))
q_mean, _ = transform(l1_v, x_u[0:1000])
idx_keep = np.std(q_mean, axis=1) > 0.1
# 2. Select dimensions
for key in ['mean_b','mean_w','logvar_b','logvar_w']:
l1_v[key] = l1_v[key][idx_keep,:]
l1_w['w0'] = l1_w['w0'][:,idx_keep]
# 3. Extract features
x_mean_u, x_logvar_u = transform(l1_v, x_u)
x_mean_l, x_logvar_l = transform(l1_v, x_l)
x_unlabeled = {'mean':x_mean_u, 'logvar':x_logvar_u, 'y':y_u}
x_labeled = {'mean':x_mean_l, 'logvar':x_logvar_l, 'y':y_l}
valid_x, _ = transform(l1_v, valid_x)
test_x, _ = transform(l1_v, test_x)
n_x = np.sum(idx_keep)
n_y = 10
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
colorImg = False
if dataset == 'svhn_2layer':
size = 32
dim_input = (size,size)
# Load model for feature extraction
path = 'models/tmp/svhn_z_x_300-500-500/'
l1_v = ndict.loadz(path+'v.ndict.tar.gz')
l1_w = ndict.loadz(path+'w.ndict.tar.gz')
f_enc, f_dec = pp.PCA_fromfile(path+'pca_params.ndict.tar.gz', True)
from anglepy.models.VAE_Z_X import VAE_Z_X
n_x = l1_v['w0'].shape[1] #=600
l1_model = VAE_Z_X(n_x=n_x, n_hidden_q=(600,600), n_z=300, n_hidden_p=(600,600), nonlinear_q='softplus', nonlinear_p='softplus', type_px='gaussian', type_qz='gaussianmarg', type_pz='gaussianmarg', prior_sd=1)
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, valid_x, valid_y, test_x, test_y = svhn.load_numpy_split(False, binarize_y=True, extra=False) #norb.load_resized(size, binarize_y=True)
#train_x = np.hstack((_train_x, extra_x))
#train_y = np.hstack((_train_y, extra_y))[:,:604000]
# create labeled/unlabeled split in training set
import anglepy.data.mnist as mnist
x_l, y_l, x_u, y_u = mnist.create_semisupervised(train_x, train_y, n_labeled)
# Extract features
# 1. Determine which dimensions to keep
def transform(v, _x):
return l1_model.dist_qz['z'](*([f_enc(_x)] + v.values() + [np.ones((1, _x.shape[1]))]))
# 2. We're keeping all latent dimensions
# 3. Extract features
x_mean_u, x_logvar_u = transform(l1_v, x_u)
x_mean_l, x_logvar_l = transform(l1_v, x_l)
x_unlabeled = {'mean':x_mean_u, 'logvar':x_logvar_u, 'y':y_u}
x_labeled = {'mean':x_mean_l, 'logvar':x_logvar_l, 'y':y_l}
valid_x, _ = transform(l1_v, valid_x)
test_x, _ = transform(l1_v, test_x)
n_x = l1_w['w0'].shape[1]
n_y = 10
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
# Init VAE model p(x,y,z)
from anglepy.models.VAE_YZ_X import VAE_YZ_X
uniform_y = True
model = VAE_YZ_X(n_x, n_y, n_hidden, n_z, n_hidden, nonlinear, nonlinear, type_px, type_qz="gaussianmarg", type_pz=type_pz, prior_sd=1, uniform_y=uniform_y)
v, w = model.init_w(1e-3)
# Init q(y|x) model
from anglepy.models.MLP_Categorical import MLP_Categorical
n_units = [n_x]+list(n_hidden)+[n_y]
model_qy = MLP_Categorical(n_units=n_units, prior_sd=1, nonlinearity=nonlinear)
u = model_qy.init_w(1e-3)
# Just test
if False:
u = ndict.loadz('u.ndict.tar.gz')
v = ndict.loadz('v.ndict.tar.gz')
w = ndict.loadz('w.ndict.tar.gz')
