def initialize_instances(filename):
"""Read the abalone.txt CSV data into a list of instances."""
print('Creating instances')
instances = []
inFile = open(filename, 'rb')
reader = csv.reader(inFile, delimiter=',')
skipHeader = True
for row in reader:
if skipHeader:
skipHeader = False
continue
# print(len(row[1:-1]))
# print(len([float(value) for value in row[1:-1]]))
instance = Instance([float(value) for value in row[1:-1]
]) #ignore the index and the label
instance.setLabel(
Instance(0 if float(row[-1]) < 15 else 1)) #set the label
instances.append(instance)
inFile.close()
print('Finished instances')
return instances
def train(oa, network, oaName, instances, measure):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
print "\nError results for %s\n---------------------------" % (oaName, )
for iteration in xrange(TRAINING_ITERATIONS):
oa.train()
error = 0.00
for instance in instances:
network.setInputValues(instance.getData())
network.run()
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
print "%0.03f" % error
def errorOnDataSet(network,ds,measure):
N = len(ds)
error = 0.
correct = 0
incorrect = 0
count = 0
for instance in ds:
count +=1
network.setInputValues(instance.getData())
network.run()
actual = instance.getLabel().getContinuous()
predicted = network.getOutputValues().get(0)
predicted = max(min(predicted,1),0)
if abs(predicted - actual) < 0.5:
correct += 1
else:
incorrect += 1
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
MSE = error/float(N)
acc = correct/float(correct+incorrect)
return MSE,acc
def train(oa, network, oaName, instances, measure = SumOfSquaresError(),
surpress_output=False,
TRAINING_ITERATIONS = 1500):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
if not surpress_output:
print "\nError results for %s every 100 " \
"iterations\n---------------------------" % (oaName,)
for i in xrange(TRAINING_ITERATIONS):
oa.train()
error = 0.00
for instance in instances:
network.setInputValues(instance.getData())
network.run()
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
if not surpress_output and i % 100 == 0:
print "%0.03f" % error
def initialize_instances(infile):
"""Read the given CSV data into a list of instances."""
instances = []
# Read in the CSV file
with open(infile, "r") as dat:
reader = csv.reader(dat)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
# TODO: Set to <= 0 to handle 0/1 labels and not just -1/1?
# assumes labels are integers from 0 to NUM_OF_CLASSES-1
label = int(float(row[-1]))
classes = [0] * NUM_OF_CLASSES
classes[label] = 1
instance.setLabel(Instance(classes))
instances.append(instance)
return instances
def errorOnDataSet(network, ds, measure):
N = len(ds)
error = 0.
correct = 0
incorrect = 0
for instance in ds:
network.setInputValues(instance.getData())
network.run()
# actual = instance.getLabel().getData().argMax()
actual = instance.getLabel().getData().get(0)
# predicted = network.getOutputValues().argMax()
predicted = network.getOutputValues().get(0)
if predicted > 0.5:
predicted = 1.0
else:
predicted = 0.0
# print("Actual = ", actual, " , Predicted = ", predicted)
if actual == predicted:
correct += 1
else:
incorrect += 1
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values))
error += measure.value(output, example)
MSE = error / float(N)
acc = correct / float(correct + incorrect)
return MSE, acc
def train(oa, network, oaName, instances, measure):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
print "\nError results for %s\n---------------------------" % (oaName, )
FILE_NAME = oaName + ".csv"
OUTPUT_FILE = os.path.join("data", FILE_NAME)
with open(OUTPUT_FILE, "wb") as results:
writer = csv.writer(results, delimiter=',')
for iteration in xrange(TRAINING_ITERATIONS):
oa.train()
error = 0.00
for instance in instances:
network.setInputValues(instance.getData())
network.run()
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values,
Instance(output_values.get(0)))
error += measure.value(output, example)
print error / len(instances)
writer.writerow([error / len(instances)])
def train(oa, network, oaName, instances, measure, fileobject):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
fileobject.write(str(oaName) + " training " + "\n")
for iteration in xrange(TRAINING_ITERATIONS):
oa.train()
error = 0.00
for instance in instances:
network.setInputValues(instance.getData())
network.run()
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
print "finished iter", iteration, "for", oaName
fileobject.write(str(oaName) + "," + str(iteration) + "," + str(error) + "\n")
def eval_instances(net, instances, measure):
# get the accuracy of the set (training, test, validation)
set_len = len(instances)
right, wrong, error = 0, 0, 0.
