def __init__(self, optimizer_id):
self.map = 'sub-maxprob-thr50-2mm' # This is the brain atlas we use for normalization (from HarvardOxford)
self.CV = 4 # The number of random subsets to test our data on
self.connectivity_metric = 'tangent' # The type of functional connectivity extraction we use
self.times_to_run = 3000 # Number of times that we randomly generate and test params before ending
self.verbose = True # Whether to print out model results after each iteration
self.csv = True # Whether to output results to a csv file or not
self.estimator_chance = 0.5 # The chance that an estimator will be included
self.shuffle_models = True # Whether to shuffle the classifier order
self.maxes = { # Set maximum values for the random parameter generator
'estimators': 2,
'mlp_layers': 3, # Maximum MLP Layers
'mlp_nodes': 150, # Maximum nodes in each MLP layer
'xgb_trees': 130, # Maximum number of XGB trees
'rf_tress': 130, # Maximum number of RF tress
'early_stopping': 3 # Maximum number of early stopping
}
self.models_consider = { # Which models to consider during optimization
'rf': True, # Include Random Forests?
'xgb': True, # Include XGB?
'mlp': True, # Include MLP?
'svc': True, # Include SVC?
'logit': True, # Include Logit?
}
self.classifier_atr_choices = { # Certain choice attributes for classifiers
'mlp': ['sgd', 'lbfgs', 'adam'], # MLP solver choices
'svc': ['rbf', 'linear', 'poly'] # SVC Kernel Choices
}
self.csvFile = 'optimizer_' + optimizer_id + '_metrics' + '.csv'
# Set the CSV file name to include some useful information
pickled_features, pickled_labels = check_and_get_pickled_data() # Check and see if biomarkers are already
# created
try:
if not pickled_features or not pickled_labels: # If we don't already have the data cached locally
masker = get_atlas_data(self.map) # Generate a mask using the HarvardOxford atlas
adhd_data = generate_train_data() # Retrieve the data from my hard drive
masked_fmris = apply_masks(adhd_data.func, masker)
features, adhd_labels = make_connectivity_biomarkers(self.connectivity_metric, adhd_data.labels,
adhd_data, masked_fmris)
# Calculate functional connectivity and combine phenotypic information as a feature. Returns a matrix
# containing phenotypic information and computed functional connectivity -> features
else:
features, adhd_labels = pickled_features, pickled_labels # If it is cached, retrieve it
except ValueError:
features, adhd_labels = pickled_features, pickled_labels # If it is cached, retrieve it
self.features = features
self.labels = adhd_labels
Helpers.write_attributes(optimizer_id, self.CV, self.times_to_run, self.estimator_chance, self.maxes,
self.classifier_atr_choices, self.models_consider)
def run_hdiutil_command(self, *args, **kwargs):
args = ['hdiutil'] + list(args)
try:
out = Helpers.run_command(*args, **kwargs)
except Exception, e:
# Some commands require the disk-image to be mounted/unmounted. If ran when it isn't it returns
# saying 'Resource temporarily unavailable'
if 'Resource temporarily unavailable' in str(e):
self.detach() if self.is_mounted() else self.attach()
out = Helpers.run_command(*args, **kwargs)
def make_connectivity_biomarkers(kind, labels, adhd200, pooled_subjects):
"""
This function takes the masked fMRI volumes and the corresponding phenotypic information (age, gender and dexterity)
and turns them into a 2D array for doing ML classification. If there is no phenotypic information available,
we exlude it from the dataset.
:param kind: (str) The type of functional connnectity we extract
:param labels: (list) The truth values for the ADHD200 dataset
:param adhd200: (ADHD200) The ADHD200 object
:param pooled_subjects: (list) The masked fMRI volumes
:return: (list) features, (list) labels
"""
new_labels = [] # Initialize a new list for containing the new labels (only labels for fMRI volumes that
# have corresponding phenotypic information
temp_features = [] # Initialize a new list for containing the new labels (only labels for fMRI volumes that
# have corresponding phenotypic information
conn_measure = ConnectivityMeasure(kind=kind, vectorize=True, discard_diagonal=True) # Generate the functional
# connectivity using the biomarker specified
connectivity = conn_measure.fit_transform(pooled_subjects) # Apply it to all of the masked fMRI scans
bar = ProgressBar(max_value=len(adhd200.func)) # Instantiate a new progressbar
ops = 0 # Set the default value of the bar to 0
for index in range(len(adhd200.func)):
phenotypic_information = Helpers.get_params(adhd200, adhd200.func[
index]) # Retrieve the corresponding phenotypic information for each fMRI
ops += 1 # Increment the bar by one
bar.update(ops) # Update the progressbar to the value of the variable "ops"
if phenotypic_information is not None: # If we found phenotypic information for that fMRI
new_labels.append(labels[index]) # Add it to the "approved" labels list
generated_features = np.array(
[Helpers.conform_1d(phenotypic_information, connectivity[index].shape[0]), connectivity[index]])
# Add the phenotypic information and the functional connectivity as a matrix. We have to
# surround the phenotypic information by 0s to make it the same shape as the connectivity (conform 1d)
temp_features.append(generated_features) # add it to the temp features
else:
continue # Skip that fMRI scan from the dataset
d3_dataset = np.array(temp_features) # Convert the 3D temp_features array to a numpy array
nsamples, nx, ny = d3_dataset.shape # Extract the dimensionality of the data
d2_functional_connectivity = d3_dataset.reshape((nsamples, nx * ny)) # Convert it to 2 dimensions
with open('pickles/features.pkl',
'wb') as features_file: # Cache the features so that we don't have to run this
# function again
dump(d2_functional_connectivity, features_file) # Dump them to the pickle file
with open('pickles/adhd_labels.pkl', 'wb') as labels_file: # Cache the biomarkers so that we don't have to run this
# function again
dump(new_labels, labels_file) # Dump them to the pickle file
return d2_functional_connectivity, new_labels # Return them
def size(self, size):
size = Helpers.get_bytes(size) if isinstance(size, str) else size
# General validation testing that size is an int and that space is available on disk
if not Helpers.is_float(size):
raise Exception('Invalid argument. Size must be an integer')
elif size >= Helpers.bytes_available():
raise Exception('Invalid argument. Size is too large, not enough space.')