pass
# Progress hook
t0 = time.time()
def hook(t, u, v, w, ll):
# Get classification error of validation and test sets
def error(dataset_x, dataset_y):
_, _, _z = model_qy.gen_xz(u, {'x':dataset_x}, {})
return np.sum( np.argmax(_z['py'], axis=0) != np.argmax(dataset_y, axis=0)) / (0.0 + dataset_y.shape[1])
valid_error = error(valid_x, valid_y)
test_error = error(test_x, test_y)
# Log
ndict.savez(u, logdir+'u')
ndict.savez(v, logdir+'v')
ndict.savez(w, logdir+'w')
dt = time.time() - t0
print dt, t, ll, valid_error, test_error
with open(logdir+'hook.txt', 'a') as f:
print >>f, dt, t, ll, valid_error, test_error
return valid_error
# Optimize
result = optim_vae_ss_adam(alpha, model_qy, model, x_labeled, x_unlabeled, n_y, u, v, w, n_minibatches=n_minibatches, n_passes=n_passes, hook=hook)
return result
import numpy as np
from anglepy import ndict
import scipy.io as sio
import cPickle, gzip
import math
import os, sys
# load data, recognition model and generative model
print 'Loading data...'
dir = sys.argv[1]
p_type = sys.argv[5]
if p_type == 'null':
p_type = ''
v = ndict.loadz(dir + 'v' + p_type + '.ndict.tar.gz')
w = ndict.loadz(dir + 'w' + p_type + '.ndict.tar.gz')
# perturb data
print 'Loading perturbed data...'
width = 28
height = 28
denoise_tpye = 1 # sample or mean
pertub_type = int(sys.argv[2])
pertub_prob = float(sys.argv[3])
denoise_times = int(sys.argv[4]) # denoising epoch
print pertub_type, pertub_prob, denoise_times
if pertub_type == 4:
def hook(epoch, t, ll):
if epoch%10 != 0:
return
ll_valid, _ = model.est_loglik(x_valid, n_samples=L_valid, n_batch=n_batch, byteToFloat=byteToFloat)
if math.isnan(ll_valid):
print "NaN detected. Reverting to saved best parameters"
ndict.set_value(model.v, ndict.loadz(logdir+'v.ndict.tar.gz'))
ndict.set_value(model.w, ndict.loadz(logdir+'w.ndict.tar.gz'))
return
if ll_valid > ll_valid_stats[0]:
ll_valid_stats[0] = ll_valid
ll_valid_stats[1] = 0
ndict.savez(ndict.get_value(model.v), logdir+'v_best')
ndict.savez(ndict.get_value(model.w), logdir+'w_best')
else:
ll_valid_stats[1] += 1
# Stop when not improving validation set performance in 100 iterations
if False and ll_valid_stats[1] > 1000:
print "Finished"
with open(logdir+'hook.txt', 'a') as f:
print >>f, "Finished"
exit()
# Log
ndict.savez(ndict.get_value(model.v), logdir+'v')
ndict.savez(ndict.get_value(model.w), logdir+'w')
print epoch, t, ll, ll_valid
with open(logdir+'hook.txt', 'a') as f:
print >>f, t, ll, ll_valid
if gfx:
# Graphics
v = {i: model.v[i].get_value() for i in model.v}
w = {i: model.w[i].get_value() for i in model.w}
tail = '-'+str(epoch)+'.png'
image = paramgraphics.mat_to_img(f_dec(v['w0x'][:].T), dim_input, True, colorImg=colorImg)
image.save(logdir+'q_w0x'+tail, 'PNG')
image = paramgraphics.mat_to_img(f_dec(w['out_w'][:]), dim_input, True, colorImg=colorImg)
image.save(logdir+'out_w'+tail, 'PNG')
