def kmeans_builder(centroid_func):
samples_per_cluster = 50
n_cluster = 9
x, y = toy_dataset(n_cluster, samples_per_cluster)
fig = Figure()
fig.ax.scatter(x[:, 0], x[:, 1], c=y)
fig.savefig('plots/toy_dataset_real_labels.png')
fig.ax.scatter(x[:, 0], x[:, 1])
fig.savefig('plots/toy_dataset.png')
k_means = KMeans(n_cluster=n_cluster, max_iter=100, e=1e-8)
centroids, membership, i = k_means.fit(x, centroid_func)
assert centroids.shape == (n_cluster, 2), \
('centroids for toy dataset should be numpy array of size {} X 2'
.format(n_cluster))
assert membership.shape == (samples_per_cluster * n_cluster,), \
'membership for toy dataset should be a vector of size {}'.format(len(membership))
assert type(i) == int and i > 0, \
'Number of updates for toy datasets should be integer and positive'
print('[success] : kmeans clustering done on toy dataset')
print('Toy dataset K means clustering converged in {} steps'.format(i))
fig = Figure()
fig.ax.scatter(x[:, 0], x[:, 1], c=membership)
fig.ax.scatter(centroids[:, 0], centroids[:, 1], c='red')
fig.savefig('plots/toy_dataset_predicted_labels.png')
def kmeans_image_compression():
im = plt.imread('baboon.tiff')
N, M = im.shape[:2]
im = im / 255
# convert to RGB array
data = im.reshape(N * M, 3)
k_means = KMeans(n_cluster=16, max_iter=100, e=1e-6)
centroids, _, i = k_means.fit(data)
print('RGB centroids computed in {} iteration'.format(i))
new_im = transform_image(im, centroids)
assert new_im.shape == im.shape, \
'Shape of transformed image should be same as image'
mse = np.sum((im - new_im)**2) / (N * M)
print('Mean square error per pixel is {}'.format(mse))
plt.imsave('plots/compressed_baboon.png', new_im)
np.savez('results/k_means_compression.npz',
im=im,
centroids=centroids,
step=i,
new_image=new_im,
pixel_error=mse)
def B4(pca=False):
'''
Evaluate using NMI and visualize in 2D.
'''
fnames = [
'digits-embedding.csv', 'digits-embedding-2467.csv',
'digits-embedding-67.csv'
]
nmi = zeros(len(fnames))
for i, k, fname in zip([0, 1, 2], [8, 4, 2], fnames):
raw = genfromtxt(fname, delimiter=',')
X = raw[:, 2:]
y = get_normalized_labels(raw[:, 1])
kmeans = KMeans(n_clusters=k)
ind = kmeans.fit(X, y)
_, _, nmi[i] = kmeans.get_evals()
figure()
perm = permutation(X.shape[0])[:1000]
X = X[perm]
ind = ind[perm]
colors = rand(k, 3)[ind, :]
scatter(X[:, 0], X[:, 1], c=colors, alpha=0.9, s=30)
print(fnames)
print("NMI =", nmi)
show()
def test_predict(self):
test_samples = [[-3, -3], [3, 3], [-1, -1], [1, 1]]
expected_predictions = [0, 1, 0, 1]
k_means = KMeans(num_clusters=self.num_clusters, seed=1)
k_means.fit(self.data)
predictions = k_means.predict(test_samples)
self.assertEqual(expected_predictions, predictions)
def __init__(self,
K_max,
embedding_mats,
vec_ids_dict,
durations_dict,
landmarks_dict,
n_slices_min=0,
n_slices_max=20,
min_duration=0,
p_boundary_init=0.5,
init_assignments="rand",
wip=0):
# Attributes from parameters
self.n_slices_min = n_slices_min
self.n_slices_max = n_slices_max
self.wip = wip
# Process embeddings into a single matrix, and vec_ids into a list (entry for each utterance)
embeddings, vec_ids, ids_to_utterance_labels = process_embeddings(
embedding_mats,
vec_ids_dict #, n_slices_min=n_slices_min
)
self.ids_to_utterance_labels = ids_to_utterance_labels
N = embeddings.shape[0]
# Initialize `utterances`
lengths = [len(landmarks_dict[i]) for i in ids_to_utterance_labels]
landmarks = [landmarks_dict[i] for i in ids_to_utterance_labels]
durations = [durations_dict[i] for i in ids_to_utterance_labels]
self.utterances = Utterances(lengths,
vec_ids,
durations,
landmarks,
p_boundary_init=p_boundary_init,
n_slices_min=n_slices_min,
n_slices_max=n_slices_max,
min_duration=min_duration)
# Embeddings in the initial segmentation
init_embeds = []
for i in range(self.utterances.D):
init_embeds.extend(self.utterances.get_segmented_embeds_i(i))
init_embeds = np.array(init_embeds, dtype=int)
init_embeds = init_embeds[np.where(init_embeds != -1)]
print("No. initial embeddings: {}".format(init_embeds.shape[0]))
# Initialize the K-means components
assignments = -1 * np.ones(N, dtype=int)
if init_assignments == "rand":
assignments[init_embeds] = np.random.randint(
0, K_max, len(init_embeds))
elif init_assignments == "spread":
n_init_embeds = len(init_embeds)
assignment_list = (
range(K_max) *
int(np.ceil(float(n_init_embeds) / K_max)))[:n_init_embeds]
random.shuffle(assignment_list)
assignments[init_embeds] = np.array(assignment_list)
self.acoustic_model = KMeans(embeddings, K_max, assignments)
def cluster_colors(img, n_clusters):
kmeans = KMeans(n_clusters=n_clusters)
color_vectors = cv.cvtColor(img, cv.COLOR_BGR2RGB).reshape([-1, 3])
centroids = kmeans.fit(color_vectors)
labels = kmeans.predict(color_vectors)
pred = labels.reshape(img.shape[:-1])
# Initialize img for clusters
cluster_img = np.zeros(img.shape)
for i in range(n_clusters):
cluster_img[np.where(pred == i)] = centroids[i]
cluster_img = cluster_img.astype(np.uint8)
plt.figure(figsize=(10, 10))
plt.imshow(cluster_img)
colors = ["Cluster {}".format(i) for i in range(n_clusters)]
patches = [
mpatches.Patch(color=centroids[i] / 255, label=colors[i])
for i in range(len(colors))
]
plt.legend(handles=patches,
bbox_to_anchor=(1.05, 1),
loc=2,
borderaxespad=0.)