# Different handling cases depending on if size has been assigned before
if self._size:
self.run_hdiutil_command('resize', self.path, size=Helpers.hr_bytes(size))
self._size = size
def diskutil_info(self):
UTILITY_NAME = 'diskutil'
self.attach()
response = Helpers.run_command(UTILITY_NAME, 'info', self.get_mounting_point())
non_empty_lines = [line for line in response.splitlines() if line != '']
return {line.split(':')[0].lstrip() : line.split(':')[-1].strip() for line in non_empty_lines}
def mp3(self, url):
path = Helpers.check_platform('Music')
self.create_path(path)
ydl_opts = utils.ydl_options()
with youtube_dl.YoutubeDL(ydl_opts) as ydl:
ydl.download([url])
print(colored('Download Completed', 'green'))
def mp4(self, url):
path = Helpers.check_platform('Videos')
self.create_path(path)
try:
with youtube_dl.YoutubeDL({}) as ydl:
ydl.download([url])
print(colored('Download Completed', 'green'))
except:
print(colored('something went wrong try again', 'red'))
def playlist(self, url):
playlist = pafy.get_playlist(url)
path = Helpers.check_platform() + "/Playlists/{}".format(
playlist['title'])
join_ = os.path.join(path)
file = Helpers.check_platform('Playlists')
if os.path.isdir(file) == True:
pass
else:
os.mkdir(file)
if os.path.isdir(path) == True:
pass
else:
os.mkdir(join_)
os.chdir(join_)
utils.playlist_info(url)
with youtube_dl.YoutubeDL({}) as ydl:
ydl.download([url])
def run(self):
"""
Run the model self.times_to_run times using random parameters. Export the results to a CSV file
"""
for times in range(0, self.times_to_run): # Loop through the number of times we have to run
output = { # Initialize an empty dictionary containing the results from each iteration
'accuracies': [],
'f1s_positive': [],
'precisions_positive': [],
'recalls_positive': [],
'f1s_negative': [],
'precisions_negative': [],
'recalls_negative': [],
'true_negative': [],
'false_positive': [],
'false_negative': [],
'true_positive': []
}
random_attributes = self._random_args() # Generate random model parameters
layer_order = self._find_order(random_attributes)
for cv_run in range(self.CV):
accuracy, positive_metrics, negative_metrics, confusion_metrics = run_model(
self.features, self.labels,
random_attributes, verbose=True
)
# Run the model and get metrics from that run
output['accuracies'].append(accuracy) # Add this iteration's metrics to the CV array
output['f1s_positive'].append(positive_metrics['f1'])
output['f1s_negative'].append(negative_metrics['f1'])
output['precisions_positive'].append(positive_metrics['precision'])
output['precisions_negative'].append(negative_metrics['precision'])
output['recalls_negative'].append(negative_metrics['recall'])
output['recalls_positive'].append(positive_metrics['recall'])
output['true_negative'].append(confusion_metrics['true_negative'])
output['false_positive'].append(confusion_metrics['false_positive'])
output['false_negative'].append(confusion_metrics['false_negative'])
output['true_positive'].append(confusion_metrics['true_positive'])
print 'Ran {0} times (iteration {1})'.format(times, cv_run), random_attributes
data = Helpers.generate_csv_data(layer_order, output['accuracies'],
[output['f1s_negative'], output['f1s_positive']],
[output['precisions_negative'], output['precisions_positive']],
[output['recalls_negative'], output['recalls_positive']],
[output['true_negative'], output['false_positive'],
output['false_negative'], output['true_positive']])
# Generate the dictionary for the CSV File
self._csv_writer(random_attributes, data) # Write the data to a file
def generate_data_model(self, image_info):
ext = self.path.split('.')[-1]
options = {
'volname' : 'Volume Name',
'fs' : 'File System Personality',
'size' : 'Total Size'
}
options = {k: image_info[v] for k, v in options.items()}
str_size = ' '.join(options['size'].split(' ')[:2])
options['size'] = Helpers.get_bytes(str_size)
options['type'] = ext if ext != 'dmg' else 'UDIF'
return options
def test_jss_stage(self):
driver = self.driver
WebDriverWait(driver, 10).until_not(lambda x: x.find_element_by_xpath(
'//*[@style="display: block;"]').is_displayed)
helper = Helpers()
helper.field(self, driver.find_element(By.ID, l.search_ref),
time_stamp)
driver.find_element_by_xpath(
'//*[@id="downloadProjects-form"]//*[@data-target="list"]').click(
)
WebDriverWait(driver, 10).until_not(lambda el: el.find_element(
By.XPATH, '//*[@id="tasks-table"]/tbody/tr[2]').is_displayed)
time.sleep(2)
project_ref_num = driver.find_element_by_xpath(
'//*[@id="tasks-table"]/tbody/tr/td[7]/a')
project_ref_num.click()
time.sleep(2)
WebDriverWait(driver, 10).until(
lambda x: x.find_element_by_id(l.project_code).is_displayed())
assert driver.find_element(By.ID, l.project_code).is_displayed()
auth = Authenticate()
auth.delete_project(time_stamp)
def _csv_writer(self, iteration_input, iteration_output):
"""
Write outputs to csv file
:param iteration_input: (dict) the parameters that were into the model
:param iteration_output: (dict)the returned result from the CV
:param csvFile: (string) path to a csv file for outputting
:return: None
"""
if self.csv:
is_new_file = not exists(self.csvFile) # Check if the file exists so we know whether to write the header
with open(self.csvFile, 'a') as csv_file: # Open the tsv file for appending
writer = DictWriter(csv_file,
fieldnames=Helpers.fieldnames,
delimiter=',') # Initialize a tsv writer (using dictionary)
if is_new_file:
writer.writeheader() # If the file is new, create a header
writer.writerow(
Helpers.merge_two_dicts(iteration_input, iteration_output)) # Write a new merged dictionary
def download_type():
music_type = input(colored('Press A for Audio V for Video P for Playlist : > ', 'green'))
print(colored('processing you download request ...........', 'blue'))
if music_type == "A" or music_type == "a":
Helpers.save_url_(url)
Audio.mp3(url)
elif music_type == 'V' or music_type == 'v':
Helpers.save_url_(url)
Audio.mp4(url)
elif music_type == 'P' or music_type == 'p':
Helpers.save_url(url)
Audio.playlist(url)
else:
main()
def change_volname(old_name, new_name):
Helpers.run_command('diskutil', 'rename', old_name, new_name)
def run_disk_util_command(self, *args, **kwargs):
out = Helpers.run_command(*args, **kwargs)
def main(save_path, params):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
sub2vec = params['sub2vec']
subdict = params['subdic']
dataset = params['data']
nlayers = params['nlayers']
train_emb = params['train_emb']
sub_dim = params['sub_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
# save settings
shutil.copyfile('config.py', '%s/config.py' % save_path)
use_subs = sub_dim > 0
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset,
no_training_set=False,
use_subs=use_subs,
subdict=subdict)
print "building minibatch loaders ...", datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')
batch_loader_train = MiniBatchLoader.MiniBatchLoader(data.training,
BATCH_SIZE,
sample=1)
batch_loader_val = MiniBatchLoader.MiniBatchLoader(data.validation,
BATCH_SIZE)
print "building network ...", datetime.now().strftime('%Y-%m-%d %H:%M:%S')
W_init, embed_dim, = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
S_init, sub_dim = Helpers.load_sub_embeddings(data.dictionary[1], sub2vec)
m = model.Model(nlayers, data.vocab_size, data.num_chars, W_init, S_init,
nhidden, embed_dim, dropout, train_emb, sub_dim, use_feat,
gating_fn)
print "training ...", datetime.now().strftime('%Y-%m-%d %H:%M:%S')
num_iter = 0
max_acc = 0.
