# END OF MODULE 2
# TESTING PHASE
start_time = time.time()
score_test = compute_score(X_test, Y_test)
t_test = regr.predict(score_test)
print 'original t_test is in ', min(t_test), '..', max(t_test)
t_test[t_test > 1] = max(t_test[t_test < 1])
t_test[t_test < 0] = min(
t_test[t_test > 0]) # ! Keep t_test in [0,1]
print 'corrected t_test is in ', min(t_test), '..', max(t_test)
# Predict label
metrics = predict_label(score_test,
Y_test,
t_test,
seed,
num_classes,
verbose=1)
time_profiles['test'].append(time.time() - start_time)
all_metrics.append(metrics)
except KeyboardInterrupt:
pass
# Store all_metrics and print estimates
np.save(osp.join('metrics', snapshot_name + '_allmetrics.npy'),
all_metrics)
np.save(osp.join('metrics', snapshot_name + '_time'), time_profiles)
print '\nFINAL ESTIMATES FOR', snapshot_name, 'IN', len(
regr.fit(score_train, t_train)
time_profiles['train_module2'].append(time.time()-start_time)
# END OF MODULE 2
# TESTING PHASE
start_time = time.time()
score_test = compute_score(X_test, Y_test)
t_test = regr.predict(score_test)
print 'original t_test is in ', min(t_test), '..', max(t_test)
t_test[t_test>1] = max(t_test[t_test<1])
t_test[t_test<0] = min(t_test[t_test>0]) # ! Keep t_test in [0,1]
print 'corrected t_test is in ', min(t_test), '..', max(t_test)
# Predict label
metrics = predict_label(score_test, Y_test, t_test, seed, num_classes, verbose=1)
time_profiles['test'].append(time.time()-start_time)
all_metrics.append(metrics)
except KeyboardInterrupt:
pass
# Store all_metrics and print estimates
np.save(osp.join('metrics',snapshot_name + '_allmetrics.npy'), all_metrics)
np.save(osp.join('metrics',snapshot_name + '_time'), time_profiles)
print '\nFINAL ESTIMATES FOR', snapshot_name,'IN',len(all_metrics),'RUNS'
estimate_metrics(all_metrics)
def main(reps, pretrained_w_path, do_module1, init_seed=0, load_t=0, num_epochs=200,
batchsize=96, fine_tune=0, patience=500, lr_init = 1e-3, optim='adagrad', toy=0,
num_classes=23):
res_root = '/home/hoa/Desktop/projects/resources'
X_path=osp.join(res_root, 'datasets/msrcv2/Xaug_b01c.npy')
Y_path=osp.join(res_root, 'datasets/msrcv2/Y.npy')
MEAN_IMG_PATH=osp.join(res_root, 'models/ilsvrc_2012_mean.npy')
snapshot=50 # save model after every `snapshot` epochs
drop_p=0.5 # drop out prob.
lambda2=0.0005/2 # l2-regularizer constant
# step=patience/4 # decay learning after every `step` epochs
lr_patience=60 # for learning rate schedule, if optim=='momentum'
if toy: # unit testing
num_epochs=10
data_multi=3
reps = 2
#drop_p=0
#lambda2=0
# Create name tag for the experiment
if fine_tune:
full_or_tune = 'tune' # description tag for storing associated files
else:
full_or_tune = 'full'
time_stamp=time.strftime("%y%m%d%H%M%S", time.localtime())
snapshot_root = '../snapshot_models/'
snapshot_name = str(num_classes)+'alex'+time_stamp+full_or_tune
# LOADING DATA
print 'LOADING DATA ...'
X = np.load(X_path)
Y = np.load(Y_path)
if X.shape[1]!=3:
X = b01c_to_bc01(X)
N = len(Y)
print 'Raw X,Y shape', X.shape, Y.shape
if len(X) != len(Y):
print 'Inconsistent number of input images and labels. X is possibly augmented.'
MEAN_IMG = np.load(MEAN_IMG_PATH)
MEAN_IMG_227 = skimage.transform.resize(
np.swapaxes(np.swapaxes(MEAN_IMG,0,1),1,2), (227,227), mode='nearest', preserve_range=True)
MEAN_IMG = np.swapaxes(np.swapaxes(MEAN_IMG_227,1,2),0,1).reshape((1,3,227,227))
all_metrics = [] # store metrics in each run
time_profiles = {
'train_module1': [],
'train_module1_eff': [],
'train_module2': [],
'test': []
} # record training and testing time
# PREPARE THEANO EXPRESSION FOR BOTH MODULES
print 'COMPILING THEANO EXPRESSION ...'
