j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
jkeyword = jkeywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j:j +
keyword_len]:
if have_dic:
if keyword[0] in d:
f, s = d[keyword[0]]
s.add(jkeyword)
d[keyword[0]] = f, s
else:
d[keyword[0]] = print_features(
keyword[0]), set([jkeyword])
print "B\t" + print_features(
keyword[0]) + "\t" + jkeyword
#print keyword[0] + "\tB\t" + str(i+1) + "\t" + str(k+1)
for l in keyword[1:]:
if have_dic:
if l in d:
f, s = d[l]
s.add(jkeyword)
d[l] = f, s
else:
d[l] = print_features(l), set([jkeyword])
print "I\t" + print_features(l) + "\t" + jkeyword
#print l + "\tI\t" + str(i+1) + "\t" + str(k+1)
found = True
j += keyword_len
for i in range(len(lines)):
if i % 1000 == 0:
sys.stderr.write(str(i) + "/" + str(len(lines)) + "\n")
line = dict(lines[i])
if 'EKYWD' in line and 'EABST' in line:
abstract = line['EABST']
keywords = re.split('\t', line['EKYWD'])
abstract = word_tokenize(abstract)
keywords = [word_tokenize(keyword) for keyword in keywords]
j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j:j + keyword_len]:
print "B\t" + print_features(keyword[0])
for l in keyword[1:]:
print "I\t" + print_features(l)
found = True
j += keyword_len
if found:
break
if j >= len(abstract):
break
print "O\t" + print_features(abstract[j])
j += 1
sys.stderr.write("Finished\n")
abstract = line["EABST"]
keywords = re.split("\t", line["EKYWD"])
abstract = word_tokenize(abstract)
keywords = [word_tokenize(keyword) for keyword in keywords]
j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j : j + keyword_len]:
if have_dic:
if keyword[0] in d:
print "B\t" + d[keyword[0]]
else:
print "B\t" + print_features(keyword[0])
else:
print "B\t" + print_features(keyword[0])
# print "B\t" + print_features(keyword[0]) + "\t" + jkeyword
# print keyword[0] + "\tB\t" + str(i+1) + "\t" + str(k+1)
for l in keyword[1:]:
if have_dic:
if l in d:
print "I\t" + d[l]
else:
print "I\t" + print_features(l)
else:
print "I\t" + print_features(l)
# print "I\t" + print_features(l) + "\t" + jkeyword
# print l + "\tI\t" + str(i+1) + "\t" + str(k+1)
found = True
keywords = [word_tokenize(keyword) for keyword in keywords]
j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
jkeyword = jkeywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j:j+keyword_len]:
if have_dic:
if keyword[0] in d:
f, s = d[keyword[0]]
s.add(jkeyword)
d[keyword[0]] = f, s
else:
d[keyword[0]] = print_features(keyword[0]), set([jkeyword])
print "B\t" + print_features(keyword[0]) + "\t" + jkeyword
#print keyword[0] + "\tB\t" + str(i+1) + "\t" + str(k+1)
for l in keyword[1:]:
if have_dic:
if l in d:
f, s = d[l]
s.add(jkeyword)
d[l] = f, s
else:
d[l] = print_features(l), set([jkeyword])
print "I\t" + print_features(l) + "\t" + jkeyword
#print l + "\tI\t" + str(i+1) + "\t" + str(k+1)
found = True
j += keyword_len
if found:
for i in range(len(lines)):
if i % 1000 == 0:
sys.stderr.write(str(i) + "/" + str(len(lines)) + "\n")
line = dict(lines[i])
if "EKYWD" in line and "EABST" in line and "KYWD" in line:
keywords = re.split("\t", line["EKYWD"])
jkeywords = re.split("\t", line["KYWD"])
if len(keywords) == len(jkeywords):
keywords = [word_tokenize(keyword) for keyword in keywords]
for k in range(len(keywords)):
keyword = keywords[k]
jkeyword = jkeywords[k]
for word in keyword:
if word in d:
f, s = d[word]
s.add(jkeyword)
d[word] = f, s
else:
d[word] = print_features(word), set([jkeyword])
sys.stderr.write("Printing dict\n")
for k, (f, s) in d.iteritems():
line = k + "\t"
line += f
for j in s:
line += "\t" + j
print line
sys.stderr.write("Finished\n");
if len(args) == 0:
f = sys.stdin
else:
f = open(args[0])
d = dict()
i = 0
for line in f:
if i % 20000 == 0:
sys.stderr.write("Entry: " + str(i) + "\n")
i += 1
line = re.split('\t', line)
jterm = line[1]
eterm = word_tokenize(line[2])
for token in eterm:
if token in d:
d[token].add(jterm)
else:
d[token] = set([jterm])
sys.stderr.write(str(i) + "\n")
sys.stderr.write(str(len(d)) + "\n")
for k, v in d.iteritems():
sys.stdout.write(k)
sys.stdout.write("\t" + print_features(k))
for j in v:
sys.stdout.write('\t' + j)
sys.stdout.write('\n')
def main():
model_choices = [
'PerceptronModel', 'SoftmaxRegressionModel', 'ConvNetModel'
]
solver_choices = [
'PerceptronSolver', 'GradientDescentSolver',
'StochasticGradientDescentSolver',
'MinibatchStochasticGradientDescentSolver'
]
data_choices = [
'tinyMnistDataset', 'medMnistDataset', 'largeMnistDataset',
'mnistDataset', 'datasetA', 'datasetB'
]
parser = argparse.ArgumentParser(
description='Input the arguments to train the neural net.')
parser.add_argument('-m',
'--model',
choices=model_choices,
default='SoftmaxRegressionModel',
help='Perceptron or neural net model')
parser.add_argument('-s',
'--solver',
choices=solver_choices,
default='MinibatchStochasticGradientDescentSolver',
help='Solver to train the model')
parser.add_argument(
'-d',
'--data',
choices=data_choices,
default='medMnistDataset',
help='Dataset to use for training',
)
parser.add_argument(
'-f',
'--weight_file',
default=None,
help='File name (.npz) of weights to use to initialize the model')
parser.add_argument('-i',
'--iterations',
default=10,
type=int,
help='Maximum iterations to run training')
parser.add_argument('-l',
'--learning_rate',
nargs='+',
default=[0.001],
type=float,
help='Learning rate to use for the solver')
parser.add_argument(
'-b',
'--batch_size',
nargs='+',
default=[32],
type=int,
help=
'Minibatch size to use when iterating the training and validation data'
)
parser.add_argument('-u',
'--momentum',
nargs='+',
default=[0.0],
type=float,
help='Momentum to use for the solver')
parser.add_argument('-w',
'--weight_decay',
default=1e-3,
type=float,
help='Coefficient for l2 regularization on the loss')
parser.add_argument('-bn',
'--batch_norm',
action='store_true',
help='Batch normalization')
parser.add_argument('--no-shuffle',
action='store_true',
help='Disables shuffling of data')
parser.add_argument('--no-graphics',
action='store_true',
help='Turns off plots')
parser.add_argument(
'-p',
'--plot_interval',
default=100,
type=int,
help='Only plot only every this often (in terms of iterations)')
parser.add_argument('--print_features',
action='store_true',
help='Print high weight features')
parser.add_argument(
'--feature_extractor',
choices=['enhancedFeatureExtractor', 'basicFeatureExtractor'],
help='Feature extractor function to use for mnist images')
args = parser.parse_args()
# Parse args and print information
if args.model == 'PerceptronModel':
args.solver = 'PerceptronSolver'
print("data:\t\t" + args.data)
print("model:\t\t" + args.model)
print("solver:\t\t" + args.solver)
train_data, val_data, test_data = get_data(args)
# Load weights if applicable
if args.weight_file is not None:
print("loading parameter values from %s" % args.weight_file)
init_param_values_file = np.load(args.weight_file)
init_param_values = [
init_param_values_file['arr_%d' % i]
for i in range(len(init_param_values_file.files))
]
else:
init_param_values = None
# train and validate
hyperparams = [args.learning_rate, args.momentum, args.batch_size]
if all([len(hyperparam) == 1 for hyperparam in hyperparams
]): # train and validate using a single set of hyperparameters
model = get_model(args, train_data)
if init_param_values is not None:
model.set_param_values(init_param_values)
solver = get_solver(args)
print("Training...")