deltas = []
logger = open(save_path + '/log', 'a', 0)
if os.path.isfile('%s/best_model.p' % save_path):
print 'loading previously saved model', datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')
m.load_model('%s/best_model.p' % save_path)
print "model loaded"
else:
print 'saving init model', datetime.now().strftime('%Y-%m-%d %H:%M:%S')
m.save_model('%s/model_init.p' % save_path)
print 'loading init model', datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')
m.load_model('%s/model_init.p' % save_path)
for epoch in xrange(NUM_EPOCHS):
print "epochs training ...", datetime.now().strftime(
'%Y-%m-%d %H:%M:%S')
estart = time.time()
new_max = False
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_train:
loss, tr_acc, probs = m.train(dw, dt, qw, qt, c, a, m_dw, m_qw, tt,
tm, m_c, cl)
message = "Epoch %d TRAIN loss=%.4e acc=%.4f elapsed=%.1f" % (
epoch, loss, tr_acc, time.time() - estart)
print message
logger.write(message + '\n')
num_iter += 1
if num_iter % VALIDATION_FREQ == 0:
total_loss, total_acc, n, n_cand = 0., 0., 0, 0.
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_val:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm,
m_c, cl)
loss, acc, probs = outs[:3]
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
n += bsize
print('validate on ', str(n) + 'validation data')
val_acc = total_acc / n
if val_acc > max_acc:
max_acc = val_acc
m.save_model('%s/best_model.p' % save_path)
new_max = True
message = "Epoch %d VAL loss=%.4e acc=%.4f max_acc=%.4f" % (
epoch, total_loss / n, val_acc, max_acc)
print message
logger.write(message + '\n')
m.save_model('%s/model_%d.p' % (save_path, epoch))
message = "After Epoch %d: Train acc=%.4f, Val acc=%.4f" % (
epoch, tr_acc, val_acc)
print message
logger.write(message + '\n')
# learning schedule
if epoch >= 2:
m.anneal()
# stopping criterion
if not new_max:
break
logger.close()
def _random_args(self, consider_mlp=True, consider_svc=True, consider_logit=True, consider_xgb=True,
consider_rf=True, consider_early_stopping=True):
"""
Generate random parameters for testing
:param consider_mlp: (bool) whether or not to include multi layer perceptron in the optimization
:param consider_svc: (bool) whether or not to include SVC in the optimization
:param consider_logit: (bool) whether or not to include Logistic Regression in the optimization
:param consider_xgb: (bool) whether or not to include gradient boosting in the optimization
:param consider_rf: (bool) whether or not to include random forests in the optimization
:param consider_early_stopping: (bool) whether or not to randomize the "down" iterations required to stop a model train
:return: (dict) a dictionary contating the model parameters (MLP Solver, MLP Layers, XGB Estimators, number of
Logistic Regressions and SVC kernel)
"""
mlp = Helpers.decision(probability=self.estimator_chance) # Decide whether to include MLP
svc = Helpers.decision(probability=self.estimator_chance) # Decide whether to include SVC
xgb = Helpers.decision(probability=self.estimator_chance) # Decide whether to include XGB
rf = Helpers.decision(probability=self.estimator_chance) # Decide whether to include RF
logit = choice([0, 1, 2, 3]) # Decide whether to include one logit, 2 logit, or none
active_classifiers = [] # Keep a count so we know how many active estimators we have
if mlp and self.models_consider['svc']:
num_mlp = randint(0, self.maxes[
'estimators']) # How many MLP classifiers we should use in this round of testing
mlp_layer_schema = []
mlp_solvers = []
for _ in range(num_mlp): # Loop through all of the MLP classifiers we chose to consider
temp_schema = []
mlp_solvers.append(choice(self.classifier_atr_choices['mlp'])) # Randomly choose an MLP algorithm
number_of_layers = randint(1, self.maxes['mlp_layers'])
# Randomly generate the number of layers between 1 and 3
active_classifiers.append(
Helpers.reversed_initial_structure['mlp']) # Append so we keep track of active estimators
for layer in range(number_of_layers): # Loop through all of the layers
nodes_in_layer = randint(1, self.maxes['mlp_nodes'])
# Generate the random number of nodes in each layer (up to max)
temp_schema.append(nodes_in_layer) # Add it to the array containing the MLP layer schema
mlp_layer_schema.append(temp_schema)
else:
mlp_layer_schema = None
mlp_solvers = None
if svc and self.models_consider['svc']:
num_svc = randint(0, self.maxes[
'estimators']) # Randomly generate the number of SVC classifiers we want to use
svc_kernels = []
for _ in range(num_svc): # Loop through all of the SVC estimators we chose to consider
svc_kernels.append(choice(self.classifier_atr_choices['svc'])) # Randomly choose a kernel for SVC
active_classifiers.append(
Helpers.reversed_initial_structure['svc']) # Append so we keep track of active estimators
else:
svc_kernels = None
if xgb and self.models_consider['xgb']:
num_xgb = randint(0, self.maxes['estimators'])
xgb_estimators = []
for _ in range(num_xgb):
xgb_estimators.append(
randint(1, self.maxes['xgb_trees'])) # Generate a random number of XGB estimators (0 < num estim < 130)
active_classifiers.append(
Helpers.reversed_initial_structure['xgb']) # Append so we keep track of active estimators
else:
xgb_estimators = None
if self.models_consider['logit']:
if logit == 1:
number_of_logit_regressions = randint(1, self.maxes['estimators']), 0 # Generate one group of logistic