input_var = T.tensor4('inputs')
target_var = T.imatrix('targets')
network = build_model(num_classes=num_classes, input_var=input_var)
# Create a loss expression for training
prediction = lasagne.layers.get_output(network)
loss = lasagne.objectives.binary_crossentropy(prediction, target_var)
weights = lasagne.layers.get_all_params(network, regularizable=True)
l2reg = theano.shared(floatX(lambda2))*T.sum([T.sum(w ** 2) for w in weights])
loss = loss.mean() + l2reg
lr = theano.shared(np.array(lr_init, dtype=theano.config.floatX))
lr_decay = np.array(1./3, dtype=theano.config.floatX)
# Create update expressions for training
params = lasagne.layers.get_all_params(network, trainable=True)
# last-layer case is actually very simple:
# `params` above is a list of all (W,b)-pairs
# Therefore last layer's (W,b) is params[-2:]
if fine_tune == 7: # tuning params from fc7 to fc8
params = params[-2:]
# elif fine_tune == 6: # tuning params from fc6 to fc8
# params = params[-4:]
# TODO adjust for per-layer training with local_lr
if optim=='momentum':
updates = lasagne.updates.nesterov_momentum(loss, params, learning_rate=lr, momentum=0.9)
elif optim=='rmsprop':
updates = lasagne.updates.rmsprop(loss, params, learning_rate=lr, rho=0.9, epsilon=1e-06)
elif optim=='adam':
updates = lasagne.updates.adam(
loss, params, learning_rate=lr, beta1=0.9, beta2=0.999, epsilon=1e-08)
elif optim=='adagrad':
updates = lasagne.updates.adagrad(loss, params, learning_rate=lr, epsilon=1e-06)
# Create a loss expression for validation/testing
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.binary_crossentropy(test_prediction,
target_var)
test_loss = test_loss.mean() + l2reg
# zero-one loss with threshold t = 0.5 for reference
# zero_one_loss = T.abs_((test_prediction > theano.shared(floatX(0.5))) - target_var).sum(axis=1)
#zero_one_loss /= target_var.shape[1].astype(theano.config.floatX)
#zero_one_loss = zero_one_loss.mean()
# Compile a function performing a backward pass (training step) on a mini-batch (by giving
# the updates dictionary) and returning the corresponding training loss:
bwd_fn = theano.function([input_var, target_var], loss, updates=updates,)
# Compile a second function performing a forward pass,
# returns validation loss, 0/1 Error, score i.e. Xout:
fwd_fn = theano.function([input_var, target_var], test_loss)
# Create a theano function for computing score
score = lasagne.layers.get_output(network, deterministic=True)
score_fn = theano.function([input_var], score)
def compute_score(X, Y, batchsize=batchsize, shuffle=False):
out = np.zeros(Y.shape)
batch_id = 0
for batch in iterate_minibatches(X, Y, batchsize, shuffle=False):
inputs, _ = batch
# Flip random half of the batch
flip_idx = np.random.choice(len(inputs),size=len(inputs)/2,replace=False)
if len(flip_idx)>1:
inputs[flip_idx] = inputs[flip_idx,:,:,::-1]
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
if len(inputs)==batchsize:
out[batch_id*batchsize : (batch_id+1)*batchsize] = score_fn(inputs)
batch_id += 1
else:
out[batch_id*batchsize : ] = score_fn(inputs)
return out
try:
# MAIN LOOP FOR EACH RUN
for seed in np.arange(reps)+init_seed:
# reset learning rate
lr.set_value(lr_init)
print '\nRUN', seed, '...'
# Split train/val/test set
indicies = np.arange(len(Y))
Y_train_val, Y_test, idx_train_val, idx_test = train_test_split(
Y, indicies, random_state=seed, train_size=float(2)/3)
Y_train, Y_val, idx_train, idx_val = train_test_split(
Y_train_val, idx_train_val, random_state=seed)
print "Train/val/test set size:",len(idx_train),len(idx_val),len(idx_test)
idx_aug_train = data_aug(idx_train, mode='aug', isMat='idx', N=N)
Xaug_train = X[idx_aug_train]
Yaug_train = data_aug(Y_train, mode='aug', isMat='Y', N=N)
idx_aug_val = data_aug(idx_val, mode='aug', isMat='idx', N=N)
Xaug_val = X[idx_aug_val]
Yaug_val = data_aug(Y_val, mode='aug', isMat='Y', N=N)
# Module 2 training set is composed of module 1 training and validation set
idx_aug_train_val = data_aug(idx_train_val, mode='aug', isMat='idx', N=N)
Xaug_train_val = X[idx_aug_train_val]
Yaug_train_val = data_aug(Y_train_val, mode='aug', isMat='Y', N=N)
# Test set
X_test = X[idx_test]
# Y_test is already returned in the first train_test_split
print "Augmented train/val/test set size:",len(Xaug_train),len(Yaug_val), len(X_test)
print "Augmented (X,Y) dtype:", Xaug_train.dtype, Yaug_val.dtype
print "Processed Mean image:",MEAN_IMG.dtype,MEAN_IMG.shape
if toy: # try to overfit a tiny subset of the data
Xaug_train = Xaug_train[:batchsize*data_multi + batchsize/2]
Yaug_train = Yaug_train[:batchsize*data_multi + batchsize/2]
Xaug_val = Xaug_val[:batchsize + batchsize/2]
Yaug_val = Yaug_val[:batchsize + batchsize/2]
# Init by pre-trained weights, if any
if len(pretrained_w_path)>0:
layer_list = lasagne.layers.get_all_layers(network) # 22 layers
if pretrained_w_path.endswith('pkl'):
# load reference_net
# use case: weights initialized from pre-trained reference nets
f = open(pretrained_w_path, 'r')
w_list = pickle.load(f) # list of 11 (W,b)-pairs
f.close()
lasagne.layers.set_all_param_values(layer_list[-3], w_list[:-2])
