def test_easy_forward_propagation(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, 0, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
y = nn.forward([3, 22])
self.assertEqual(len(y), 2)
self.assertEqual(y, [0.5, 0.5])
genome = GenomeMock([(2, 4, 1, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, 0, True)], 2, 2)
nn.generate_network(genome)
y = nn.forward([3, 22])
self.assertEqual(y[0], 0.5)
self.assertAlmostEqual(y[1], 0.9926085)
genome = GenomeMock([(2, 4, 1, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, -2, True)], 2, 2)
nn.generate_network(genome)
y = nn.forward([3, 22])
self.assertEqual(y[0], 0.5)
self.assertAlmostEqual(y[1], 0.00739157)
genome = GenomeMock([(2, 4, 1, True), (1, 3, 0, False),
(2, 3, 0, False), (1, 4, -2, True)], 2, 2)
nn.generate_network(genome)
y = nn.forward([3, 22])
self.assertEqual(y[0], 0.5)
self.assertAlmostEqual(y[1], 0.00739157)
def test_input_neurons_have_input_signal(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, 0, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
nn.forward([3, 22])
self.assertEqual(nn._input_neurons[1]._input_signals, [3])
self.assertEqual(nn._input_neurons[2]._input_signals, [22])
def test_input_length_exception(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, 0, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
with self.assertRaises(Exception) as e:
nn.forward([1])
self.assertEqual(str(e.exception), "Expected 2 inputs, got 1 instead")
def test_conections(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, 0, True), (2, 3, 0, True),
(1, 4, 0, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
self.assertEqual(nn._genome.get_connections(), [(1, 3, 0, True),
(1, 4, 0, True),
(2, 3, 0, True),
(2, 4, 0, True)])
def test_connections_creation(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, -3, True),
(2, 3, 4, True), (1, 4, 22, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
self.assertEqual(nn._connections, {
(2, 4): 0,
(1, 3): -3,
(2, 3): 4,
(1, 4): 22
})
def test_hard_forward_propagation(self):
genome = GenomeMock([(1, 5, 3, True), (2, 5, -2, True),
(1, 6, -1, True), (5, 6, -3.4, True),
(3, 6, 4, True), (6, 4, 5, True)], 3, 1)
nn = NeuralNetwork()
nn.generate_network(genome)
y = nn.forward([0.2, 2, -0.02])
self.assertAlmostEqual(y[0], 0.5144, places=4)
genome = GenomeMock([(1, 5, 3, True),
(2, 5, -2, True), (1, 7, -1, True),
(5, 7, -3.4, True), (3, 7, 4, True),
(7, 6, 2, True), (6, 4, 0.3, True)], 3, 1)
nn.generate_network(genome)
y = nn.forward([0.2, 2, -0.02])
self.assertAlmostEqual(y[0], 0.6778, places=4)
def test_node_creation(self):
genome = GenomeMock([(2, 4, 0, True), (1, 3, -3, True),
(2, 3, 4, True), (1, 4, 22, True),
(1, 5, 3, True)], 2, 2)
nn = NeuralNetwork()
nn.generate_network(genome)
self.assertEqual(1 in nn._neurons, True)
self.assertEqual(2 in nn._neurons, True)
self.assertEqual(3 in nn._neurons, True)
self.assertEqual(4 in nn._neurons, True)
self.assertEqual(5 in nn._neurons, True)
self.assertEqual(1 in nn._input_neurons, True)
self.assertEqual(2 in nn._input_neurons, True)
self.assertEqual(3 in nn._input_neurons, False)
self.assertEqual(4 in nn._input_neurons, False)
self.assertEqual(5 in nn._input_neurons, False)
self.assertEqual(1 in nn._output_neurons, False)
self.assertEqual(2 in nn._output_neurons, False)
self.assertEqual(3 in nn._output_neurons, True)
self.assertEqual(4 in nn._output_neurons, True)
self.assertEqual(5 in nn._output_neurons, False)
def test_evolve_xor(self):
print("testing advanced xor")
Group._GROUP_ID = 0
Generation._GENERATION_ID = 0
specie = Group()
c1 = ConnectionGene(1, 3, enabled=True)
c2 = ConnectionGene(2, 3, enabled=True)