# regressions but leave the other blank
for _ in range(number_of_logit_regressions[0]):
active_classifiers.append(
Helpers.reversed_initial_structure['logit1']) # Append so we keep track of active estimators
elif logit == 2:
number_of_logit_regressions = randint(1, self.maxes['estimators']), randint(0, self.maxes['estimators'])
# Generate two groups of a random number of logistic regressions
for _ in range(number_of_logit_regressions[0]):
active_classifiers.append(
Helpers.reversed_initial_structure['logit1']) # Append so we keep track of active estimators
for _ in range(number_of_logit_regressions[1]):
active_classifiers.append(
Helpers.reversed_initial_structure['logit2']) # Append so we keep track of active estimators
elif logit == 3:
number_of_logit_regressions = 0, randint(1, self.maxes['estimators']) # Generate one group of logistic
for _ in range(number_of_logit_regressions[1]):
active_classifiers.append(
Helpers.reversed_initial_structure['logit2']) # Append so we keep track of active estimators
# regressions but leave the other blank
else:
number_of_logit_regressions = 0, 0
active_classifiers.append(
Helpers.reversed_initial_structure[
'logit3']) # Add the constant logistic regressions to the active classifiers list
if rf and consider_rf:
number_of_rfs = randint(0, self.maxes['estimators']) # Generate the number of RFs to consider
rf_estims = []
for _ in range(number_of_rfs): # For each RF classifier
active_classifiers.append(
Helpers.reversed_initial_structure['rf']) # Add it to the active classifiers list
rf_estims.append(randint(1, self.maxes['rf_tress'])) # Add the random number of estimators
else:
rf_estims = None
if consider_early_stopping:
early_stopping_iterations = randint(1, self.maxes['early_stopping']) # Randomly select the number of layers
# required to stop the model iteration
else:
early_stopping_iterations = 2
if self.shuffle_models:
positions = sample(active_classifiers, len(active_classifiers))
# Shuffle the indexes of estimators in the config
else:
positions = active_classifiers
final_parameters = {
'mlp_layers': mlp_layer_schema,
'mlp_solver': mlp_solvers,
'svc_kernel': svc_kernels,
'xgb_estimators': xgb_estimators,
'logistic_regressions': number_of_logit_regressions,
'rf_estimators': rf_estims,
'early_stopping_iterations': early_stopping_iterations,
'positions': positions,
}
print final_parameters
return final_parameters # Return the final dictionary as a result
def main(load_path, params, mode='test'):
regularizer = params['regularizer']
rlambda = params['lambda']
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
subsample = params['subsample']
base_model = params['model']
char_dim = params['char_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
# load settings
shutil.copyfile('%s/config.py' % load_path, 'config.py')
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset)
inv_vocab = data.inv_dictionary
print("building minibatch loaders ...")
if mode == 'test':
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.test, BATCH_SIZE, data.dictionary)
else:
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.validation, BATCH_SIZE, data.dictionary)
print("building network ...")
W_init, embed_dim = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
m = eval(base_model).Model(nlayers, data.vocab_size, data.num_chars,
W_init, regularizer, rlambda, nhidden,
embed_dim, dropout, train_emb, subsample,
char_dim, use_feat, data.dictionary[4])
m.load_model('%s/best_model.p' % load_path)
print("testing ...")
pr = np.zeros((len(batch_loader_test.questions),
batch_loader_test.max_num_cand)).astype('float32')
fids, attns = [], []
total_loss, total_acc, n = 0., 0., 0
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames, match_feat, use_char, use_char_q in batch_loader_test:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm, m_c, cl,
match_feat, use_char, use_char_q)
loss, acc, probs = outs[:3]
attns += [[fnames[0], probs[0, :]] + [o[0, :, :] for o in outs[3:]]
] # store one attention
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
pr[n:n + bsize, :] = probs
fids += fnames
n += bsize
logger = open(load_path + '/log', 'a', 0)
message = '%s Loss %.4e acc=%.4f' % (mode.upper(), total_loss / n,
total_acc / n)
print message
logger.write(message + '\n')
logger.close()
np.save('%s/%s.probs' % (load_path, mode), np.asarray(pr))
pkl.dump(attns, open('%s/%s.attns' % (load_path, mode), 'w'))
f = open('%s/%s.ids' % (load_path, mode), 'w')
for item in fids:
f.write(item + '\n')
f.close()
def main(save_path, params):
regularizer = params['regularizer']
rlambda = params['lambda']
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
subsample = params['subsample']
base_model = params['model']
char_dim = params['char_dim']
use_feat = params['use_feat']
train_cut = params['train_cut']
gating_fn = params['gating_fn']
# save settings
shutil.copyfile('config.py','%s/config.py'%save_path)
use_chars = char_dim>0
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset, use_chars=use_chars)
print("building minibatch loaders ...")
batch_loader_train = MiniBatchLoader.MiniBatchLoader(data.training, BATCH_SIZE, data.dictionary,
sample=train_cut, max_qry_len=85)
batch_loader_val = MiniBatchLoader.MiniBatchLoader(data.validation, BATCH_SIZE, data.dictionary, max_qry_len=85)
batch_loader_test = MiniBatchLoader.MiniBatchLoader(data.test, BATCH_SIZE, data.dictionary)
print("building network ...")