plt.show()
return kmeans
def kmeans_toy():
x, y = toy_dataset(4)
fig = Figure()
fig.ax.scatter(x[:, 0], x[:, 1], c=y)
fig.savefig('plots/toy_dataset_real_labels.png')
fig.ax.scatter(x[:, 0], x[:, 1])
fig.savefig('plots/toy_dataset.png')
n_cluster = 4
k_means = KMeans(n_cluster=n_cluster, max_iter=100, e=1e-8)
centroids, membership, i = k_means.fit(x)
assert centroids.shape == (n_cluster, 2), \
('centroids for toy dataset should be numpy array of size {} X 2'
.format(n_cluster))
assert membership.shape == (50 * n_cluster,), \
'membership for toy dataset should be a vector of size 200'
assert type(i) == int and i > 0, \
'Number of updates for toy datasets should be integer and positive'
print('[success] : kmeans clustering done on toy dataset')
print('Toy dataset K means clustering converged in {} steps'.format(i))
fig = Figure()
fig.ax.scatter(x[:, 0], x[:, 1], c=membership)
fig.ax.scatter(centroids[:, 0], centroids[:, 1], c='red')
fig.savefig('plots/toy_dataset_predicted_labels.png')
np.savez('results/k_means_toy.npz',
centroids=centroids,
step=i,
membership=membership,
y=y)
def test_fit_with_different_initial_centroids(self):
expected_labels = [0, 0, 0, 1, 1, 1]
expected_centroids = [[-1.6666667, -1.6666667], [1.6666667, 1.6666667]]
k_means = KMeans(num_clusters=self.num_clusters, seed=0)
k_means.fit(self.data)
self.assertEqual(expected_labels, k_means.labels_)
np.testing.assert_almost_equal(expected_centroids, k_means.centroids_)
def _initialise_prams(self, X):
# Get initial clusters using Kmeans
kmeans = KMeans(k=self.k, max_iters=500)
kmeans.fit(X)
kmeans_preds = kmeans.predict(X)
N, col_length = X.shape
mixture_labels = np.unique(kmeans_preds)
initial_mean = np.zeros((self.k, col_length))
initial_cov = np.zeros((self.k, col_length, col_length))
initial_pi = np.zeros(self.k)
for index, mixture_label in enumerate(mixture_labels):
mixture_indices = (kmeans_preds == mixture_label)
Nk = X[mixture_indices].shape[0]
# Initial pi
initial_pi[index] = Nk / N
# Intial mean
initial_mean[index, :] = np.mean(X[mixture_indices], axis=0)
# Initial covariance
de_meaned = X[mixture_indices] - initial_mean[index, :]
initial_cov[index] = np.dot(initial_pi[index] * de_meaned.T,
de_meaned) / Nk
assert np.sum(initial_pi) == 1
return initial_pi, initial_mean, initial_cov
def test02_non_fitted_model_raises_not_fitted_error_message(self):
model = KMeans(k=2)
try:
model.predict(np.array([[1, 0], [0, 1]]))
self.fail()
except Exception as e:
self.assertEqual(str(e), KMeans.NOT_FITTED_ERROR_MESSAGE)
def cluster_newsgroups():
""" Cluster newsgroup categories. """
from kmeans import KMeans
from similarity import simMatrix
corpus, dictionary = build_dictionary(bigram=True)
tfidf = TFIDF(dictionary)
newsgroups = tfidf.vectorize(corpus)
dictionary = tfidf.dictionary
categories = sorted(corpus.keys())
N = 6
print "\n{}-Most Common Words".format(N)
for index, category in enumerate(categories):
nlargest = np.argpartition(newsgroups[index, :], -N)[-N:]
nlargest = nlargest[np.argsort(newsgroups[index, nlargest])][::-1]
print "{:>24} {}".format(category, dictionary[nlargest])
print
K = 3
km = KMeans(n_clusters=K)
km.fit(newsgroups)
labels = km.labels_
print "\nKMeans Label Assignment, K = {}".format(K)
for category, label, in zip(categories, labels):
print int(label), category
simMatrix(newsgroups).plot().show()
def main():
# NOTE(Jovan): Load data
data = pd.read_csv("data/skincancer.csv", delimiter=',', index_col=0)
mort = data.Mort.values
lat = data.Lat.values
lon = data.Long.values
# NOTE(Jovan): Init LinearRegression and predict
lin_reg = LinearRegression(lat, mort)
hawaii = lin_reg.predict(20)
print("Prediction for hawaii[lat=20]:", hawaii)
# NOTE(Jovan): Init KMeans and add lat and long points
k_means = KMeans()
for i, j in zip(lat, lon):
k_means.points.append(Point(i, j))
k_means.split(2, 0.01)
# NOTE(Jovan): Plot clusters
fig = plt.figure()
ax = fig.add_axes([0,0,1,1])
# NOTE(Jovan): First clusters
for p in k_means._clusters[0].points:
ax.scatter(p.x, p.y, c="#ff0000")
# NOTE(Jovan): Second clusters
for p in k_means._clusters[1].points:
ax.scatter(p.x, p.y, c="#00ff00")
# NOTE(Jovan): Plot cluster centers
center1 = k_means._clusters[0].center
center2 = k_means._clusters[1].center
ax.scatter(center1.x, center1.y, marker="P", c="#ff0000")
ax.scatter(center2.x, center2.y, marker="P", c="#00ff00")
plt.show()
def spectral(X, sigma, k, centroids):
"""
Ng谱聚类算法
:param X: 数据点
:param sigma: 参数
:param k: 参数
:return: accu聚类精度
"""
(n, d) = X.shape
L_sym, L = get_L(X, k, sigma)
eig, eigvec = np.linalg.eig(L_sym) # eigvec按列
# eig_index = np.argsort(eig)[1:d+1]
eig_index = np.argsort(eig)[:d] # 最小的d个特征值的索引
U = eigvec[:, eig_index]
T = np.zeros(U.shape)
for i in range(n):
for j in range(d):
T[i][j] = U[i][j] / np.linalg.norm(U[i])