_x = {'y': np.random.multinomial(1, [1./n_y]*n_y, size=144).T}
_, _, _z_confab = model.gen_xz(_x, {}, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples'+tail, 'PNG')
_, _, _z_confab = model.gen_xz(y_sample, z_sample, n_batch=144)
image = paramgraphics.mat_to_img(f_dec(_z_confab['x']), dim_input, colorImg=colorImg)
image.save(logdir+'samples_fixed'+tail, 'PNG')
if n_z == 2:
import ImageFont
import ImageDraw
n_width = 10
submosaic_offset = 15
submosaic_width = (dim_input[1]*n_width)
submosaic_height = (dim_input[0]*n_width)
mosaic = Image.new("RGB", (submosaic_width*mosaic_w, submosaic_offset+submosaic_height*mosaic_h))
for digit in range(0,n_y):
if digit >= mosaic_h*mosaic_w: continue
_x = {}
n_batch_plot = n_width*n_width
_x['y'] = np.zeros((n_y,n_batch_plot))
_x['y'][digit,:] = 1
_z = {'z':np.zeros((2,n_width**2))}
for i in range(0,n_width):
for j in range(0,n_width):
_z['z'][0,n_width*i+j] = scipy.stats.norm.ppf(float(i)/n_width+0.5/n_width)
_z['z'][1,n_width*i+j] = scipy.stats.norm.ppf(float(j)/n_width+0.5/n_width)
_x, _, _z_confab = model.gen_xz(_x, _z, n_batch=n_batch_plot)
x_samples = _z_confab['x']
image = paramgraphics.mat_to_img(f_dec(x_samples), dim_input, colorImg=colorImg, tile_spacing=(0,0))
#image.save(logdir+'samples_digit_'+str(digit)+'_'+tail, 'PNG')
mosaic_x = (digit%mosaic_w)*submosaic_width
mosaic_y = submosaic_offset+int(digit/mosaic_w)*submosaic_height
mosaic.paste(image, (mosaic_x, mosaic_y))
draw = ImageDraw.Draw(mosaic)
draw.text((1,1),"Epoch #"+str(epoch)+" Loss="+str(int(ll)))
#plt.savefig(logdir+'mosaic'+tail, format='PNG')
mosaic.save(logdir+'mosaic'+tail, 'PNG')
def main(n_passes, n_labeled, n_z, n_hidden, dataset, seed, alpha,
n_minibatches, comment):
'''
Learn a variational auto-encoder with generative model p(x,y,z)=p(y)p(z)p(x|y,z)
And where 'x' is always observed and 'y' is _sometimes_ observed (hence semi-supervised).
We're going to use q(y|x) as a classification model.
'''
import time
logdir = 'results/learn_yz_x_ss_' + dataset + '_' + str(n_z) + '-' + str(
n_hidden) + '_nlabeled' + str(n_labeled) + '_alpha' + str(
alpha) + '_seed' + str(seed) + '_' + comment + '-' + str(
int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print('logdir:', logdir)
print(sys.argv[0], n_labeled, n_z, n_hidden, dataset, seed, comment)
np.random.seed(seed)
# Init data
if dataset == 'mnist_2layer':
size = 28
dim_input = (size, size)
# Load model for feature extraction
path = 'models/mnist_z_x_50-500-500_longrun/' #'models/mnist_z_x_50-600-600/'
l1_v = ndict.loadz(path + 'v.ndict.tar.gz')
l1_w = ndict.loadz(path + 'w.ndict.tar.gz')
n_h = (500, 500)
from anglepy.models.VAE_Z_X import VAE_Z_X
l1_model = VAE_Z_X(n_x=28 * 28,
n_hidden_q=n_h,
n_z=50,
n_hidden_p=n_h,
nonlinear_q='softplus',
nonlinear_p='softplus',
type_px='bernoulli',
type_qz='gaussianmarg',
type_pz='gaussianmarg',
prior_sd=1)
# Load dataset
import anglepy.data.mnist as mnist