# exclude (W,b) of fc8
# BIG NOTE: don't be confused, it's pure coincident that layer_list
# and w_list have the same index here. The last element of layer_list are
# [.., fc6, drop6, fc7, drop7, fc8], while w_list are
# [..., W, b, W, b, W, b] which, eg w_list[-4] and w_list[-3] correspond to
# params that are associated with fc7 i.e. params that connect drop6 to fc7
elif pretrained_w_path.endswith('npz'):
# load self-trained net
# use case: continue training from a snapshot model
with np.load(pretrained_w_path) as f: # NOTE: only load snapshot of the same `seed`
# w_list = [f['arr_%d' % i] for i in range(len(f.files))]
w_list = [f.items()['arr_%d' % i] for i in range(len(f.files))] # load from bkviz, one-time use
lasagne.layers.set_all_param_values(network, w_list)
elif pretrained_w_path.endswith('/'): # init from 1 of the 30 snapshots
from os import listdir
import re
files = [f for f in listdir(pretrained_w_path) if osp.isfile(osp.join(pretrained_w_path, f))]
for file_name in files:
regex_seed = 'full%d_' %seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
print snapshot_name
with np.load(osp.join(pretrained_w_path,snapshot_name)+'.npz') as f:
w_list = [f['arr_%d' % i] for i in range(len(f.files))]
lasagne.layers.set_all_param_values(network, w_list)
# START MODULE 1
module1_time = 0
if do_module1:
print 'MODULE 1'
training_history={}
training_history['iter_training_loss'] = []
training_history['iter_validation_loss'] = []
training_history['training_loss'] = []
training_history['validation_loss'] = []
training_history['learning_rate'] = []
# http://deeplearning.net/tutorial/gettingstarted.html#early-stopping
# early-stopping parameters
n_train_batches = Xaug_train.shape[0] / batchsize
if Xaug_train.shape[0] % batchsize != 0:
n_train_batches += 1
patience = patience # look as this many examples regardless
patience_increase = 2 # wait this much longer when a new best is found
lr_patience_increase = 1.01
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant; a significant test
# MIGHT be better
validation_frequency = min(n_train_batches, patience/2)
# go through this many
# minibatches before checking the network
# on the validation set; in this case we
# check every epoch
best_params = None
epoch_validation_loss = 0 # indicates that valid_loss has not been computed yet
best_validation_loss = np.inf
best_iter = -1
lr_iter = -1
test_score = 0.
start_time = time.time()
done_looping = False
epoch = 0
# Finally, launch the training loop.
print("Starting training...")
# We iterate over epochs:
print("\nEpoch\tTrain Loss\tValid Loss\tBest-ValLoss-and-Iter\tTime\tL.Rate")
sys.setrecursionlimit(10000)
try: # Early-stopping implementation
while (not done_looping) and (epoch<num_epochs):
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(Xaug_train, Yaug_train, batchsize, shuffle=True):
inputs, targets = batch
# Horizontal flip half of the images
bs = inputs.shape[0]
indices = np.random.choice(bs, bs / 2, replace=False)
inputs[indices] = inputs[indices, :, :, ::-1]
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
train_err_batch = bwd_fn(inputs, targets)
train_err += train_err_batch
train_batches += 1
iter_now = epoch*n_train_batches + train_batches
training_history['iter_training_loss'].append(train_err_batch)
training_history['iter_validation_loss'].append(epoch_validation_loss)
if (iter_now+1) % validation_frequency == 0:
# a full pass over the validation data:
val_err = 0
#zero_one_err = 0
val_batches = 0
for batch in iterate_minibatches(Xaug_val, Yaug_val, batchsize, shuffle=False):
inputs, targets = batch
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
val_err_batch = fwd_fn(inputs, targets)
val_err += val_err_batch
val_batches += 1
epoch_validation_loss = val_err / val_batches
if epoch_validation_loss < best_validation_loss:
if epoch_validation_loss < best_validation_loss*improvement_threshold:
patience = max(patience, iter_now * patience_increase)
# lr_patience *= lr_patience_increase
best_params = lasagne.layers.get_all_param_values(network)
best_validation_loss = epoch_validation_loss
best_iter = iter_now
lr_iter = best_iter
else: # decay learning rate if optim=='momentum'
if optim=='momentum' and (iter_now - lr_iter) > lr_patience:
lr.set_value(lr.get_value() * lr_decay)
lr_iter = iter_now
if patience <= iter_now:
done_looping = True
break
# Record training history
training_history['training_loss'].append(train_err / train_batches)
training_history['validation_loss'].append(epoch_validation_loss)
training_history['learning_rate'].append(lr.get_value())
epoch_time = time.time() - start_time
module1_time += epoch_time
# Then we print the results for this epoch:
print("{}\t{:.6f}\t{:.6f}\t{:.6f}\t{}\t{:.3f}\t{}".format(
epoch+1,
training_history['training_loss'][-1],
training_history['validation_loss'][-1],
best_validation_loss,
best_iter+1,
epoch_time,
training_history['learning_rate'][-1]
))
if (epoch+1)%snapshot==0: # TODO try to save weights at best_iter
snapshot_path_string = snapshot_root+snapshot_name+str(seed)+'_'+str(iter_now+1)
try: # use case: terminate experiment before reaching `reps`
np.savez(snapshot_path_string+'.npz', *best_params)
np.savez(snapshot_path_string+'_history.npz', training_history)