for i in instances:
net.setInputValues(i.getData())
net.run()
# should only need first output binary class
truth = i.getLabel().getContinuous()
n_out = net.getOutputValues().get(0)
if int(truth) == int(n_out):
right += 1
else:
wrong += 1
output = i.getLabel()
output_values = net.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
accuracy = float(right) / float(set_len)
error = error / float(set_len)
return accuracy, error
def error_on_data_set(network, ds, measure, ugh=False):
N = len(ds)
error = 0.
correct = 0
incorrect = 0
actuals = []
predicteds = []
for instance in ds:
network.setInputValues(instance.getData())
network.run()
actual_out = instance.getLabel()
predicted_out = network.getOutputValues()
predicted = []
actual = []
for j in range(0, predicted_out.size()):
predicted.append(max(min(predicted_out.get(j), 1), 0))
if sum([round(cur) for cur in predicted]) > 1:
print "FOUND TWO ONES : {}".format(
[round(cur) for cur in predicted])
elif sum([round(cur) for cur in predicted]) == 0:
print "ALL ZEROS : {}".format(
[round(cur) for cur in predicted])
for k in range(0, actual_out.getData().size()):
actual.append(round(actual_out.getData().get(k)))
if ugh:
print "label: {}".format(instance.getLabel())
print "actual: {}, predicted: {}".format(actual_out, predicted_out)
predicteds.append([round(cur) for cur in predicted])
actuals.append([max(min(cur, 1), 0) for cur in actual])
ind = max(xrange(len(predicted)), key=predicted.__getitem__)
if actual[ind] == 1:
correct += 1
if ugh:
print "CORRECT"
else:
incorrect += 1
if ugh:
print "INCORRECT"
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values))
error += measure.value(output, example)
if ugh:
print "error: {}".format(measure.value(output, example))
MSE = error / float(N)
acc = correct / float(correct + incorrect)
precision, recall, f1 = f1_score(actuals, predicteds)
if ugh:
print "MSE: {}, acc: {}, f1: {} (precision: {}, recall: {})".format(
MSE, acc, f1, precision, recall)
import sys
sys.exit(0)
return MSE, acc, f1
def errorOnDataSet(network, ds, measure):
N = len(ds)
error = 0.
correct = 0
incorrect = 0
false_positives = 0.0
false_negatives = 0.0
true_positives = 0.0
true_negatives = 0.0
for instance in ds:
network.setInputValues(instance.getData())
network.run()
actual = instance.getLabel().getContinuous()
predicted = network.getOutputValues().get(0)
predicted = max(min(predicted, 1), 0)
# Measure type of error for F1 score
if actual == 0.0 and predicted >= 0.5:
false_positives += 1.0
if actual == 0.0 and predicted < 0.5:
true_negatives += 1.0
if actual == 1.0 and predicted >= 0.5:
true_positives += 1.0
if actual == 1.0 and predicted < 0.5:
false_negatives += 1.0
if abs(predicted - actual) < 0.5:
correct += 1
else:
incorrect += 1
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
MSE = error / float(N)
acc = correct / float(correct + incorrect)
try:
precision = true_positives / (true_positives + false_positives)
except ZeroDivisionError:
precision = 0.0
try:
recall = true_positives / (true_positives + false_negatives)
except ZeroDivisionError:
recall = 0.0
try:
F1 = 2.0 * ((precision * recall) / (precision + recall))
except ZeroDivisionError:
F1 = 0.0
return MSE, acc, F1
def initialize_instances():
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
with open(TRAIN_FILE, "r") as abalone:
reader = csv.reader(abalone)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if int(row[-1]) == 0 else 1))
instances.append(instance)
return instances
def get_test_instances():
"""Read the optdigits test CSV data into a list of instances."""