# load train and test sets
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy_split(
size, binarize_y=True)
# create labeled/unlabeled split in training set
x_l, y_l, x_u, y_u = mnist.create_semisupervised(
train_x, train_y, n_labeled)
# Extract features
# 1. Determine which dimensions to keep
def transform(v, _x):
return l1_model.dist_qz['z'](*([_x] + list(v.values()) +
[np.ones((1, _x.shape[1]))]))
q_mean, _ = transform(l1_v, x_u[0:1000])
idx_keep = np.std(q_mean, axis=1) > 0.1
# 2. Select dimensions
for key in ['mean_b', 'mean_w', 'logvar_b', 'logvar_w']:
l1_v[key] = l1_v[key][idx_keep, :]
l1_w['w0'] = l1_w['w0'][:, idx_keep]
# 3. Extract features
x_mean_u, x_logvar_u = transform(l1_v, x_u)
x_mean_l, x_logvar_l = transform(l1_v, x_l)
x_unlabeled = {'mean': x_mean_u, 'logvar': x_logvar_u, 'y': y_u}
x_labeled = {'mean': x_mean_l, 'logvar': x_logvar_l, 'y': y_l}
valid_x, _ = transform(l1_v, valid_x)
test_x, _ = transform(l1_v, test_x)
n_x = np.sum(idx_keep)
n_y = 10
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
colorImg = False
if dataset == 'svhn_2layer':
size = 32
dim_input = (size, size)
# Load model for feature extraction
path = 'models/tmp/svhn_z_x_300-500-500/'
l1_v = ndict.loadz(path + 'v.ndict.tar.gz')
l1_w = ndict.loadz(path + 'w.ndict.tar.gz')
f_enc, f_dec = pp.PCA_fromfile(path + 'pca_params.ndict.tar.gz', True)
from anglepy.models.VAE_Z_X import VAE_Z_X
n_x = l1_v['w0'].shape[1] #=600
l1_model = VAE_Z_X(n_x=n_x,
n_hidden_q=(600, 600),
n_z=300,
n_hidden_p=(600, 600),
nonlinear_q='softplus',
nonlinear_p='softplus',
type_px='gaussian',
type_qz='gaussianmarg',
type_pz='gaussianmarg',
prior_sd=1)
# SVHN dataset
import anglepy.data.svhn as svhn
size = 32
train_x, train_y, valid_x, valid_y, test_x, test_y = svhn.load_numpy_split(
False, binarize_y=True,
extra=False) #norb.load_resized(size, binarize_y=True)
#train_x = np.hstack((_train_x, extra_x))
#train_y = np.hstack((_train_y, extra_y))[:,:604000]
# create labeled/unlabeled split in training set
import anglepy.data.mnist as mnist
x_l, y_l, x_u, y_u = mnist.create_semisupervised(
train_x, train_y, n_labeled)
# Extract features
# 1. Determine which dimensions to keep
def transform(v, _x):
return l1_model.dist_qz['z'](*([f_enc(_x)] + list(v.values()) +
[np.ones((1, _x.shape[1]))]))
# 2. We're keeping all latent dimensions
# 3. Extract features
x_mean_u, x_logvar_u = transform(l1_v, x_u)
x_mean_l, x_logvar_l = transform(l1_v, x_l)
x_unlabeled = {'mean': x_mean_u, 'logvar': x_logvar_u, 'y': y_u}
x_labeled = {'mean': x_mean_l, 'logvar': x_logvar_l, 'y': y_l}
valid_x, _ = transform(l1_v, valid_x)
test_x, _ = transform(l1_v, test_x)
n_x = l1_w['w0'].shape[1]
n_y = 10
type_pz = 'gaussianmarg'
type_px = 'gaussian'
nonlinear = 'softplus'
# Init VAE model p(x,y,z)
from anglepy.models.VAE_YZ_X import VAE_YZ_X
uniform_y = True
model = VAE_YZ_X(n_x,
n_y,