W_init, embed_dim, = Helpers.load_word2vec_embeddings(data.dictionary[0], word2vec)
m = eval(base_model).Model(nlayers, data.vocab_size, data.num_chars, W_init,
regularizer, rlambda, nhidden, embed_dim, dropout, train_emb, subsample,
char_dim, use_feat, data.dictionary[4])
print("training ...")
num_iter = 0
max_acc = 0.
deltas = []
test_acc = 0.
logger = open(save_path+'/log','a',0)
# if os.path.isfile('%s/best_model.p'%save_path):
# print('loading previously saved model')
# m.load_model('%s/best_model.p'%save_path)
# else:
# print('saving init model')
# m.save_model('%s/model_init.p'%save_path)
# print('loading init model')
# m.load_model('%s/model_init.p'%save_path)
for epoch in xrange(NUM_EPOCHS):
estart = time.time()
new_max = False
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames, match_feat, use_char, use_char_q in batch_loader_train:
loss, tr_acc, probs = m.train(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm, m_c, cl, match_feat, use_char, use_char_q)
# message = "Epoch %d TRAIN loss=%.4e acc=%.4f elapsed=%.1f" % (
# epoch, loss, tr_acc, time.time()-estart)
# print message
# logger.write(message+'\n')
if num_iter % VALIDATION_FREQ == 0:
total_loss, total_acc, n, n_cand = 0., 0., 0, 0.
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames, match_feat, use_char, use_char_q in batch_loader_val:
outs = m.validate(dw, dt, qw, qt, c, a,
m_dw, m_qw, tt, tm, m_c, cl, match_feat, use_char, use_char_q)
loss, acc, probs = outs[:3]
bsize = dw.shape[0]
total_loss += bsize*loss
total_acc += bsize*acc
n += bsize
val_acc = total_acc/n
if val_acc > max_acc:
max_acc = val_acc
m.save_model('%s/best_model.p'%save_path)
temp_acc, temp_n = 0.0, 0
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames, match_feat, use_char, use_char_q in batch_loader_test:
outs = m.validate(dw, dt, qw, qt, c, a,
m_dw, m_qw, tt, tm, m_c, cl, match_feat, use_char, use_char_q)
_, acc, _ = outs[:3]
bsize = dw.shape[0]
temp_acc += bsize * acc
temp_n += bsize
test_acc = temp_acc / temp_n
new_max = True
message = "Epoch %d VAL loss=%.4e acc=%.4f max_acc=%.4f test=%.4f" % (
epoch, total_loss/n, val_acc, max_acc, test_acc)
print message
logger.write(message+'\n')
num_iter += 1
m.save_model('%s/model_%d.p'%(save_path,epoch))
message = "After Epoch %d: Train acc=%.4f, Val acc=%.4f" % (epoch, tr_acc, val_acc)
print message
logger.write(message+'\n')
# learning schedule
if epoch >=2:
m.anneal()
# stopping criterion
if not new_max:
break
logger.close()
import argparse
import os
import sys
from pathlib import Path
import pdfplumber
from tld import is_tld
from tld.utils import update_tld_names
from utils import Helpers, Termcolors
__author__ = "DFIRSec (@pulsecode)"
__version__ = "v0.0.8"
__description__ = "Extract Indicators of Compromise (IOCs) from PDF documents."
helper = Helpers()
tc = Termcolors()
# update/sync tld names
update_tld_names()
# Base directory
parent = Path(__file__).resolve().parent
def extractor(pdf):
size = os.path.getsize(pdf)
large = round(size / (1024 * 1024))
if size > 10240000:
sys.exit(
f"{tc.RED}[ERROR]{tc.RESET} Limit file size to 10 MB or less. Your file is {large:,} MB."
def main(load_path, params, mode='test'):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
char_dim = params['char_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
ent_setup = params['ent_setup']
data_path = params['data_path']
# save settings
shutil.copyfile('config.py', '%s/config_test.py' % load_path)
use_chars = char_dim > 0
if dataset == "clicr":
dp = DataPreprocessor.DataPreprocessorClicr()
#dataset_path = "/mnt/b5320167-5dbd-4498-bf34-173ac5338c8d/Datasets/bmj_case_reports_data/dataset_json_concept_annotated/"
#dataset_path = "data/"
data = dp.preprocess(data_path,
ent_setup=ent_setup,
no_training_set=True)
elif dataset == "clicr_novice":
dp = DataPreprocessor.DataPreprocessorNovice()
data = dp.preprocess(data_path,
ent_setup=ent_setup,
no_training_set=True)
else:
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(data_path, no_training_set=True)
inv_vocab = data.inv_dictionary
assert os.path.exists(params["test_file"] if mode ==
"test" else params["validation_file"])
print("building minibatch loaders ...")
if mode == 'test':
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.test, BATCH_SIZE)
else:
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.validation, BATCH_SIZE)
f_to_cand = {i[-1]: i[3] for i in batch_loader_test.questions}
print("building network ...")
W_init, embed_dim = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
m = GAReader.Model(nlayers,
data.vocab_size,
data.num_chars,
W_init,
nhidden,
embed_dim,
dropout,
train_emb,
char_dim,
use_feat,
gating_fn,
save_attn=False)
print("model load path")
print('%s/best_model.p' % load_path)
m.load_model('%s/best_model.p' % load_path)
print("testing ...")
pr = np.zeros((len(batch_loader_test.questions),
batch_loader_test.max_num_cand)).astype('float32')
fids, attns = [], []
pred_ans = {}
total_loss, total_acc, n = 0., 0., 0
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_test:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm, m_c, cl)
loss, acc, probs = outs[:3]
attns += [[fnames[0], probs[0, :]] + [o[0, :, :] for o in outs[3:]]
] # store one attention
for f in range(len(fnames)):
pred_cand = probs[f].argmax()
pred_a_ids = f_to_cand[fnames[f]][pred_cand]
pred_a = " ".join([inv_vocab[i] for i in pred_a_ids])
if ent_setup == "ent-anonym" and (dataset == "clicr"
or dataset == "clicr_novice"):
relabeling_dicts = data.test_relabeling_dicts if mode == 'test' else data.val_relabeling_dicts
pred_a = relabeling_dicts[fnames[f]][pred_a]
pred_ans[fnames[f]] = pred_a
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
pr[n:n + bsize, :] = probs
fids += fnames
n += bsize
if (params["dataset"] == "clicr" or params["dataset"] == "clicr_plain" or params["dataset"] == "clicr_novice") \
and (mode == 'test' or mode == 'validation'):
print("writing predictions")
preds_data = utils.to_output_preds(pred_ans)
preds_filepath = load_path + '/{}.preds'.format(mode)
utils.write_preds(preds_data, file_name=preds_filepath)
utils.external_eval(preds_filepath,
preds_filepath + ".scores",
params["test_file"]
if mode == "test" else params["validation_file"],
extended=True)
logger = open(load_path + '/log.test', 'a')
message = '%s Loss %.4e acc=%.4f' % (mode.upper(), total_loss / n,
total_acc / n)
print(message)
logger.write(message + '\n')
logger.close()
np.save('%s/%s.probs' % (load_path, mode), np.asarray(pr))
pickle.dump(attns, open('%s/%s.attns' % (load_path, mode), 'wb'))
f = open('%s/%s.ids' % (load_path, mode), 'w')
for item in fids:
f.write(item + '\n')
f.close()
def main(save_path, params):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
char_dim = params['char_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
out = 'out'
# save settings
shutil.copyfile('config.py', '%s/config.py' % save_path)
use_chars = char_dim > 0
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset, no_training_set=False, use_chars=use_chars)
word_dictionary = data.dictionary[0]
the_index = word_dictionary['the']
#print('the index : {}'.format(word_dictionary['the']))
idx_to_word = dict([(v, k) for (k, v) in word_dictionary.iteritems()])
words = [idx_to_word[i] for i in sorted(idx_to_word.keys())]
print("building minibatch loaders ...")