Y = T
# visual(Y, k=k, sigma=sigma, save=1)
cluster = KMeans(2, 100, centroids)
cluster.fit(Y)
labels = cluster.labels
if labels[0] == 0:
n1 = 100 - sum(labels[:100])
n2 = sum(labels[100:])
else:
n1 = sum(labels[:100])
n2 = 100 - sum(labels[100:])
accu = (n1 + n2) / n
print('---------------------sigma=%.2f, k=%d, accu=%.4f' %
(sigma, k, accu))
return accu
def __init__(self,
n_cluster: int,
data: np.ndarray,
use_kmeans: bool = False,
w: float = 0.9,
c1: float = 0.5,
c2: float = 0.3,
flag: int = 1,
weights: list = None):
index = np.random.choice(list(range(len(data))), n_cluster)
self.centroids = data[index].copy()
if use_kmeans:
kmeans = KMeans(n_cluster=n_cluster, init_pp=False)
kmeans.fit(data)
self.centroids = kmeans.centroid.copy()
self.best_position = self.centroids.copy()
self.best_score = quantization_error(self.centroids, self._predict(data), data)
self.flag=flag
if self.flag%2==1:
self.best_sse = calc_sse(self.centroids, self._predict(data), data)
else:
self.best_sse = calc_sse2(self.centroids, self._predict(data), data, weights)
self.velocity = np.zeros_like(self.centroids)
self._w = w
self._c1 = c1
self._c2 = c2
def test_select_initial_centroids(self):
expected_initial_centroids = [[2, 1], [-1, -2]]
k_means = KMeans(num_clusters=self.num_clusters, seed=3)
k_means.fit(self.data)
initial_centroids = k_means._select_initial_centroids(self.data)
self.assertEqual(expected_initial_centroids, initial_centroids)
self.assertEqual(self.num_clusters, len(initial_centroids))
def main2():
df = pd.read_csv('credit_card_data.csv')
df = df.fillna(df.median())
original_data = df.iloc[:, 1:].values
data = copy.deepcopy(original_data)
columns = list(df.columns)[1:] # lista naziva kolona
print(columns)
# min_max_data(df, columns)
normalizacija(data) # radimo normalizaciju nad ucitanim podacima
pca = PCA()
pca.fit(data)
# odredjujem na koliiko cu da smanjim dimenzionalnost
plt.plot(range(1, 18), pca.explained_variance_ratio_.cumsum(), marker='x', linestyle='--')
plt.xlabel('Components') # features
plt.ylabel('Variance')
plt.show()
components = 7 # vidimo iz plota
pca = PCA(n_components=components)
pca.fit(data)
scores = pca.transform(data)
# print(scores) # ima onoliko komponenti koliko smo stavili
# pokazujemo da prve dve dimenzije uticu najvise na grafik
plt.bar(range(pca.n_components_), pca.explained_variance_ratio_, color='black')
plt.xlabel('PCA components')
plt.ylabel('Variance %') # procenat koliko uticu na grafik, da tako kazemo
plt.xticks(range(pca.n_components_))
plt.show()
# dobijam optimal k = 5 za 500 prvih ucitanih
# za sve ucitane dobijam 6
# optimal_k_plot(data)
broj_klastera = 6
k_means = MyKMeans(n_clusters=broj_klastera, max_iter=100)
k_means.fit(scores, normalize=False)
klaster_indeksi = k_means.klaster_indeksi
print(klaster_indeksi)
lista_klastera_sa_originalnim_podacima = [] # lista klastera sa originalnim podacima
for i in range(broj_klastera):
lista_klastera_sa_originalnim_podacima.append([])
for i in range(len(original_data)):
lista_klastera_sa_originalnim_podacima[klaster_indeksi[i]].append(original_data[i])
# printujem osobine i stablo odlucivanja
print_descriptions(lista_klastera_sa_originalnim_podacima, columns)
# print_decision_tree(original_data, klaster_indeksi, columns)
print_clusters_description()
# iscrtavamo tacke
plot_2_D(k_means)
def main():
tagged_words = brown.tagged_words()
words_corpus = brown.words()
word2vec = Word2Vec()
word2vec.train(words_corpus)
word_vecs = [word2vec.word2vec(word) for word in words_corpus]
n_clusters = 10 # random number for now
kmeans = KMeans(n_clusters)
kmeans.compute(word_vecs)
# word-cluster HMM
p_word = {}
p_cluster = {}
p_cluster_given_word = None # softmax
p_word_given_cluster = None # joint probability formula
p_transition_cluster = None # count
p_initial_cluster = None # count
# cluster-tag HMM
p_cluster_given_tag = None # softmax
p_transition_tag = None # count from tagged data
p_initial_tag = None # count from tagged data
hmm_word_cluster = HMM(p_initial_cluster, p_transition_cluster, p_word_given_cluster)
hmm_cluster_tag = HMM(p_initial_tag, p_transition_tag, p_cluster_given_tag)
words = []
clusters = hmm_word_cluster.viterbi(words)
tags = hmm_cluster_tag.viterbi(clusters)
def main():
filepath = "./data/self_test.csv"
#filepath = "./data/self_test_petit.csv"
#filepath = "./data/iris.csv"
# chargement des données
data, labels = load_dataset(filepath)
# initialisation de l'objet KMeans
kmeans = KMeans(n_clusters=3,
max_iter=100,
early_stopping=True,
tol=1e-6,
display=True)
# calcule les clusters
kmeans.fit(data)
# calcule la pureté de nos clusters
score = kmeans.score(data, labels)
print("Pureté : {}".format(score))
input("Press any key to exit...")
def test_whole(self):
"""
Tests the score method.