plot_loss(training_history, snapshot_path_string+'_loss.png')
# plot_conv_weights(lasagne.layers.get_all_layers(network)[1],
# snapshot_path_string+'_conv1weights_')
except KeyboardInterrupt, TypeError:
print 'Did not save', snapshot_name+str(seed)+'_'+str(iter_now+1)
pass
epoch += 1
except KeyboardInterrupt, MemoryError: # Sadly this can only catch KeyboardInterrupt
pass
print 'Training finished or KeyboardInterrupt (Training is never finished, only abandoned)'
module1_time_eff = module1_time / iter_now * best_iter
print('Total and Effective training time are {:.0f} and {:.0f}').format(
module1_time, module1_time_eff)
time_profiles['train_module1'].append(module1_time)
time_profiles['train_module1_eff'].append(module1_time_eff)
# Save model after num_epochs or KeyboardInterrupt
if (epoch+1)%snapshot!=0: # to avoid duplicate save
snapshot_path_string = snapshot_root+snapshot_name+str(seed)+'_'+str(iter_now+1)
if not toy:
try: # use case: terminate experiment before reaching `reps`
print 'Saving model...'
np.savez(snapshot_path_string+'.npz', *best_params)
np.savez(snapshot_path_string+'_history.npz', training_history)
plot_loss(training_history, snapshot_path_string+'_loss.png')
# plot_conv_weights(lasagne.layers.get_all_layers(network)[1],
# snapshot_path_string+'_conv1weights_')
except KeyboardInterrupt, TypeError:
print 'Did not save', snapshot_name+str(seed)+'_'+str(iter_now+1)
pass
# And load them again later on like this:
#with np.load('../snapshot_models/23alex16042023213910.npz') as f:
# param_values = [f['arr_%d' % i] for i in range(len(f.files))] # or
# training_history = f['arr_0'].items()
# lasagne.layers.set_all_param_values(network, param_values)
# END OF MODULE 1
# START MODULE 2
print '\nMODULE 2'
if not do_module1:
if pretrained_w_path.endswith('pkl'):
snapshot_name = str(num_classes)+'alexOTS' # short for "off-the-shelf init"
elif pretrained_w_path.endswith('npz'): # Resume from a SINGLE snapshot
# extract name pattern, e.g. '23alex16042023213910full10'
# from string '../snapshot_models/23alex16042023213910full10_100.npz'
import re
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+"
match = re.search(regex, pretrained_w_path)
snapshot_name = match.group(0)
elif pretrained_w_path.endswith('/'): # RESUMED FROM TRAINED MODULE 1 (ONE-TIME USE)
from os import listdir
import re
files = [f for f in listdir(pretrained_w_path) if osp.isfile(osp.join(pretrained_w_path, f))]
for file_name in files:
regex_seed = 'full%d_' %seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
print snapshot_name
with np.load(osp.join(pretrained_w_path,snapshot_name)+'.npz') as f:
w_list = [f['arr_%d' % i] for i in range(len(f.files))]
lasagne.layers.set_all_param_values(network, w_list)
else: # MAIN BRANCH - assume do_module1 is True AND have run `snapshot` epochs
if (epoch+1)>snapshot:
with np.load(snapshot_path_string+'.npz') as f: # reload the best params for module 1
w_list = [f['arr_%d' % i] for i in range(len(f.files))]
lasagne.layers.set_all_param_values(network, w_list)
score_train = compute_score(Xaug_train_val, Yaug_train_val)
start_time = time.time()
if load_t: # Server failed at the wrong time. We only have t backed-up
if pretrained_w_path.endswith('/'):
from os import listdir
import re
files = [f for f in listdir(pretrained_w_path) if osp.isfile(osp.join(pretrained_w_path, f))]
for file_name in files:
regex_seed = 'full%d_' %seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
t_train = np.load(osp.join('t','{0}.npy'.format(snapshot_name)))
else: # MAIN BRANCH
thresholds = Threshold(score_train, Yaug_train_val)
thresholds.find_t_for() # determine t_train for each score_train. It will take a while
t_train = np.asarray(thresholds.t)
print 't_train is in ', t_train.min(), '..', t_train.max()
# `thresholds` holds t_train vector in .t attribute
print('t_train produced in {:.3f}s').format(time.time()-start_time)
np.save('t/'+snapshot_name+str(seed)+'.npy', t_train)
# Predictive model for t
regr = linear_model.RidgeCV(cv=5)
# Ridge() is LinearClassifier() with L2-reg
regr.fit(score_train, t_train)
time_profiles['train_module2'].append(time.time()-start_time)
# END OF MODULE 2
# TESTING PHASE
start_time = time.time()
score_test = compute_score(X_test, Y_test)
t_test = regr.predict(score_test)
print 'original t_test is in ', min(t_test), '..', max(t_test)
t_test[t_test>1] = max(t_test[t_test<1])
t_test[t_test<0] = min(t_test[t_test>0]) # ! Keep t_test in [0,1]
print 'corrected t_test is in ', min(t_test), '..', max(t_test)
# Predict label
metrics = predict_label(score_test, Y_test, t_test, seed, num_classes, verbose=1)
time_profiles['test'].append(time.time()-start_time)
all_metrics.append(metrics)
def main(reps,
pretrained_w_path,
do_module1,
init_seed=0,
load_t=0,
num_epochs=200,
batchsize=96,
fine_tune=0,
patience=500,
lr_init=1e-3,
optim='adagrad',
toy=0,
num_classes=23):
res_root = '/home/hoa/Desktop/projects/resources'
X_path = osp.join(res_root, 'datasets/msrcv2/Xaug_b01c.npy')
Y_path = osp.join(res_root, 'datasets/msrcv2/Y.npy')
MEAN_IMG_PATH = osp.join(res_root, 'models/ilsvrc_2012_mean.npy')
snapshot = 50 # save model after every `snapshot` epochs
drop_p = 0.5 # drop out prob.