c3 = ConnectionGene(2, 3, enabled=True)
c4 = ConnectionGene(2, 3, enabled=True)
c5 = ConnectionGene(2, 3, enabled=True)
c6 = ConnectionGene(2, 3, enabled=True)
c7 = ConnectionGene(2, 3, enabled=True)
c8 = ConnectionGene(2, 3, enabled=True)
c9 = ConnectionGene(2, 3, enabled=True)
c10 = ConnectionGene(2, 3, enabled=True)
c11 = ConnectionGene(2, 3, enabled=True)
c12 = ConnectionGene(2, 3, enabled=True)
c13 = ConnectionGene(2, 3, enabled=True)
c14 = ConnectionGene(2, 3, enabled=True)
c15 = ConnectionGene(2, 3, enabled=True)
c16 = ConnectionGene(2, 3, enabled=True)
c17 = ConnectionGene(2, 3, enabled=True)
c18 = ConnectionGene(2, 3, enabled=True)
c19 = ConnectionGene(2, 3, enabled=True)
c20 = ConnectionGene(2, 3, enabled=True)
c21 = ConnectionGene(2, 3, enabled=True)
c22 = ConnectionGene(2, 3, enabled=True)
c23 = ConnectionGene(2, 3, enabled=True)
c24 = ConnectionGene(2, 3, enabled=True)
c25 = ConnectionGene(2, 3, enabled=True)
c26 = ConnectionGene(2, 3, enabled=True)
c27 = ConnectionGene(2, 3, enabled=True)
c28 = ConnectionGene(2, 3, enabled=True)
c29 = ConnectionGene(2, 3, enabled=True)
c30 = ConnectionGene(2, 3, enabled=True)
c31 = ConnectionGene(2, 3, enabled=True)
c31 = ConnectionGene(2, 3, enabled=True)
c33 = ConnectionGene(2, 3, enabled=True)
for i in range(10):
specie.add_genome(
Genome([
[1, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[1, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[1, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[1, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[2, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[2, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[2, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[2, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[3, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[3, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[3, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[3, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[4, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[4, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[4, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[4, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[5, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[5, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[5, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[5, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[6, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[6, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[6, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[6, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[7, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[7, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[7, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[7, 12,
random.normalvariate(mu=0.0, sigma=1.0), True],
[8, 9, random.normalvariate(mu=0.0, sigma=1.0), True],
[8, 10,
random.normalvariate(mu=0.0, sigma=1.0), True],
[8, 11,
random.normalvariate(mu=0.0, sigma=1.0), True],
[8, 12,
random.normalvariate(mu=0.0, sigma=1.0), True]
], 8, 4))
mutation_coefficients = {
'add_connection': 0.5,
'split_connection': 0.2,
'change_weight': 0.8,
'new_connection_abs_max_weight': 1.0,
'max_weight_mutation': 0.25
}
compatibility_coefficients = {
'excess_factor': 1.0,
'disjoint_factor': 1.0,
'weight_difference_factor': 0.5
}
log = Logger()
gen = Generation([specie],
mutation_coefficients=mutation_coefficients,
compatibility_coefficients=compatibility_coefficients,
logger=log)
i = 1
while i < 8:
print(i)
gen = gen.create_new_generation()
i += 1
best_nn = NeuralNetwork(Generation.best_genome)