batch_loader_train = MiniBatchLoader.MiniBatchLoader(data.training,
BATCH_SIZE,
sample=1.0)
batch_loader_val = MiniBatchLoader.MiniBatchLoader(data.validation,
BATCH_SIZE)
print("building network ...")
W_init, embed_dim, = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
#print('the embedding : {}'.format(W_init[the_index]))
#print(W_init[0:5])
print("running GAReader ...")
m = GAReader.Model(nlayers, data.vocab_size, data.num_chars, W_init,
nhidden, embed_dim, dropout, train_emb, char_dim,
use_feat, gating_fn, words).build_network()
m.compile(optimizer=tf.keras.optimizers.Adam(lr=LEARNING_RATE,
clipnorm=GRAD_CLIP),
loss=tf.keras.losses.categorical_crossentropy,
metrics=[tf.keras.metrics.categorical_accuracy])
#tf.enable_eager_execution(config=tf.ConfigProto(allow_soft_placement = True))
with tf.Graph().as_default():
with tf.Session(config=tf.ConfigProto(
allow_soft_placement=True)) as sess:
K.set_session(sess)
#with tf.device('/gpu:0:'):
tensorboard = TensorBoardCustom(log_dir="logs", words=words)
modelcheckpoint = tf.keras.callbacks.ModelCheckpoint(
'output/weights.{epoch:02d}-{val_loss:.2f}.hdf5')
writer = tf.summary.FileWriter("logs")
def schedule(epoch, lr):
if epoch >= 3:
return lr * 0.5
else:
return lr
lrate = LearningRateScheduler(schedule, verbose=1)
for epoch in xrange(NUM_EPOCHS):
for (inputs, a) in batch_loader_train:
[dw, qw, m_dw, m_qw, c, m_c, cl] = inputs
m = GAReader.Model(nlayers, data.vocab_size,
data.num_chars, W_init, nhidden,
embed_dim, dropout, train_emb, char_dim,
use_feat, gating_fn,
words).build_network()
m.compile(optimizer=tf.keras.optimizers.Adam(
lr=LEARNING_RATE, clipnorm=GRAD_CLIP),
loss=tf.keras.losses.categorical_crossentropy,
metrics=[tf.keras.metrics.categorical_accuracy])
#print(dw.shape)
#print('dw : {}'.format(dw))
#print('qw : {}'.format(qw))
#print('m_dw : {}'.format(m_dw))
#print('m_qw : {}'.format(m_qw))
#print('c : {}'.format(c))
#print([idx_to_word[i] for i in dw[0, :, 0].tolist()])
train_summary = m.train_on_batch(
inputs,
to_categorical(a, batch_loader_train.max_num_cand))
print(m.get_weights()[0])
print('epoch: {}, train loss: {}, train acc: {}'.format(
epoch, train_summary[0], train_summary[1]))
lr = tf.summary.scalar('learning_rate', LEARNING_RATE)
summary = tf.summary.merge_all()
s = sess.run(summary)
writer.add_summary(s)
writer.close()
import youtube_dl
import os
import getpass
import pafy
from termcolor import colored
from utils import Helpers
user = getpass.getuser()
utils = Helpers()
class Music:
@staticmethod
def create_path(path):
if not os.path.exists(path):
os.mkdir(path)
os.chdir(path)
os.chdir(path)
def mp3(self, url):
path = Helpers.check_platform('Music')
self.create_path(path)
ydl_opts = utils.ydl_options()
with youtube_dl.YoutubeDL(ydl_opts) as ydl:
ydl.download([url])
print(colored('Download Completed', 'green'))
def mp4(self, url):
path = Helpers.check_platform('Videos')
self.create_path(path)
try:
def main(load_path, params, mode='test'):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
char_dim = params['char_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset, no_training_set=True)
inv_vocab = data.inv_dictionary
print("building minibatch loaders ...")
if mode == 'test':
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.test, BATCH_SIZE)
else:
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.validation, BATCH_SIZE)
print("building network ...")
W_init, embed_dim = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
m = Reader.Model(nlayers,
data.vocab_size,
data.num_chars,
W_init,
nhidden,
embed_dim,
dropout,
train_emb,
char_dim,
use_feat,
gating_fn,
save_attn=True)
m.load_model('%s/best_model.p' % load_path)
print("testing ...")