lambda2 = 0.0005 / 2 # l2-regularizer constant
# step=patience/4 # decay learning after every `step` epochs
lr_patience = 60 # for learning rate schedule, if optim=='momentum'
if toy: # unit testing
num_epochs = 10
data_multi = 3
reps = 2
#drop_p=0
#lambda2=0
# Create name tag for the experiment
if fine_tune:
full_or_tune = 'tune' # description tag for storing associated files
else:
full_or_tune = 'full'
time_stamp = time.strftime("%y%m%d%H%M%S", time.localtime())
snapshot_root = '../snapshot_models/'
snapshot_name = str(num_classes) + 'alex' + time_stamp + full_or_tune
# LOADING DATA
print 'LOADING DATA ...'
X = np.load(X_path)
Y = np.load(Y_path)
if X.shape[1] != 3:
X = b01c_to_bc01(X)
N = len(Y)
print 'Raw X,Y shape', X.shape, Y.shape
if len(X) != len(Y):
print 'Inconsistent number of input images and labels. X is possibly augmented.'
MEAN_IMG = np.load(MEAN_IMG_PATH)
MEAN_IMG_227 = skimage.transform.resize(np.swapaxes(
np.swapaxes(MEAN_IMG, 0, 1), 1, 2), (227, 227),
mode='nearest',
preserve_range=True)
MEAN_IMG = np.swapaxes(np.swapaxes(MEAN_IMG_227, 1, 2), 0, 1).reshape(
(1, 3, 227, 227))
all_metrics = [] # store metrics in each run
time_profiles = {
'train_module1': [],
'train_module1_eff': [],
'train_module2': [],
'test': []
} # record training and testing time
# PREPARE THEANO EXPRESSION FOR BOTH MODULES
print 'COMPILING THEANO EXPRESSION ...'
input_var = T.tensor4('inputs')
target_var = T.imatrix('targets')
network = build_model(num_classes=num_classes, input_var=input_var)
# Create a loss expression for training
prediction = lasagne.layers.get_output(network)
loss = lasagne.objectives.binary_crossentropy(prediction, target_var)
weights = lasagne.layers.get_all_params(network, regularizable=True)
l2reg = theano.shared(floatX(lambda2)) * T.sum(
[T.sum(w**2) for w in weights])
loss = loss.mean() + l2reg
lr = theano.shared(np.array(lr_init, dtype=theano.config.floatX))
lr_decay = np.array(1. / 3, dtype=theano.config.floatX)
# Create update expressions for training
params = lasagne.layers.get_all_params(network, trainable=True)
# last-layer case is actually very simple:
# `params` above is a list of all (W,b)-pairs
# Therefore last layer's (W,b) is params[-2:]
if fine_tune == 7: # tuning params from fc7 to fc8
params = params[-2:]
# elif fine_tune == 6: # tuning params from fc6 to fc8
# params = params[-4:]
# TODO adjust for per-layer training with local_lr
if optim == 'momentum':
updates = lasagne.updates.nesterov_momentum(loss,
params,
learning_rate=lr,
momentum=0.9)
elif optim == 'rmsprop':
updates = lasagne.updates.rmsprop(loss,
params,
learning_rate=lr,
rho=0.9,
epsilon=1e-06)
elif optim == 'adam':
updates = lasagne.updates.adam(loss,
params,
learning_rate=lr,
beta1=0.9,
beta2=0.999,
epsilon=1e-08)
elif optim == 'adagrad':
updates = lasagne.updates.adagrad(loss,
params,
learning_rate=lr,
epsilon=1e-06)
# Create a loss expression for validation/testing
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.binary_crossentropy(test_prediction,
target_var)
test_loss = test_loss.mean() + l2reg
# zero-one loss with threshold t = 0.5 for reference
# zero_one_loss = T.abs_((test_prediction > theano.shared(floatX(0.5))) - target_var).sum(axis=1)
#zero_one_loss /= target_var.shape[1].astype(theano.config.floatX)
#zero_one_loss = zero_one_loss.mean()
# Compile a function performing a backward pass (training step) on a mini-batch (by giving
# the updates dictionary) and returning the corresponding training loss:
bwd_fn = theano.function(
[input_var, target_var],
loss,
updates=updates,
)
# Compile a second function performing a forward pass,
# returns validation loss, 0/1 Error, score i.e. Xout:
fwd_fn = theano.function([input_var, target_var], test_loss)
# Create a theano function for computing score
score = lasagne.layers.get_output(network, deterministic=True)
score_fn = theano.function([input_var], score)
def compute_score(X, Y, batchsize=batchsize, shuffle=False):
out = np.zeros(Y.shape)
batch_id = 0
for batch in iterate_minibatches(X, Y, batchsize, shuffle=False):
inputs, _ = batch
# Flip random half of the batch
flip_idx = np.random.choice(len(inputs),
size=len(inputs) / 2,
replace=False)
if len(flip_idx) > 1:
inputs[flip_idx] = inputs[flip_idx, :, :, ::-1]
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
if len(inputs) == batchsize:
out[batch_id * batchsize:(batch_id + 1) *
batchsize] = score_fn(inputs)
batch_id += 1
else:
out[batch_id * batchsize:] = score_fn(inputs)
return out