print(best_nn.forward([0, 1, 1, 0, 0, 1, 1, 0]))
print(str(best_nn._genome.fitness) + "/" + str(256 * 4))
def test_simple_xor(self):
print("testing simple xor")
Group._GROUP_ID = 0
Generation._GENERATION_ID = 0
specie = Group()
for i in range(16):
for j in range(17, 21):
ConnectionGene(i + 1, j, enabled=True)
connection_list = []
z = 0
for i in range(16):
for j in range(17, 21):
connection_list.append([
i + 1, j,
random.normalvariate(mu=0.0, sigma=1.0), True, z
])
z += 1
print(connection_list)
for i in range(10):
specie.add_genome(
Genome(
[[1, 3,
random.normalvariate(mu=0.0, sigma=1.0), True, 0],
[2, 3,
random.normalvariate(mu=0.0, sigma=1.0), True, 1]], 2,
1))
mutation_coefficients = {
'add_connection': 0.5,
'split_connection': 0.2,
'change_weight': 0.8,
'new_connection_abs_max_weight': 1.0,
'max_weight_mutation': 0.5
}
compatibility_coefficients = {
'excess_factor': 1.0,
'disjoint_factor': 1.0,
'weight_difference_factor': 2.0
}
log = Logger()
gen = Generation([specie],
mutation_coefficients=mutation_coefficients,
compatibility_coefficients=compatibility_coefficients,
logger=log)
i = 1
while i < 150:
print(i)
gen = gen.create_new_generation()
i += 1
best_nn = NeuralNetwork(Generation.best_genome)
a = (best_nn.forward([0.0, 0.0]))
b = (best_nn.forward([0.0, 1.0]))
c = (best_nn.forward([1.0, 0.0]))
d = (best_nn.forward([1.0, 1.0]))
print(a)
print(b)
print(c)
print(d)
print(4.0 - (a[0] - 0)**2 - (b[0] - 1)**2 - (c[0] - 1)**2 -
(d[0] - 0)**2)
print(best_nn._genome.fitness)
groups_count = []
for generation_log in gen.logger.log.values():
groups_count.append(len(generation_log.groups_log))
plt.plot(list(gen.logger.log.keys()), groups_count)
plt.xlabel("Generation")
plt.ylabel("Number of groups")
plt.title("Groups amount change over evolution")
plt.savefig("plot of gen count")
plt.clf()
last_gen_groups_fitness = []
for fit in gen.logger.log[gen.id -
1].groups_fitness_scores_log.values():
last_gen_groups_fitness.append(fit[0][2])
plt.plot(list(gen.logger.log[gen.id - 1].groups_log.keys()),
last_gen_groups_fitness, 'ro')
plt.xlabel("Group")
plt.ylabel("Group adjusted fitness")
plt.title("Adjusted fitness of groups in last generation")
plt.savefig("plot of last gen fitness")
plt.clf()
plt.plot(list(Generation.best_fitnesses.keys()),
list(Generation.best_fitnesses.values()))
plt.xlabel("Generation")
plt.ylabel("Fitness score")
plt.title("Fitness score progression")
plt.savefig("plot of fitness")
from nn.neuralnetwork import NeuralNetwork
import numpy as np
X = np.array([[0, 0], [0, 1], [1, 0], [1, 1]])
y = np.array([[0], [1], [1], [0]])
nn = NeuralNetwork([2, 2, 1], alpha=0.5)
nn.fit(X, y, epochs=20000)
for (x, target) in zip(X, y):
pred = nn.predict(x)[0][0]
step = 1 if pred > 0.5 else 0
print("[INFO] data={}, ground-truth={}, pred={:.4f}, step={}".format(
x, target[0], pred, step))
from nn.neuralnetwork import NeuralNetwork
from sklearn.preprocessing import LabelBinarizer
from sklearn.model_selection import train_test_split
from sklearn.metrics import classification_report
from sklearn import datasets
print('[INFO] loading MNST (sample) dataset...')
digits = datasets.load_digits()
data = digits.data.astype('float')
data = (data - data.min()) / (data.max() - data.min())
print(f'[INFO] samples: {data.shape[0]}, dim: {data.shape[1]}')
(trainX, testX, trainY, testY) = train_test_split(data,
digits.target,
test_size=0.25)
trainY = LabelBinarizer().fit_transform(trainY)
testY = LabelBinarizer().fit_transform(testY)
print('[INFO] training network...')
nn = NeuralNetwork([trainX.shape[1], 32, 16, 10])
print(f'[INFO] {nn}')
nn.fit(trainX, trainY, epochs=1000)
print('[INFO] evaluating network...')