"""
X, y, centers = generate_cluster_samples()
n_samples = X.shape[0]
n_features = X.shape[1]
k = centers.shape[0]
# run N_TRIALS, pick best model
best_model = None
for i in range(N_TRIALS):
kmeans = KMeans(k, N_ITER)
kmeans.fit(X)
if best_model is None:
best_model = kmeans
elif kmeans.score(X) < best_model.score(X):
best_model = kmeans
# check sum squared errors
sum_squared_errors = best_model.score(X)
self.assertLess(sum_squared_errors / n_samples, EPS)
# compare centers to expected centers
smallest_distances = find_smallest_distances(
best_model.cluster_centers, centers)
for distance in smallest_distances:
self.assertLess(distance, EPS)
def do_KMeans_clustering(N_cluster, X, device): """ This function will use KMeans Clustering method to label training data according to its proximity with a cluster Input: N_cluster: number of cluster estimated by Gap Statistics X: Training data for the input layer Output: cluster_label: label assigned to every point over_coef: this will be used in the oversampling method to increase number of points in the less densed cluster region """ X = X.to(device) #Instantiating kmeans object kmeans = KMeans(n_clusters=N_cluster, mode='euclidean', verbose=1) cluster_label = kmeans.fit_predict(X) #Calculating the size of cluster (number of data near the cluster centroid) cluster_size = torch.zeros(N_cluster, dtype=torch.int32).to(device) for cluster in range(N_cluster): cluster_size[cluster] = len(torch.where(cluster_label==cluster)[0]) over_coef = torch.zeros(N_cluster, dtype=torch.int32).to(device) for cluster in range(N_cluster): over_coef[cluster] = torch.clone((max(cluster_size))/cluster_size[cluster]).to(device) if over_coef[cluster] > 10: over_coef[cluster] = 10 return cluster_label.cpu(), over_coef.cpu()
def B1(pca=False):
'''
Plot WC_SSD and SC over K.
'''
K = [2, 4, 6, 8, 16, 32]
fnames = [
'digits-embedding.csv', 'digits-embedding-2467.csv',
'digits-embedding-67.csv'
]
wc_ssd_val = zeros((len(fnames), len(K)))
sc_val = zeros((len(fnames), len(K)))
for i, fname in enumerate(fnames):
X = genfromtxt(fname, delimiter=',')[:, 2:]
for j, k in enumerate(K):
kmeans = KMeans(n_clusters=k)
kmeans.fit(X)
wc_ssd_val[i, j], sc_val[i, j], _ = kmeans.get_evals()
# Plot WC_SSD
figure()
for i, fname in enumerate(fnames):
plot(K, wc_ssd_val[i], label=fname)
legend()
title('WC_SSD v.s. K')
figure()
for i, fname in enumerate(fnames):
plot(K, sc_val[i], label=fname)
legend()
title('SC v.s. K')
show()
def __init_parameters(self):
N = self.X.shape[0]
n_features = self.X.shape[1]
kmeans = KMeans(n_clusters=self.n_components, n_init=5)
kmeans.fit(self.X)
# mu, means for each component
self.means_ = kmeans.cluster_centers_
# sigma, covariances for each component
self.covariances_ = np.zeros(
[self.n_components, n_features, n_features])
# pi, weights for each component
self.weights_ = np.zeros(self.n_components)
for k in range(self.n_components):
logic = (kmeans.labels_ == k)
Nk = logic.sum()
# otherwise error
if Nk > 1:
Xk = self.X[logic]
self.covariances_[k] = np.cov(Xk.T)
self.weights_[k] = Nk / N
# gamma(Znk)
self.gamma = np.zeros([N, self.n_components])
# log_likelihood
self.lower_bound_ = -np.inf
return self
def kmeans_image_compression():
print("[+] K-Means Image Compression")
im = plt.imread('baboon.tiff')
N, M = im.shape[:2]
im = im / 255
# convert to RGB array
data = im.reshape(N * M, 3)
# print(im)
k_means = KMeans(n_cluster=16, max_iter=100, e=1e-6)
centroids, _, i = k_means.fit(data)
# print(centroids.shape)
print('[+] RGB centroids computed in {} iteration'.format(i))
new_im = transform_image(im, centroids)
assert new_im.shape == im.shape, \
'Shape of transformed image should be same as image'
mse = np.sum((im - new_im)**2) / (N * M)
print('[+] Mean square error per pixel is {}\n'.format(mse))
plt.imsave('plots/compressed_baboon.png', new_im)
def test_cluster_points_two_cluster(self):
test_vector = self.create_test_data_vector()
kmeans = KMeans(test_vector, 2)
test_point0 = datapoint.DataPoint()
test_point0.add_dimension(1.1)
test_point0.add_dimension(2.1)
test_point0.add_dimension(3.1)
test_point1 = datapoint.DataPoint()
test_point1.add_dimension(3.1)
test_point1.add_dimension(1.1)
test_point1.add_dimension(2.1)
test_cluster = datapoint.DataVector()
test_cluster.add_point(test_point0)
test_cluster.add_point(test_point1)
self.assertEqual(
[1.0, 2.0, 3.0],
kmeans.cluster_points(test_cluster)[0].data_points[0].coordinates)
self.assertEqual(
[2.0, 3.0, 1.0],
kmeans.cluster_points(test_cluster)[0].data_points[1].coordinates)
self.assertEqual(
[3.0, 1.0, 2.0],
kmeans.cluster_points(test_cluster)[1].data_points[0].coordinates)
def test_assign_points(self):
"""
Tests initialize methods of the KMeans class.