pr = np.zeros((len(batch_loader_test.questions),
batch_loader_test.max_num_cand)).astype('float32')
fids, attns = [], []
total_loss, total_acc, n = 0., 0., 0
result = {}
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_test:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm, m_c, cl)
loss, acc, probs = outs[:3]
attns += [[fnames[0], probs[0, :]] + [o[0, :, :] for o in outs[3:]]
] # store one attention
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
pr[n:n + bsize, :] = probs
fids += fnames
n += bsize
answer = probs.argmax(1)
for it in range(len(fnames)):
tid = fnames[it].split('/')[-1].split('.')[0].strip()
result[eval(tid)] = answer[it]
print tid, answer[it]
print('probs----', probs)
#print('a----', a)
print('fnames----', fnames)
print len(result)
with open('raw.txt', 'w') as ff:
for i in range(1, 2501):
ff.write(str(result[i]) + '\n')
logger = open(load_path + '/log', 'a', 0)
message = '%s Loss %.4e acc=%.4f' % (mode.upper(), total_loss / n,
total_acc / n)
print message
logger.write(message + '\n')
logger.close()
np.save('%s/%s.probs' % (load_path, mode), np.asarray(pr))
pkl.dump(attns, open('%s/%s.attns' % (load_path, mode), 'w'))
f = open('%s/%s.ids' % (load_path, mode), 'w')
for item in fids:
f.write(item + '\n')
f.close()
def main(load_path, params, mode='test'):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['data']
nlayers = params['nlayers']
sub2vec = params['sub2vec']
train_emb = params['train_emb']
sub_dim = params['sub_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
use_subs = sub_dim > 0
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(dataset, no_training_set=True, use_subs=use_subs)
inv_vocab = data.inv_dictionary
print("building minibatch loaders ...")
if mode == 'test':
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.test, BATCH_SIZE)
else:
batch_loader_test = MiniBatchLoader.MiniBatchLoader(
data.validation, BATCH_SIZE)
print("building network ...")
W_init, embed_dim = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
S_init, sub_dim = Helpers.load_sub_embeddings(data.dictionary[1], sub2vec)
m = model.Model(nlayers,
data.vocab_size,
data.num_chars,
W_init,
S_init,
nhidden,
embed_dim,
dropout,
train_emb,
sub_dim,
use_feat,
gating_fn,
save_attn=True)
m.load_model('%s/best_model.p' % load_path)
print("testing ...")
pr = np.zeros((len(batch_loader_test.questions),
batch_loader_test.max_num_cand)).astype('float32')
fids, attns = [], []
total_loss, total_acc, n = 0., 0., 0
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_test:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm, m_c, cl)
loss, acc, probs = outs[:3]
attns += [[fnames[0], probs[0, :]] + [o[0, :, :] for o in outs[3:]]
] # store one attention
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
fids += fnames
n += bsize
print("step" + str(n) + ",acc" + str(acc))
logger = open(load_path + '/log', 'a', 0)
message = '%s Loss %.4e acc=%.4f' % (mode.upper(), total_loss / n,
total_acc / n)
print message
logger.write(message + '\n')
logger.close()
np.save('%s/%s.probs' % (load_path, mode), np.asarray(pr))
pkl.dump(attns, open('%s/%s.attns' % (load_path, mode), 'w'))
f = open('%s/%s.ids' % (load_path, mode), 'w')
for item in fids:
f.write(item + '\n')
f.close()
def main(save_path, params, mode='train'):
word2vec = params['word2vec']
dataset = params['dataset']
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess_rc(params, dataset)
print("building minibatch loaders ...")
batch_loader_train = MiniBatchLoader.MiniBatchLoaderMention(
params, data.training, params['batch_size'])
batch_loader_val = MiniBatchLoader.MiniBatchLoaderMention(
params,
data.validation,
params['batch_size'],
shuffle=False,
ensure_answer=False)
batch_loader_test = MiniBatchLoader.MiniBatchLoaderMention(
params,
data.test,
params['batch_size'],
shuffle=False,
ensure_answer=False)
print("building network ...")
W_init, embed_dim, = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
m = GA.Model(params, W_init, embed_dim)
print("training ...")
num_iter = 0
max_acc = 0.0
min_loss = 1e5
logger = open(save_path + '/log', 'a', 0)
train_writer = tf.summary.FileWriter(os.path.join(save_path, 'train'))
val_writer = tf.summary.FileWriter(os.path.join(save_path, 'val'))
if params['reload_']:
print('loading previously saved model')
saves = pkl.load(open('%s/checkpoints.p' % save_path))
m.load_model('%s/best_model.p' % save_path, saves[-1])
# train
if mode == 'train':
saves = []
for epoch in xrange(params['num_epochs']):
estart = time.time()
stop_flag = False
for example in batch_loader_train:
loss, tr_acc, probs, summary = m.train(*example[:-2])
if num_iter % params['logging_frequency'] == 0:
message = (
"Epoch %d TRAIN loss=%.4e acc=%.4f elapsed=%.1f" %
(epoch, loss, tr_acc, time.time() - estart))
print(message)
logger.write(message + '\n')
train_writer.add_summary(summary, num_iter)
num_iter += 1
if num_iter % params['validation_frequency'] == 0:
total_loss, total_acc, n = 0., 0., 0.
for example in batch_loader_val:
outs = m.validate(*example[:-2])
loss, acc, probs = outs[:3]
bsize = example[0].shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
n += bsize
val_acc = total_acc / n
print("11111111111 ", val_acc)
if val_acc > max_acc:
max_acc = val_acc
save_id = num_iter
print("111111111111111111111111111111")
sv = m.save_model('%s/best_model.p' % save_path,
save_id)
saves.append(save_id)
new_max = True
val_loss = total_loss / n
message = "Epoch %d VAL loss=%.4e acc=%.4f max_acc=%.4f" % (
epoch, val_loss, val_acc, max_acc)
print(message)
logger.write(message + '\n')
_add_summary(val_writer, val_loss, "loss", num_iter)
_add_summary(val_writer, val_acc, "accuracy", num_iter)
# stopping
if val_loss < min_loss: min_loss = val_loss
if params['stopping_criterion'] and (
val_loss - min_loss) / min_loss > 0.3:
stop_flag = True
break
if num_iter % params["anneal_frequency"] == 0:
m.anneal()
#m.save_model('%s/model_%d.p'%(save_path,epoch))
message = "After Epoch %d: Train acc=%.4f, Val acc=%.4f" % (
epoch, tr_acc, max_acc)
print(message)
logger.write(message + '\n')
if stop_flag: break
# record all saved models
pkl.dump(saves, open('%s/checkpoints.p' % save_path, 'w'))
# test
mode = 'test' if mode in ['train', 'test'] else 'val'
print("testing ...")