n_hidden,
n_z,
n_hidden,
nonlinear,
nonlinear,
type_px,
type_qz="gaussianmarg",
type_pz=type_pz,
prior_sd=1,
uniform_y=uniform_y)
v, w = model.init_w(1e-3)
# Init q(y|x) model
from anglepy.models.MLP_Categorical import MLP_Categorical
n_units = [n_x] + list(n_hidden) + [n_y]
model_qy = MLP_Categorical(n_units=n_units,
prior_sd=1,
nonlinearity=nonlinear)
u = model_qy.init_w(1e-3)
# Just test
if False:
u = ndict.loadz('u.ndict.tar.gz')
v = ndict.loadz('v.ndict.tar.gz')
w = ndict.loadz('w.ndict.tar.gz')
pass
# Progress hook
t0 = time.time()
def hook(t, u, v, w, ll):
# Get classification error of validation and test sets
def error(dataset_x, dataset_y):
_, _, _z = model_qy.gen_xz(u, {'x': dataset_x}, {})
return np.sum(
np.argmax(_z['py'], axis=0) != np.argmax(dataset_y, axis=0)
) / (0.0 + dataset_y.shape[1])
valid_error = error(valid_x, valid_y)
test_error = error(test_x, test_y)
# Log
ndict.savez(u, logdir + 'u')
ndict.savez(v, logdir + 'v')
ndict.savez(w, logdir + 'w')
dt = time.time() - t0
print(dt, t, ll, valid_error, test_error)
with open(logdir + 'hook.txt', 'a') as f:
print(dt, t, ll, valid_error, test_error, file=f)
return valid_error
# Optimize
result = optim_vae_ss_adam(alpha,
model_qy,
model,
x_labeled,
x_unlabeled,
n_y,
u,
v,
w,
n_minibatches=n_minibatches,
n_passes=n_passes,
hook=hook)
return result
type_px = 'gaussian'
nonlinear = 'softplus'
n_y = 10
n_batch_w = 10
colorImg = True
binarize = False
if True:
n_hidden = (500,500)
n_z = 300
dir = 'models/svhn_yz_x_300-500-500/'
from anglepy.models import GPUVAE_YZ_X
model = GPUVAE_YZ_X(None, n_x, n_y, n_hidden, n_z, n_hidden[::-1], nonlinear, nonlinear, type_px, type_qz=type_qz, type_pz=type_pz, prior_sd=100, init_sd=1e-2)
w = ndict.loadz(dir+'w_best.ndict.tar.gz')
v = ndict.loadz(dir+'v_best.ndict.tar.gz')
ndict.set_value(model.w, w)
ndict.set_value(model.v, v)
# PCA
f_enc, f_dec = pp.PCA_fromfile(dir+'pca_params.ndict.tar.gz')
if dataset == 'mnist':
# MNIST
import anglepy.data.mnist as mnist
train_x, train_y, valid_x, valid_y, test_x, test_y = mnist.load_numpy(size=28, binarize_y=True)
f_enc, f_dec = lambda x:x, lambda x:x
n_x = 28*28
dim_input = (28,28)
from anglepy import ndict
import scipy.io as sio
import cPickle, gzip
import math
import os, sys
# load data, recognition model and generative model
print "Loading data..."
f = gzip.open("data/mnist/mnist_28.pkl.gz", "rb")
(x_train, t_train), (x_valid, t_valid), (x_test, t_test) = cPickle.load(f)
f.close()
dir = sys.argv[1]
v = ndict.loadz(dir + "v_best.ndict.tar.gz")
w = ndict.loadz(dir + "w_best.ndict.tar.gz")
# choose number of images to transform and number of images to do visualization
num_trans = 1000
num_show = 300
data = (x_test[:num_trans, :]).T
pertub_label = np.ones(data.shape)
# perturb data
print "Loading perturbed data..."
width = 28
height = 28
denoise_tpye = 1 # sample or mean
pertub_type = int(sys.argv[2])