"""
X, y, centers = generate_cluster_samples()
n_samples = X.shape[0]
k = centers.shape[0]
kmeans = KMeans(k, N_ITER)
# Set cluster centers so that assignment is deterministic
kmeans.cluster_centers = centers
assignments, distances = kmeans.assign_points(X)
# check assignment array shape
self.assertEqual(assignments.ndim, 1)
self.assertEqual(assignments.shape[0], n_samples)
# check distances array shape
self.assertEqual(distances.ndim, 1)
self.assertEqual(distances.shape[0], n_samples)
# check that assignments only include valid cluster indices (0 <= idx < k)
self.assertTrue(
np.all(np.logical_and(assignments < k, assignments >= 0)))
# Check cluster assignments are correct
self.assertTrue(np.all(assignments[:25] == 0))
self.assertTrue(np.all(assignments[25:50] == 1))
self.assertTrue(np.all(assignments[50:75] == 2))
self.assertTrue(np.all(assignments[75:] == 3))
def test_initialize(self):
"""
Tests initialize methods of the KMeans class.
"""
k = 3
n_samples = 100
n_features = 10
for i in range(N_TRIALS):
X = np.random.randn(n_samples, n_features)
kmeans = KMeans(k, N_ITER)
kmeans.initialize_clusters(X)
# ensure that the cluster_centers matrix has the right shape
self.assertEqual(kmeans.cluster_centers.ndim, 2)
self.assertEqual(kmeans.cluster_centers.shape[0], k)
self.assertEqual(kmeans.cluster_centers.shape[1], n_features)
# Check that every center is one the points in X.
# Calculcate the distances between every cluster center
# and every point in X. Find the closest matches.
# Checks that the distances are nearly 0.0
distances = find_smallest_distances(X, kmeans.cluster_centers)
for d in distances:
self.assertAlmostEqual(d, 0.0)
def cluster_newsgroups():
""" Cluster newsgroup categories. """
from kmeans import KMeans
from similarity import simMatrix
corpus, dictionary = build_dictionary(bigram=True)
tfidf = TFIDF(dictionary)
newsgroups = tfidf.vectorize(corpus)
dictionary = tfidf.dictionary
categories = sorted(corpus.keys())
N = 6
print "\n{}-Most Common Words".format(N)
for index, category in enumerate(categories):
nlargest = np.argpartition(newsgroups[index,:], -N)[-N:]
nlargest = nlargest[np.argsort(newsgroups[index,nlargest])][::-1]
print "{:>24} {}".format(category, dictionary[nlargest])
print
K = 3
km = KMeans(n_clusters=K)
km.fit(newsgroups)
labels = km.labels_
print "\nKMeans Label Assignment, K = {}".format(K)
for category, label, in zip(categories, labels):
print int(label), category
simMatrix(newsgroups).plot().show()
def test_kmeans(self):
locations = [[1, 1], [1, 2], [2, 1], [1, 3], [3, 1], [2, 2], [10, 10],
[10, 20], [20, 10], [10, 30], [30, 10], [20, 20]]
clusterer = KMeans(2)
clusterer.train(locations)
def plot_elbow(interval, data, random_seed=None):
inertia = []
for n_clusters in interval:
clf = KMeans(k=n_clusters, init='kmeans++', random_seed=random_seed)
clf.fit(data)
inertia.append(clf.inertia)
plot_metrics(interval, inertia, 'Elbow method', 'Number of clusters (K)',
'Sum of Squared Error')
def test06_fit_two_clusters(self):
np.random.seed(1)
model = KMeans(k=2, init=init.forgy_initialization)
data = np.array([[-1.0, 0.0], [-1.001, 0.0], [-0.999, 0.0], [0.0, 1.0],
[0.0, 0.999], [0.0, 1.001]])
model.fit(data)
self.assertEquals(model.predict(data), [1, 1, 1, 0, 0, 0])
def test_fit(self):
expected_labels = [0, 0, 0, 1, 1, 1]
expected_centroids = [[-1.6666667, -1.6666667], [1.6666667, 1.6666667]]
expected_inertia = 2.6666667
k_means = KMeans(num_clusters=self.num_clusters, seed=1)
k_means.fit(self.data)
self.assertEqual(expected_labels, k_means.labels_)
np.testing.assert_almost_equal(expected_centroids, k_means.centroids_)
self.assertAlmostEqual(expected_inertia, k_means.inertia_)
def squared_clustering_errors(inputs, k):
"""finds the total squared error from k-means clustering the inputs"""
clusterer = KMeans(k)
clusterer.train(inputs)
means = clusterer.means()
assignments = map(clusterer.classify, inputs)
return sum(squared_distance(input, means[cluster])
for input, cluster in zip(inputs, assignments))
def task3(dataset):
dimensions = len(dataset.training[0].data)
print('k-means')
for k in [9, 10, 20]:
kmeans = KMeans(dimensions, k)
kmeans.train(dataset.training)
predictions = [kmeans(x) for x in dataset.testing]
print('k=', k, ' ', sep='', end='')
print_error(predictions, dataset.testing)
def process_articles(input_file, num_partitions=8):
sc = SparkContext()
try:
input_rdd = sc.textFile(input_file)
vectorized_docs = CorpusVectorizer(input_rdd).vectorize_corpus()
centroids = KMeans(vectorized_docs).centroids
print >> sys.stdout, centroids.take(4)
except Exception as e:
print >> sys.stderr, "Unable to load file"
print >> sys.stderr, e
sys.exit(0)
def ClusterQueryDoc(dataset,rankerPath,feature_count, path_train_dataset, path_test_dataset, iterations, click_model, clusterData,queryDataPath,from_var,to_var):
C = Fake(dataset, path_train_dataset, rankerPath,feature_count)
C.Save()
bestRankersFile = 'QueryData/'+dataset+'.data'
KM = KMeans(from_var, to_var, bestRankersFile, dataset)