solver.solve(*(train_data + val_data +
[model, pacman_display_callback(train_data)]))
else: # do hyperparameter search
# cartesian product of hyperparameters
hyperparams = list(itertools.product(*hyperparams))
model, best_hyperparams = search_hyperparams(
*(train_data + val_data + zip(*hyperparams)),
iterations=args.iterations,
model_class=get_model_class(args),
init_param_values=init_param_values,
use_bn=args.batch_norm)
print(
'Best model is trained with these hyperparameters: learning_rate=%r, momentum=%r, batch_size=%r'
% tuple(best_hyperparams))
if args.print_features and args.model == 'PerceptronModel' and 'mnist' in args.data.lower(
):
for l in model.legal_labels:
highest_weighted_features = model.find_high_weight_features(l)
features.print_features(highest_weighted_features)
if 'mnist' in args.data.lower() and args.feature_extractor is not None:
def get_data_labels_pred(data):
features = data[0]
labels = np.argmax(data[1], axis=-1)
predictions = model.classify(features)
return features, labels, predictions
trainData, trainLabels, trainPredictions = get_data_labels_pred(
train_data)
validationData, validationLabels, validationPredictions = get_data_labels_pred(
val_data)
features.analysis(model, trainData, trainLabels, trainPredictions,
validationData, validationLabels,
validationPredictions)
print("Computing accuracies")
if train_data[0].shape[
0] <= 10000: # compute training accuracy only for small datasets (otherwise computing this is too slow)
print("Train accuracy: %.1f%%" % (100.0 * model.accuracy(*train_data)))
print("Validation accuracy: %.1f%%" % (100.0 * model.accuracy(*val_data)))
print("Test accuracy: %.1f%%" % (100.0 * model.accuracy(*test_data)))
raw_input('Press enter to exit')
j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j:j+keyword_len]:
for l in range(keyword_len):
this_word = keyword[l]
this_pos = pos_abstract[j+l][1]
out = ""
if l == 0:
out += "B\t"
else:
out += "I\t"
out += print_features(this_word)
out += "\tPOS=" + this_pos
if this_pos in taking_pos and this_word in d:
out += "\t" + d[this_word]
print out
found = True
j += keyword_len
if found:
break
if j >= len(abstract):
break
this_word = abstract[j]
this_pos = pos_abstract[j][1]
out = "O\t" + print_features(this_word)
out += "\tPOS=" + this_pos
if this_pos in taking_pos and this_word in d:
j = 0
while j < len(abstract):
found = False
for k in range(len(keywords)):
keyword = keywords[k]
keyword_len = len(keyword)
if keyword_len > 0 and keyword == abstract[j:j + keyword_len]:
for l in range(keyword_len):
this_word = keyword[l]
this_pos = pos_abstract[j + l][1]
out = ""
if l == 0:
out += "B\t"
else:
out += "I\t"
out += print_features(this_word)
out += "\tPOS=" + this_pos
if this_pos in taking_pos and this_word in d:
out += "\t" + d[this_word]
print out
found = True
j += keyword_len
if found:
break
if j >= len(abstract):
break
this_word = abstract[j]
this_pos = pos_abstract[j][1]
out = "O\t" + print_features(this_word)
out += "\tPOS=" + this_pos
if this_pos in taking_pos and this_word in d:
d = dict()
for i in range(len(lines)):
if i % 1000 == 0:
sys.stderr.write(str(i) + "/" + str(len(lines)) + "\n")
line = dict(lines[i])
if "EKYWD" in line and "EABST" in line and "KYWD" in line:
keywords = re.split("\t", line["EKYWD"])
jkeywords = re.split("\t", line["KYWD"])
if len(keywords) == len(jkeywords):
keywords = [word_tokenize(keyword) for keyword in keywords]
for k in range(len(keywords)):
keyword = keywords[k]
jkeyword = jkeywords[k]
for word in keyword:
if word in d:
f, s = d[word]
s.add(jkeyword)
d[word] = f, s
else:
d[word] = print_features(word), set([jkeyword])
sys.stderr.write("Printing dict\n")
for k, (f, s) in d.iteritems():
line = k + "\t"
line += f
for j in s:
line += "\t" + j
print line
sys.stderr.write("Finished\n")