try:
# MAIN LOOP FOR EACH RUN
for seed in np.arange(reps) + init_seed:
# reset learning rate
lr.set_value(lr_init)
print '\nRUN', seed, '...'
# Split train/val/test set
indicies = np.arange(len(Y))
Y_train_val, Y_test, idx_train_val, idx_test = train_test_split(
Y, indicies, random_state=seed, train_size=float(2) / 3)
Y_train, Y_val, idx_train, idx_val = train_test_split(
Y_train_val, idx_train_val, random_state=seed)
print "Train/val/test set size:", len(idx_train), len(
idx_val), len(idx_test)
idx_aug_train = data_aug(idx_train, mode='aug', isMat='idx', N=N)
Xaug_train = X[idx_aug_train]
Yaug_train = data_aug(Y_train, mode='aug', isMat='Y', N=N)
idx_aug_val = data_aug(idx_val, mode='aug', isMat='idx', N=N)
Xaug_val = X[idx_aug_val]
Yaug_val = data_aug(Y_val, mode='aug', isMat='Y', N=N)
# Module 2 training set is composed of module 1 training and validation set
idx_aug_train_val = data_aug(idx_train_val,
mode='aug',
isMat='idx',
N=N)
Xaug_train_val = X[idx_aug_train_val]
Yaug_train_val = data_aug(Y_train_val, mode='aug', isMat='Y', N=N)
# Test set
X_test = X[idx_test]
# Y_test is already returned in the first train_test_split
print "Augmented train/val/test set size:", len(Xaug_train), len(
Yaug_val), len(X_test)
print "Augmented (X,Y) dtype:", Xaug_train.dtype, Yaug_val.dtype
print "Processed Mean image:", MEAN_IMG.dtype, MEAN_IMG.shape
if toy: # try to overfit a tiny subset of the data
Xaug_train = Xaug_train[:batchsize * data_multi +
batchsize / 2]
Yaug_train = Yaug_train[:batchsize * data_multi +
batchsize / 2]
Xaug_val = Xaug_val[:batchsize + batchsize / 2]
Yaug_val = Yaug_val[:batchsize + batchsize / 2]
# Init by pre-trained weights, if any
if len(pretrained_w_path) > 0:
layer_list = lasagne.layers.get_all_layers(
network) # 22 layers
if pretrained_w_path.endswith('pkl'):
# load reference_net
# use case: weights initialized from pre-trained reference nets
f = open(pretrained_w_path, 'r')
w_list = pickle.load(f) # list of 11 (W,b)-pairs
f.close()
lasagne.layers.set_all_param_values(
layer_list[-3], w_list[:-2])
# exclude (W,b) of fc8
# BIG NOTE: don't be confused, it's pure coincident that layer_list
# and w_list have the same index here. The last element of layer_list are
# [.., fc6, drop6, fc7, drop7, fc8], while w_list are
# [..., W, b, W, b, W, b] which, eg w_list[-4] and w_list[-3] correspond to
# params that are associated with fc7 i.e. params that connect drop6 to fc7
elif pretrained_w_path.endswith('npz'):
# load self-trained net
# use case: continue training from a snapshot model
with np.load(
pretrained_w_path
) as f: # NOTE: only load snapshot of the same `seed`
# w_list = [f['arr_%d' % i] for i in range(len(f.files))]
w_list = [
f.items()['arr_%d' % i]
for i in range(len(f.files))
] # load from bkviz, one-time use
lasagne.layers.set_all_param_values(network, w_list)
elif pretrained_w_path.endswith(
'/'): # init from 1 of the 30 snapshots
from os import listdir
import re
files = [
f for f in listdir(pretrained_w_path)
if osp.isfile(osp.join(pretrained_w_path, f))
]
for file_name in files:
regex_seed = 'full%d_' % seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
print snapshot_name
with np.load(
osp.join(pretrained_w_path, snapshot_name)
+ '.npz') as f:
w_list = [
f['arr_%d' % i]
for i in range(len(f.files))
]
lasagne.layers.set_all_param_values(
network, w_list)
# START MODULE 1
module1_time = 0
if do_module1:
print 'MODULE 1'
training_history = {}
training_history['iter_training_loss'] = []
training_history['iter_validation_loss'] = []
training_history['training_loss'] = []
training_history['validation_loss'] = []
training_history['learning_rate'] = []
# http://deeplearning.net/tutorial/gettingstarted.html#early-stopping
# early-stopping parameters
n_train_batches = Xaug_train.shape[0] / batchsize
if Xaug_train.shape[0] % batchsize != 0:
n_train_batches += 1
patience = patience # look as this many examples regardless
patience_increase = 2 # wait this much longer when a new best is found
lr_patience_increase = 1.01
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant; a significant test
# MIGHT be better
validation_frequency = min(n_train_batches, patience / 2)
# go through this many
# minibatches before checking the network
# on the validation set; in this case we
# check every epoch
best_params = None
epoch_validation_loss = 0 # indicates that valid_loss has not been computed yet
best_validation_loss = np.inf
best_iter = -1
lr_iter = -1
test_score = 0.