(queryToCluster, clusterToRanker) = KM.runScript()
g=GroupRanker(path_train_dataset,path_test_dataset,feature_count,iterations,click_model,dataset,clusterData,queryDataPath)
g.groupRanker()
def _compute_k_means_clusters(data, similarity_calculator, similarity_diff_threshold):
computed_clusters = {}
k_means = KMeans(data.persons, similarity_calculator)
for personID in data.originalPeople:
friends_of_person = data.persons.getPerson(personID).getFriends()
if len(friends_of_person) > 250:
k = 12
else:
k = 6
clusters = k_means.computeClusters(friends_of_person, k, similarity_diff_threshold)
computed_clusters[personID] = clusters
return computed_clusters
def calculate_em(X, n_clusters, diag=False, ridge=1e-10, verbose=False, max_iterations=100):
"""
Returns mu, sigma and tpi
"""
n_samples, n_features = X.shape
# Initialise the data using kmeans
k_means = KMeans(k=n_clusters)
k_means_labels, _ = k_means.fit(X.copy())
k_means_cluster_centers = k_means.centers_
# OK, so we've got the centers and the labels. Let's now compute the EM
# algorithm
tau = np.zeros((n_samples, n_clusters))
mu = np.zeros((n_clusters, n_features))
sigma = np.zeros((n_clusters, n_features, n_features))
p = np.zeros((n_clusters, n_samples))
# FIXME shouldbe able to do the following using pure matric arithmetics
for i, element in enumerate(k_means_labels):
tau[i, element] = 1
for j in range(max_iterations):
old_mu = mu.copy()
for i in range(n_clusters):
mu[i] = (tau[:, i].reshape((tau.shape[0], 1)) * X).sum(axis=0) / (tau[:, i]).sum()
for i in range(n_clusters):
a = 0
for n in range(n_samples):
b = (X[n, :] - mu[i]).reshape((2, 1))
if diag:
a += tau[n, i] * np.dot(b.T, b)
else:
a += tau[n, i] * np.dot(b, b.T)
if diag:
sigma[i, :] = a.mean() / tau[:, i].sum() * np.identity(mu.shape[1])
else:
sigma[i, :] = a / tau[:, i].sum()
tpi = tau.sum(axis=1) / n_samples
for i in range(n_clusters):
p[i, :] = _calculate_normal(X, mu[i, :], sigma[i, :])
for i in range(n_clusters):
tau.T[i, :] = tpi[i] * p[i, :] / (tpi * p).sum(axis=0)
if ((old_mu - mu) ** 2).sum() < ridge:
if verbose:
print "break at iterations %d" % j
break
return mu, sigma, tpi
class Reducer:
def __init__(self):
self.k = int(self.params.get("k", "10"))
self.max_iterations = int(self.params.get("max_iterations", "100"))
self.kmeans = KMeans(self.k, self.max_iterations)
def __call__(self, key, values):
# convert input to numpy_array and feed the vectors to KMeans instance
for _vid, _vector_array in enumerate(values):
_vector_array = numpy.array(_vector_array)
self.kmeans.add_vector(_vid, _vector_array)
self.kmeans.initialize()
for _cluster in self.kmeans.run():
for item in _cluster:
yield item.cid, item
def apply_decluster(self):
"""
apply window method to the whole catalog and write mainshocks on file
"""
# get instances of classes we'll need
catalog = Catalog()
kmeans = KMeans()
# from the catalog we want, get earthquakes array on memory
earthquake_array = catalog.get_earthquake_array('../catalogs/new_jma.txt')
# decluster array, separating mainshocks and aftershocks
declustered_array = kmeans.do_kmeans(earthquake_array)
# record the mainshocks on a catalog
catalog.record_mainshocks(declustered_array, file_write='../results/mainshocks.txt', file_read='../catalogs/jma.txt')
def main(args):
df = pd.read_csv(args.data_csv)
data = np.array(df[['X', 'Y']])
plt.clf()
plt.scatter(data[:, 0], data[:, 1], s=3, color='blue')
if args.algorithm == 'gmm':
gmm = GaussianMixtureModel(args.num_clusters)
gmm.fit(data)
y = gmm.predict_cluster(data)
else:
km = KMeans(args.num_clusters)
km.fit(data)
y = km.predict(data)
plt.scatter(data[:, 0], data[:, 1], c=y)
plt.show()
def apply_decluster_smaller(self):
"""
apply window method to a smaller catalog and write mainshocks on file
"""
# get instances of classes we'll need
catalog = Catalog()
kmeans = KMeans()
# obtain a smaller catalog, so we can run this function faster
catalog.get_smaller_catalog(300)
# from the catalog we want, get earthquakes array on memory
earthquake_array = catalog.get_earthquake_array()
# decluster array, separating mainshocks and aftershocks
declustered_array = kmeans.do_kmeans(earthquake_array, 25)
# record the mainshocks on a catalog
catalog.record_mainshocks(declustered_array, file_write='../results/mainshocks.txt', file_read='../catalogs/reduced_jma.txt')
def kmeans():
filename = 0
threshold = 0
numClusters = 4
filename = 'data/4clusters.csv'
kmeans = KMeans(filename, numClusters)
clusters = kmeans.cluster()
formatted = dict()
for i, cluster in enumerate(clusters):
formatted[i] = []
for point in cluster:
#f_cluster = dict()
#f_cluster[point[0]] = point[1]
#formatted[i].append(f_cluster)
formatted[i].append(point)
print formatted
return {'clusters':formatted, 'k':len(formatted), 'get_url': app.get_url}