instances = []
with open(TEST_FILE, "r") as f:
reader = csv.reader(f)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if int(row[-1]) == 0 else 1))
instances.append(instance)
return instances
def train(oa,
network,
oaName,
train_set,
test_set,
measure,
max_iterations=TRAINING_ITERATIONS):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
train_instances = train_set.getInstances()
test_instances = test_set.getInstances()
fname = 'out/error/%s.csv' % (oaName)
with open(fname, 'w') as f:
# print "\nError results for %s\n---------------------------" % (oaName,)
for iteration in xrange(max_iterations):
oa.train()
train_error = test_error = 0.00
for train_instance in train_instances:
network.setInputValues(train_instance.getData())
network.run()
output = train_instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values,
Instance(output_values.get(0)))
train_error += measure.value(output, example)
for test_instance in test_instances:
network.setInputValues(test_instance.getData())
network.run()
output = test_instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values,
Instance(output_values.get(0)))
test_error += measure.value(output, example)
train_error_norm = train_error / len(train_instances)
test_error_norm = test_error / len(test_instances)
f.write("%d,%0.05f,%0.05f\n" %
(iteration, train_error_norm, test_error_norm))
print('Error written to %s' % (fname))
def train(oa, network, oaName, instances, measure):
"""Train a given network on a set of instances.
:param OptimizationAlgorithm oa:
:param BackPropagationNetwork network:
:param str oaName:
:param list[Instance] instances:
:param AbstractErrorMeasure measure:
"""
#print "\nError results for %s\n---------------------------" % (oaName,)
# training error each iteration
iterdata = []
training_time = 0.
for iteration in TRAINING_ITERATIONS:
#if oaName == "GA" and iteration >= int(len(TRAINING_ITERATIONS)/5):
# continue
if iteration >= int(len(TRAINING_ITERATIONS) / 5):
break
start = time.time()
oa.train()
end = time.time()
training_time += end - start
if iteration % interval != 0:
continue
correct, incorrect = 0, 0
error = 0.
for instance in instances[:1000]:
network.setInputValues(instance.getData())
network.run()
actual = instance.getLabel().getContinuous()
predicted = network.getOutputValues().get(0)
if abs(predicted - actual) < 0.5:
correct += 1
else:
incorrect += 1
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
#print "output, example,error",output, example,measure.value(output, example)
accuracy = 1. * correct / (correct + incorrect)
iterdata.append([iteration, accuracy, error, training_time])
# print 'iteration,accuracy,error,training_time',iteration,accuracy,error,training_time
return iterdata
def initialize_instances(infile):
instances = []
with open(infile, "r") as dat:
reader = csv.reader(dat)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) <= 0 else 1))
instances.append(instance)
return instances
def get_error(data, network, measure):
error = 0.00
for j, instance in enumerate(data):
network.setInputValues(instance.getData())
network.run()
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
return error
def maybe_serialize(file, force=False):
serialized_file = os.path.splitext(file)[0] + '.ser'
if not os.path.isfile(serialized_file) or force:
stdout.write("Serializing Data-Set...\n\n")
with open(file, "r") as pima:
reader_list = list(csv.reader(pima))
stdout.write("Some sample, un-shuffled data: \n%s\n\n" % reader_list[:3])
normalize_data(reader_list)
random.shuffle(reader_list)
number_of_instances = len(reader_list)
train_instances = []
for row in reader_list[:int(number_of_instances *
TRAIN_TEST_SPLIT_RATIO)]:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) == -1 else 1))
train_instances.append(instance)
test_instances = []
for row in reader_list[int(number_of_instances *