start_time = time.time()
done_looping = False
epoch = 0
# Finally, launch the training loop.
print("Starting training...")
# We iterate over epochs:
print(
"\nEpoch\tTrain Loss\tValid Loss\tBest-ValLoss-and-Iter\tTime\tL.Rate"
)
sys.setrecursionlimit(10000)
try: # Early-stopping implementation
while (not done_looping) and (epoch < num_epochs):
# In each epoch, we do a full pass over the training data:
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(Xaug_train,
Yaug_train,
batchsize,
shuffle=True):
inputs, targets = batch
# Horizontal flip half of the images
bs = inputs.shape[0]
indices = np.random.choice(bs,
bs / 2,
replace=False)
inputs[indices] = inputs[indices, :, :, ::-1]
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(
theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
train_err_batch = bwd_fn(inputs, targets)
train_err += train_err_batch
train_batches += 1
iter_now = epoch * n_train_batches + train_batches
training_history['iter_training_loss'].append(
train_err_batch)
training_history['iter_validation_loss'].append(
epoch_validation_loss)
if (iter_now + 1) % validation_frequency == 0:
# a full pass over the validation data:
val_err = 0
#zero_one_err = 0
val_batches = 0
for batch in iterate_minibatches(
Xaug_val,
Yaug_val,
batchsize,
shuffle=False):
inputs, targets = batch
# Substract mean image
inputs = (inputs - MEAN_IMG).astype(
theano.config.floatX)
# MEAN_IMG is broadcasted numpy-way, take note if want theano expression instead
val_err_batch = fwd_fn(inputs, targets)
val_err += val_err_batch
val_batches += 1
epoch_validation_loss = val_err / val_batches
if epoch_validation_loss < best_validation_loss:
if epoch_validation_loss < best_validation_loss * improvement_threshold:
patience = max(
patience,
iter_now * patience_increase)
# lr_patience *= lr_patience_increase
best_params = lasagne.layers.get_all_param_values(
network)
best_validation_loss = epoch_validation_loss
best_iter = iter_now
lr_iter = best_iter
else: # decay learning rate if optim=='momentum'
if optim == 'momentum' and (
iter_now - lr_iter) > lr_patience:
lr.set_value(lr.get_value() * lr_decay)
lr_iter = iter_now
if patience <= iter_now:
done_looping = True
break
# Record training history
training_history['training_loss'].append(train_err /
train_batches)
training_history['validation_loss'].append(
epoch_validation_loss)
training_history['learning_rate'].append(
lr.get_value())
epoch_time = time.time() - start_time
module1_time += epoch_time
# Then we print the results for this epoch:
print("{}\t{:.6f}\t{:.6f}\t{:.6f}\t{}\t{:.3f}\t{}".
format(epoch + 1,
training_history['training_loss'][-1],
training_history['validation_loss'][-1],
best_validation_loss, best_iter + 1,
epoch_time,
training_history['learning_rate'][-1]))
if (
epoch + 1
) % snapshot == 0: # TODO try to save weights at best_iter
snapshot_path_string = snapshot_root + snapshot_name + str(
seed) + '_' + str(iter_now + 1)
try: # use case: terminate experiment before reaching `reps`
np.savez(snapshot_path_string + '.npz',
*best_params)
np.savez(snapshot_path_string + '_history.npz',
training_history)
plot_loss(training_history,
snapshot_path_string + '_loss.png')
# plot_conv_weights(lasagne.layers.get_all_layers(network)[1],
# snapshot_path_string+'_conv1weights_')
except KeyboardInterrupt, TypeError:
print 'Did not save', snapshot_name + str(
seed) + '_' + str(iter_now + 1)
pass
epoch += 1
except KeyboardInterrupt, MemoryError: # Sadly this can only catch KeyboardInterrupt
pass
print 'Training finished or KeyboardInterrupt (Training is never finished, only abandoned)'
module1_time_eff = module1_time / iter_now * best_iter
print('Total and Effective training time are {:.0f} and {:.0f}'
).format(module1_time, module1_time_eff)
time_profiles['train_module1'].append(module1_time)
time_profiles['train_module1_eff'].append(module1_time_eff)
# Save model after num_epochs or KeyboardInterrupt
if (epoch + 1) % snapshot != 0: # to avoid duplicate save
snapshot_path_string = snapshot_root + snapshot_name + str(
seed) + '_' + str(iter_now + 1)
if not toy:
try: # use case: terminate experiment before reaching `reps`
print 'Saving model...'