def train(self, X, Y, beta, nb_epochs=5, normalize=False, gradients=True, alpha=1e-3): # m = nb_examples # n = nb_features # k = nb_hidden (nb of neurons in hidden layer) (m, n), k = X.shape, self.nb_hidden # K-Means for input layer: self.km = KMeans(nb_cluster=k) # select k centroids from training set: self.km.train(X, nb_iters=100, init_from_train=True) # set the centroids as ours weights from of the layer: self.weights[0] = self.km.get_centroids() # calcule the activation of rbf: # in pythonic way: A = np.array([np.exp(-beta * np.sum(np.power(self.weights[0] - x, 2), axis=1)) for x in X]).reshape(m, k) # in noob way: # A, betas = np.zeros((m, k)), np.ones((k, 1)) * beta # for i in range(m): # A[i] = self.get_activation(X[i, :], betas).T # speed up the convergence and its necessary # for pseudo-inverse method if normalize: # divide each row by its sum A = A / np.sum(A, axis=1)[:,None] # for bias A = add_column_with_ones(A) if gradients: errors = [] while not reached_precision(errors, precision=1e-7): # the same process as used in linear regression, i.e. # use the gradient descent for minimize the loss function self.weights[1] = self.gradient_descent(A, Y, beta, alpha) # calculate the errors with the trained weights: errors.append(np.sum(np.power(self.predict(X, beta, normalize=normalize) - Y, 2)) / m) else: # learn the weights using pseudo-inverse function: self.weights[1] = pinv(A.T.dot(A)).dot(A.T.dot(Y)) # calculate the errors with the trained weights: errors = [0, np.sum(np.power(self.predict(X, beta, normalize=normalize) - Y, 2)) / m] return errors
def main():
dataset = _load_csv_data(CSV_PATH, CSV_COLUMN_DELIMITER)
k = 2
max_iter = 10
handler = KMeans(dataset, k=k)
handler.kmeans()
while k < max_iter:
handler.reinitialize(k=k)
handler.kmeans()
k += 1
def compare_window_kmeans(num_entries):
"""
receives a number of entries
the function applies to a catalog with that number of entries
the window method and the kmeans to decluster the catalog
the function returns a comparation, showing how much there is
of a difference between the two
Complexity: O(n^2)
"""
# obtain a smaller catalog
catalog = Catalog()
catalog.get_smaller_catalog(num_entries)
# get earthquake array of that catalog
quakes = catalog.get_earthquake_array()
# get declustered array of that catalog, according to the window method
window = Window()
window_quakes = window.decluster(quakes)
# get the number of mainshocks of that catalog, according to the kmeans clustering method
num_mainshocks = 0
for i in range(len(window_quakes)):
if window_quakes[i].is_aftershock == False:
num_mainshocks += 1
print(num_mainshocks)
# apply declustering using the kmeans method to the catalog
kmeans = KMeans()
kmeans_quakes = kmeans.do_kmeans(quakes, num_mainshocks)
# show what are the differences between both methods
for i in range(len(quakes)):
if window_quakes[i].is_aftershock != kmeans_quakes[i].is_aftershock:
print("found a difference!")
def main():
print "K-Means algorithm illustrated through the iris dataset"
print "The algorithm uses random initialization and iterates until no iris"
print "switches clusters."
print "If matplotlib is installed, the resulting clusters are illustrated"
print "in a graphical manner."
print
# import the data
irii = import_csv()
# create and initialize the algorithm
kmeans = KMeans(3, irii, euclidean_similarity)
# run the algorithm
num_iterations = kmeans.run()
print "K-Means ran in %d iterations" % (num_iterations)
print
print "SSE Values for each cluster:"
for cluster_num, sse in enumerate(kmeans.sses()):
num_members = len(kmeans.clusters[cluster_num])
print "Cluster %d (%d members): %f" % (cluster_num, num_members, sse)
print
# create a plot
try:
print "Plotting sepal length vs sepal width."
print "Colors indicate the cluster, as identified by k-means across all"
print "attributes. The symbol indicates the 'correct' group, as"
print "determined by the name of the IRIS. The black + symbols indicate"
print "the centroids."
create_plot(kmeans)
except:
print "There was a plotting error. Do you have matplotlib installed?"
def urf_games():
my_kmeans = KMeans()
results = []
results.append({"Control: Wards placed/Wards destroyed" : my_kmeans.calculate('control')})
results.append({'Damage: Physical/Magic/True' : my_kmeans.calculate('damage')})
results.append({'Economy: Gold Earned/Gold Spent' : my_kmeans.calculate('economy')})
results.append({'Kills: Kills/Deaths/Assists' : my_kmeans.calculate('kills')})
results.append({'Multi Kills: Combo Kills/Killing Sprees/Largest Killing Spree': my_kmeans.calculate('multi_kills')})
return render_template('results.html', data=results)
from kmeans import KMeans
from matplotlib import pyplot as plt
path_to_file = "casino1.jpg"
import matplotlib.image as mpimg
img = mpimg.imread(path_to_file)
pixels = [pixel for row in img for pixel in row]
clusterer = KMeans(5)
clusterer.train(pixels) # this might take a while
def recolor(pixel):
cluster = clusterer.classify(pixel) # index of the closest cluster
return clusterer.means[cluster]
new_img = [[recolor(pixel) for pixel in row] # recolor this row of pixels
for row in img]
plt.imshow(new_img)
plt.axis('off')
plt.show()