TRAIN_TEST_SPLIT_RATIO):]:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) == -1 else 1))
test_instances.append(instance)
stdout.write("Some sample, shuffled training data (after "
"normalization): "
"\n%s\n\n" % train_instances[:3])
stdout.write("Some sample, shuffled test data (after "
"normalization): \n%s\n\n" %
test_instances[:3])
stdout.write("Train Data\tTest Data\n")
stdout.write("%s\t\t%s\n" % (len(train_instances),
len(test_instances)))
save = {
TRAIN: train_instances,
TEST: test_instances,
}
outFile = io.FileOutputStream(serialized_file)
outStream = io.ObjectOutputStream(outFile)
outStream.writeObject(save)
outFile.close()
else:
stdout.write("Serialized file for data-set found.\n")
return serialized_file
def initialize_instances(filename, i):
instances = []
with open(filename, "r") as f:
reader = csv.reader(f)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(int(row[-1])))
instances.append(instance)
return instances
def read_dataset(path, pos_set):
instances = []
with open(path, 'r') as stream:
reader = csv.reader(stream)
times = 0
for row in reader:
if times:
instance = Instance([float(value) for value in row[:-1]])
label = 1 if float(row[-1]) in pos_set else 0
instance.setLabel(Instance(label))
instances.append(instance)
times += 1
return instances
def initialize_instances(infile):
"""Read the m_trg.csv CSV data into a list of instances."""
instances = []
# Read in the CSV file
with open(infile, "r") as dat:
reader = csv.reader(dat)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) < 0 else 1))
instances.append(instance)
return instances
def initialize_instances():
"""Read the data into a list of instances."""
instances = []
# Read in the CSV file
with open(INPUT_FILE, "r") as abalone:
reader = csv.reader(abalone)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(1 if row[-1] == "crisis" else 0))
instances.append(instance)
return instances
def initialize_instances():
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
# Read in the abalone.txt CSV file
with open(INPUT_FILE, "r") as abalone:
reader = csv.reader(abalone)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) < 15 else 1))
instances.append(instance)
return instances
def initialize_instances():
"""Read the gamma.txt CSV data into a list of instances."""
instances = []
# Read in the gamma.txt CSV file
with open(INPUT_FILE, "r") as gamma:
reader = csv.reader(gamma)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) == 0 else 1))
instances.append(instance)
return instances
def initialize_instances(examples):
"""Read CSV data into a list of instances."""
instances = []
# Read in the abalone.txt CSV file
with open(examples, "r") as gamma:
reader = csv.reader(gamma)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if row[-1] == 'g' else 1))
instances.append(instance)
return instances
def initialize_instances():
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
# Read in the abalone.txt CSV file
with open(INPUT_FILE, "r") as abalone:
reader = csv.reader(abalone)
for row in reader:
instance = Instance([float(value) for value in row[1:-1]])
instance.setLabel(Instance(0 if float(row[-1]) == 2 else 1)) # 2 is benign, 4 malignant
instances.append(instance)
return instances
def initialize_instances(test=False):
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
if test:
INPUT_FILE = TEST_FILE
else:
INPUT_FILE = TRAIN_FILE
with open(INPUT_FILE, "r") as chess:
reader = csv.reader(chess)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
if do_chess:
instance.setLabel(Instance(float(row[-1])))
if do_fmnist:
classes = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
index = int(row[-1])
# print "Value is: ", row[-1], " index is: ", index
classes[index] = 1.0
temp = Instance(classes)
# print "Size is: ", temp.size()
instance.setLabel(temp)
instances.append(instance)
return instances
def error_on_data_set(network, ds, measure, ugh=False):
N = len(ds)
error = 0.