np.savez(snapshot_path_string + '.npz',
*best_params)
np.savez(snapshot_path_string + '_history.npz',
training_history)
plot_loss(training_history,
snapshot_path_string + '_loss.png')
# plot_conv_weights(lasagne.layers.get_all_layers(network)[1],
# snapshot_path_string+'_conv1weights_')
except KeyboardInterrupt, TypeError:
print 'Did not save', snapshot_name + str(
seed) + '_' + str(iter_now + 1)
pass
# And load them again later on like this:
#with np.load('../snapshot_models/23alex16042023213910.npz') as f:
# param_values = [f['arr_%d' % i] for i in range(len(f.files))] # or
# training_history = f['arr_0'].items()
# lasagne.layers.set_all_param_values(network, param_values)
# END OF MODULE 1
# START MODULE 2
print '\nMODULE 2'
if not do_module1:
if pretrained_w_path.endswith('pkl'):
snapshot_name = str(
num_classes
) + 'alexOTS' # short for "off-the-shelf init"
elif pretrained_w_path.endswith(
'npz'): # Resume from a SINGLE snapshot
# extract name pattern, e.g. '23alex16042023213910full10'
# from string '../snapshot_models/23alex16042023213910full10_100.npz'
import re
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+"
match = re.search(regex, pretrained_w_path)
snapshot_name = match.group(0)
elif pretrained_w_path.endswith(
'/'): # RESUMED FROM TRAINED MODULE 1 (ONE-TIME USE)
from os import listdir
import re
files = [
f for f in listdir(pretrained_w_path)
if osp.isfile(osp.join(pretrained_w_path, f))
]
for file_name in files:
regex_seed = 'full%d_' % seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
print snapshot_name
with np.load(
osp.join(pretrained_w_path, snapshot_name)
+ '.npz') as f:
w_list = [
f['arr_%d' % i]
for i in range(len(f.files))
]
lasagne.layers.set_all_param_values(
network, w_list)
else: # MAIN BRANCH - assume do_module1 is True AND have run `snapshot` epochs
if (epoch + 1) > snapshot:
with np.load(snapshot_path_string + '.npz'
) as f: # reload the best params for module 1
w_list = [f['arr_%d' % i] for i in range(len(f.files))]
lasagne.layers.set_all_param_values(network, w_list)
score_train = compute_score(Xaug_train_val, Yaug_train_val)
start_time = time.time()
if load_t: # Server failed at the wrong time. We only have t backed-up
if pretrained_w_path.endswith('/'):
from os import listdir
import re
files = [
f for f in listdir(pretrained_w_path)
if osp.isfile(osp.join(pretrained_w_path, f))
]
for file_name in files:
regex_seed = 'full%d_' % seed
match_seed = re.search(regex_seed, file_name)
if match_seed:
regex = r"\d+[a-zA-Z]+\d+[a-zA-Z]+\d+\_\d+"
match = re.search(regex, file_name)
snapshot_name = match.group(0)
t_train = np.load(
osp.join('t', '{0}.npy'.format(snapshot_name)))
else: # MAIN BRANCH
thresholds = Threshold(score_train, Yaug_train_val)
thresholds.find_t_for(
) # determine t_train for each score_train. It will take a while
t_train = np.asarray(thresholds.t)
print 't_train is in ', t_train.min(), '..', t_train.max()
# `thresholds` holds t_train vector in .t attribute
print('t_train produced in {:.3f}s').format(time.time() -
start_time)
np.save('t/' + snapshot_name + str(seed) + '.npy', t_train)
# Predictive model for t
regr = linear_model.RidgeCV(cv=5)
# Ridge() is LinearClassifier() with L2-reg
regr.fit(score_train, t_train)
time_profiles['train_module2'].append(time.time() - start_time)
# END OF MODULE 2
# TESTING PHASE
start_time = time.time()
score_test = compute_score(X_test, Y_test)
t_test = regr.predict(score_test)
print 'original t_test is in ', min(t_test), '..', max(t_test)
t_test[t_test > 1] = max(t_test[t_test < 1])
t_test[t_test < 0] = min(
t_test[t_test > 0]) # ! Keep t_test in [0,1]
print 'corrected t_test is in ', min(t_test), '..', max(t_test)
# Predict label
metrics = predict_label(score_test,
Y_test,
t_test,
seed,
num_classes,
verbose=1)
time_profiles['test'].append(time.time() - start_time)
all_metrics.append(metrics)