try:
saves = pkl.load(open('%s/checkpoints.p' % save_path))
print('%s/checkpoints.p' % save_path)
except IOError:
def _to_num(foo):
try:
num = int(foo)
except ValueError:
return None
return num
saves = []
for directory in os.listdir(save_path):
if not os.path.isdir(os.path.join(save_path, directory)): continue
num = _to_num(directory)
if num is None: continue
saves.append(num)
saves = sorted(saves)
print("saves111111", saves)
if not saves:
print("No models saved during training!")
return
print('loading model')
m.load_model('%s/best_model.p' % save_path, saves[-1])
total_loss, total_acc, n = 0., 0., 0
answer_structure = {}
idict = data.inv_dictionary
for example in batch_loader_val:
outs = m.validate(*example[:-2])
loss, acc, probs = outs[:3]
pred_indices = np.argmax(probs, axis=1)
for i in range(len(example[-1])):
cname = str(example[-1][i]).strip()
gt_answer = example[10][i]
answer_structure[cname] = (pred_indices[i], gt_answer, probs[i, :])
bsize = example[0].shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
n += bsize
test_acc = total_acc / n
test_loss = total_loss / n
message = "TEST loss=%.4e acc=%.4f" % (test_loss, test_acc)
print(message)
logger.write(message + '\n')
pkl.dump(answer_structure,
open(os.path.join(save_path, "test_answer_structure.p"), "w"))
logger.close()
# clean up
print("Cleaning up saved models ...")
def main(save_path, params):
nhidden = params['nhidden']
dropout = params['dropout']
word2vec = params['word2vec']
dataset = params['dataset']
nlayers = params['nlayers']
train_emb = params['train_emb']
char_dim = params['char_dim']
use_feat = params['use_feat']
gating_fn = params['gating_fn']
ent_setup = params['ent_setup'] # ent, ent-anonym, no-ent
data_path = params['data_path']
# save settings
shutil.copyfile('config.py', '%s/config.py' % save_path)
use_chars = char_dim > 0
if dataset == "clicr":
dp = DataPreprocessor.DataPreprocessorClicr()
data = dp.preprocess(
#"/mnt/b5320167-5dbd-4498-bf34-173ac5338c8d/Datasets/bmj_case_reports_data/dataset_json_concept_annotated/",
data_path,
ent_setup=ent_setup,
no_training_set=False,
use_chars=use_chars)
elif dataset == "clicr_novice":
dp = DataPreprocessor.DataPreprocessorNovice()
data = dp.preprocess(data_path,
ent_setup=ent_setup,
no_training_set=False,
use_chars=use_chars)
else:
dp = DataPreprocessor.DataPreprocessor()
data = dp.preprocess(data_path,
no_training_set=False,
use_chars=use_chars)
print("building minibatch loaders ...")
batch_loader_train = MiniBatchLoader.MiniBatchLoader(data.training,
BATCH_SIZE,
sample=1.0)
batch_loader_val = MiniBatchLoader.MiniBatchLoader(data.validation,
BATCH_SIZE)
print("building network ...")
W_init, embed_dim, = Helpers.load_word2vec_embeddings(
data.dictionary[0], word2vec)
m = GAReader.Model(nlayers, data.vocab_size, data.num_chars, W_init,
nhidden, embed_dim, dropout, train_emb, char_dim,
use_feat, gating_fn)
print("training ...")
num_iter = 0
max_acc = 0.
deltas = []
logger = open(save_path + '/log', 'a')
if os.path.isfile('%s/best_model.p' % save_path):
print('loading previously saved model')
m.load_model('%s/best_model.p' % save_path)
else:
print('saving init model')
m.save_model('%s/model_init.p' % save_path)
print('loading init model')
m.load_model('%s/model_init.p' % save_path)
for epoch in range(NUM_EPOCHS):
estart = time.time()
new_max = False
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_train:
loss, tr_acc, probs = m.train(dw, dt, qw, qt, c, a, m_dw, m_qw, tt,
tm, m_c, cl)
message = "Epoch %d TRAIN loss=%.4e acc=%.4f elapsed=%.1f" % (
epoch, loss, tr_acc, time.time() - estart)
print(message)
logger.write(message + '\n')
num_iter += 1
if num_iter % VALIDATION_FREQ == 0:
total_loss, total_acc, n, n_cand = 0., 0., 0, 0.
for dw, dt, qw, qt, a, m_dw, m_qw, tt, tm, c, m_c, cl, fnames in batch_loader_val:
outs = m.validate(dw, dt, qw, qt, c, a, m_dw, m_qw, tt, tm,
m_c, cl)
loss, acc, probs = outs[:3]
bsize = dw.shape[0]
total_loss += bsize * loss
total_acc += bsize * acc
n += bsize
val_acc = total_acc / n
if val_acc > max_acc:
max_acc = val_acc
m.save_model('%s/best_model.p' % save_path)
new_max = True
message = "Epoch %d VAL loss=%.4e acc=%.4f max_acc=%.4f" % (
epoch, total_loss / n, val_acc, max_acc)
print(message)
logger.write(message + '\n')
# m.save_model('%s/model_%d.p'%(save_path,epoch))
message = "After Epoch %d: Train acc=%.4f, Val acc=%.4f" % (
epoch, tr_acc, val_acc)
print(message)
logger.write(message + '\n')
# learning schedule
if epoch >= 2:
m.anneal()
# stopping criterion
if not new_max:
break
logger.close()
def test_create_project(self):
driver = self.driver
WebDriverWait(driver, 10).until_not(lambda x: x.find_element_by_xpath(
'//*[@style="display: block;"]').is_displayed())
# project menu: get and click
self.project_menu = driver.find_element_by_id(l.projectTool)
self.assertTrue(self.project_menu.is_displayed()
and self.project_menu.is_enabled())
self.project_menu.click()
# create project click
WebDriverWait(
driver,
10).until(lambda el: el.find_element_by_id(l.CREATE_PROJECT))
driver.find_element(By.ID, l.CREATE_PROJECT).click()
# fill mandatory fields
helper = Helpers()
helper.field(self, driver.find_element(By.ID, l.project_code),
time_stamp)
helper.field(self, driver.find_element(By.ID, l.project_note),
time_stamp)
helper.field(self, driver.find_element(By.ID, l.project_address),
time_stamp)
helper.field(self, driver.find_element(By.ID, l.project_client),
time_stamp)
helper.field(self, driver.find_element(By.ID, l.project_contact),
time_stamp)
print(time_stamp)
driver.find_element_by_id(l.project_add_button).click()