predictions = nn.predict(testX)
predictions = predictions.argmax(axis=1)
print(classification_report(testY.argmax(axis=1), predictions))
# load the MNIST dataset
dataset = datasets.load_digits()
# apply min/max scaling to scale the
# pixel intensity values to the range [0, 1]
data = dataset.data.astype("float")
data = (data - data.min()) / (data.max() - data.min())
print("[INFO] samples: {}, dim: {}".format(data.shape[0],data.shape[1]))
labels = dataset.target
# split training: 75%, testing: 25%
(trainX, testX, trainY, testY) = train_test_split(data,
labels, test_size=0.25, random_state=42)
# convert labels as vector
lb = LabelBinarizer()
trainY = lb.fit_transform(trainY)
testY = lb.fit_transform(testY)
# train the network
print("[INFO] training network ...")
model = NeuralNetwork([trainX.shape[1], 32, 16, 10],alpha=0.5)
print("[INFO] {}".format(model))
model.fit(trainX, trainY, epochs=1000)
# evaluate network
print("[INFO] evaluating network...")
preds = model.predict(testX)
print(classification_report(testY.argmax(axis=1), preds.argmax(axis=1)))
def create_phenotypes(self):
for group in self.groups.values():
for genome in group.genomes:
self.phenotypes.append(NeuralNetwork(genome))
from nn.neuralnetwork import NeuralNetwork
from nn.dataset import Dataset
from nn.layer import Layer
from nn.utils import kfold_cv_generator
import numpy as np
if __name__ == '__main__':
dataset = Dataset('iris.csv')
data = dataset.data
output_real = dataset.attr
nn = NeuralNetwork()
nn.add(Layer(4))
nn.add(Layer(32, activation='relu'))
nn.add(Layer(3, activation='sigmoid'))
id_train, id_test = kfold_cv_generator(data, n_splits=8)
kf = 1
acc = []
for train_idx, test_idx in zip(id_train, id_test):
train = data.iloc[train_idx]
test = data.iloc[test_idx]
print("#FOLD: ", kf)
score = nn.learn(train,
test,
output_real,
kf,
epochs=100,
classNames = [str(x) for x in np.unique(classNames)]
# initialize the image preprocessor, load the data set from disk
# and reshape the data matrix
sp = SimplePreprocessor(32, 32)
sdl = SimpleDatasetLoader(preprocessors=[sp])
(data, labels) = sdl.load(imagePaths, verbose=100)
data = data.astype("float")
data = (data - data.min()) / (data.max() - data.min())
# construct the training and testing splits
(trainX, testX, trainY, testY) = train_test_split(data, labels, test_size=0.25)
# convert the labels from string to vertors
trainY = LabelBinarizer().fit_transform(trainY)
testY = LabelBinarizer().fit_transform(testY)
# train the network
print("[INFO] training network...")
nn = NeuralNetwork([trainX.shape[1], 64, 16, 32])
print("[INFO] {}".format(nn))
nn.fit(trainX, trainY, epochs=1000)
# evaluate the network
print("[INFO] evaluating network...")
predictions = nn.predict(testX)
print(
classification_report(testY.argmax(axis=1),
predictions.argmax(axis=1),
target_names=classNames))
#!/usr/local/bin/python3.6
## import packages
import os
import sys
sys.path.append("./nn")
from nn.neuralnetwork import NeuralNetwork
import numpy as np
import matplotlib.pyplot as plt
# create XOR datasets
X = np.array([[0, 0], [0, 1], [1, 0], [1, 1]])
y = np.array([[0], [1], [1], [0]])
Epochs = 20000
nn = NeuralNetwork([2, 2, 1], alpha=0.8)
displayLoss = nn.fit(X, y, epochs=Epochs)
# predict X
print("[INFO] Predicting on XOR...")
for (x, target) in zip(X, y):
pred = nn.predict(x)[0][0] # because p is 2d array
# encode in to 1 or 0
pred_label = 1 if pred > 0.5 else 0
print("[INFO] data={}, gt={}, pred={}, pred_label={}".format(
x, target, pred, pred_label))
# plot learning curve
plt.figure()