correct = 0
incorrect = 0
actuals = []
predicteds = []
# ugh=True
for instance in ds:
network.setInputValues(instance.getData())
# print instance
# print instance.getData()
# print instance.getLabel().getContinuous()
network.run()
actual = instance.getLabel().getContinuous()
predicted = network.getOutputValues().get(0)
# print "Predicted 1", network.getOutputValues()
predicted = max(min(predicted, 1), 0)
if ugh:
print "label: {}".format(instance.getLabel())
print "actual: {}, predicted: {}".format(actual, predicted)
predicteds.append(round(predicted))
actuals.append(max(min(actual, 1), 0))
if abs(predicted - actual) < 0.5:
correct += 1
if ugh:
print "CORRECT"
else:
incorrect += 1
if ugh:
print "INCORRECT"
output = instance.getLabel()
output_values = network.getOutputValues()
example = Instance(output_values, Instance(output_values.get(0)))
error += measure.value(output, example)
if ugh:
print "error: {}".format(measure.value(output, example))
MSE = error / float(N)
acc = correct / float(correct + incorrect)
precision, recall, f1 = f1_score(actuals, predicteds)
if ugh:
print "MSE: {}, acc: {}, f1: {} (precision: {}, recall: {})".format(
MSE, acc, f1, precision, recall)
import sys
sys.exit(0)
return MSE, acc, f1
def initialize_instances():
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
# Read in the abalone.txt CSV file
with open(INPUT_FILE, "r") as abalone:
reader = csv.reader(abalone)
for row in reader:
INPUT_LAYER = len(row) - 1
instance = Instance([float(value) for value in row[:-1]])
instance.setLabel(Instance(0 if float(row[-1]) < 0.5 else 1))
instances.append(instance)
#print instances
return instances
def initialize_instances(infile):
"""Read the given CSV data into a list of instances."""
instances = []
# Read in the CSV file
with open(infile, "r") as dat:
reader = csv.reader(dat)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
# TODO: Set to <= 0 to handle 0/1 labels and not just -1/1?
instance.setLabel(Instance(0 if float(row[-1]) < 0.001 else 1))
instances.append(instance)
return instances
def initialize_instances(file_path):
"""Read the abalone.txt CSV data into a list of instances."""
instances = []
# Read in the adult_train.txt CSV file
with open(file_path, "r") as adult:
reader = csv.reader(adult)
for row in reader:
instance = Instance([float(value) for value in row[:-1]])
# my data was already preprocessed, so this basically does nothing but appends my data to instances
instance.setLabel(Instance(0 if float(row[-1]) < 1 else 1))
instances.append(instance)
return instances
def read_data_files(self):
"""
Read a scikit data set. The entire file should be numbers, so I'm not bothering with CSV or anything fancy.
Just numbers separated by spaces.
:return: None
"""
# Set the data file names
data_file = self.dataset_name + ".data"
target_file = self.dataset_name + ".target"
# Check that the files exist
if not os.path.isfile(data_file):
raise Exception("Data file '" + data_file + "' not found")
if not os.path.isfile(data_file):
raise Exception("Target file '" + target_file + "' not found")
# Read the lines of the data and target files
if self.verbose:
print("Loading data")
d_in = open(data_file, 'r')
data_lines = d_in.readlines()
d_in.close()
t_in = open(target_file, 'r')
target_lines = t_in.readlines()
t_in.close()
# A quick check that there is a one-to-one correspondence between data and target lines
self.n_samples = len(data_lines)
if not self.n_samples == len(target_lines):
raise Exception("Data and Target lengths are not the same.")
# Interpret each data and target line pair
if self.verbose:
print("Interpreting data")
self.samples = []
self.n_features = len(data_lines[0].split())
self.n_targets = len(target_lines[0].split())
for ss in xrange(self.n_samples):
data = []
ds = data_lines[ss].split()
n_inputs = len(ds)
for val in ds:
data.append(float(val))
target = []
ds = target_lines[ss].split()
n_outputs = len(ds)
for val in ds:
target.append(float(val))
inst = Instance(data)
inst.setLabel(Instance(target))
# Do some checking before we append this
if not self.n_features == n_inputs:
raise Exception("Line " + str(ss) + ": Number of data points does not match previous lines")
if not self.n_targets == n_outputs:
raise Exception("Line " + str(ss) + ": Number of targets does not match previous lines")
# Append this data pattern
self.samples.append(inst)
# What type of classification is this?
if self.n_targets == 1:
self.out_type = "binary"
else:
self.out_type = "multiclass"