def __init__(self, n_clusters, initCent, max_iter):
self.data = np.array([])
self.belongApp = np.array([])
self.n_clusters = n_clusters
self.clf = KMeans(n_clusters, initCent, max_iter)
class ClsfCRTL(object):
def __init__(self, n_clusters, initCent, max_iter):
self.data = np.array([])
self.belongApp = np.array([])
self.n_clusters = n_clusters
self.clf = KMeans(n_clusters, initCent, max_iter)
def genDataset(self, file_name):
dataSet, belongApp = [], []
f = open(file_name, "r")
lines = f.readlines()
for line in lines:
line_elm = line.split("\t")
dataSet.append([int(line_elm[0]), 0])
belongApp.append(line_elm[1].rstrip("\n"))
self.data = np.array(dataSet)
self.belongApp = np.array(belongApp)
f.close()
def clsf(self):
self.clf.fit(self.data)
def show(self):
cents = self.clf.centroids
labels = self.clf.labels
sse = self.clf.sse
colors = ['b', 'g', 'r', 'k', 'c', 'm', 'y', '#e24fff', '#524C90', '#845868', '#00FF00', '#330000',
'#333300', '#333333', '#CC0099', '#FFFF00', '#FF99CC', '#CCCC66', '#003333', '#66FFFF']
for i in range(self.n_clusters):
index = np.nonzero(labels==i)[0]
x0 = self.data[index, 0]
x1 = self.data[index, 1]
y_i = self.belongApp[index]
for j in range(len(x0)):
plt.scatter(x0[j], x1[j], marker='o', color=colors[i])
# plt.text(x0[j],x1[j],str(y_i[j]),color=colors[i],fontdict={'weight': 'bold', 'size': 9})
plt.scatter(cents[i,0], cents[i,1], marker='x', color=colors[i], linewidths=5)
plt.title("SSE={:.2f}".format(sse))
plt.axis([0, 1600, -2, 2])
plt.show()
def showBar(self):
n = 1600
X = np.arange(n)
Y1 = (1-X/float(n) * np.random.uniform(0.5, 1.0, n))
rect = plt.bar(X, +Y1, facecolor='#524C90', edgecolor='white')
for x,y in zip(X, Y1):
plt.text(x+0.4, y+0.05, '%.2f' % y, ha='center', va='bottom')
plt.xlim(-0.5, 12.5)
plt.ylim(-0.1, +1.25)
plt.xlabel("xlabel")
plt.ylabel("ylabel")
plt.title("title")
plt.legend((rect,), ("example",))
plt.show()
def genResFile(self, i):
cents = self.clf.centroids
sse = self.clf.sse
f = open("Res" + "-" + str(i), "w")
f.write(str(cents.shape[0]) + '\n')
for cent in cents:
f.write(str(cent[0]) + '\t' + str(cent[1]) + '\n')
f.write(str(sse) + '\n')
# test
f.write("\n")
for clu in self.clf.clusterAssment:
f.write(str(clu[0]) + '\t' + str(clu[1]) + '\n')
# test
f.close()
iris_data = load_iris() # ucitavanje Iris data seta
iris_data = iris_data.data[:, 1:3] # uzima se druga i treca osobina iz data seta (sirina sepala i duzina petala)
plt.figure()
for i in range(len(iris_data)):
plt.scatter(iris_data[i, 0], iris_data[i, 1])
plt.xlabel('Sepal width')
plt.ylabel('Petal length')
plt.show()
# --- INICIJALIZACIJA I PRIMENA K-MEANS ALGORITMA --- #
# TODO 2: K-means na Iris data setu
kmeans = KMeans(n_clusters=2, max_iter=100)
kmeans.fit(iris_data, normalize=True)
colors = {0: 'red', 1: 'green'}
plt.figure()
for idx, cluster in enumerate(kmeans.clusters):
plt.scatter(cluster.center[0], cluster.center[1], c=colors[idx], marker='x', s=200) # iscrtavanje centara
for datum in cluster.data: # iscrtavanje tacaka
plt.scatter(datum[0], datum[1], c=colors[idx])
plt.xlabel('Sepal width')
plt.ylabel('Petal length')
plt.show()
# --- ODREDJIVANJE OPTIMALNOG K --- #
def doTrain(self, feats, clusters, maxIters = 1024, epsilon = 1e-4):
# Initialise using kmeans...
km = KMeans()
kmAssignment = numpy.empty(feats.shape[0],dtype=numpy.float_)
km.train(feats,clusters,assignOut = kmAssignment)
# Create the assorted data structures needed...
mix = numpy.ones(clusters,dtype=numpy.float_)/float(clusters)
mean = numpy.empty((clusters,feats.shape[1]),dtype=numpy.float_)
for c in xrange(clusters): mean[c,:] = km.getCentre(c)
sd = numpy.zeros(clusters,dtype=numpy.float_)
tempCount = numpy.zeros(clusters,dtype=numpy.int_)
for f in xrange(feats.shape[0]):
c = kmAssignment[f]
dist = ((feats[f,:] - mean[c,:])**2).sum()
tempCount[c] += 1
sd += (dist-sd)/float(tempCount[c])
sd = numpy.sqrt(sd/float(feats.shape[1]))
wv = numpy.ones((feats.shape[0],clusters),dtype=numpy.float_) # Weight vectors calculated in e-step.
pwv = numpy.empty(clusters,dtype=numpy.float_) # For convergance detection.
norms = numpy.empty(clusters,dtype=numpy.float_) # Normalising constants for the distributions, to save repeated calculation.
sqrt2pi = math.sqrt(2.0*math.pi)
# The code...
code = """
for (int iter=0;iter<maxIters;iter++)
{
// e-step - for all features calculate the weight vector (Also do convergance detection.)...
for (int c=0;c<Nmean[0];c++)
{
norms[c] = pow(sqrt2pi*sd[c], Nmean[1]);
}
bool done = true;
for (int f=0;f<Nfeats[0];f++)
{
float sum = 0.0;
for (int c=0;c<Nmean[0];c++)
{
float distSqr = 0.0;
for (int i=0;i<Nmean[1];i++)
{
float diff = FEATS2(f,i) - MEAN2(c,i);
distSqr += diff*diff;
}
pwv[c] = WV2(f,c);
float core = -0.5*distSqr / (sd[c]*sd[c]);
WV2(f,c) = mix[c]*exp(core); // Unnormalised.
WV2(f,c) /= norms[c]; // Normalisation
sum += WV2(f,c);
}
for (int c=0;c<Nmean[0];c++)
{
WV2(f,c) /= sum;
done = done && (fabs(WV2(f,c)-pwv[c])<epsilon);
}
}
if (done) break;
// Zero out mix,mean and sd, ready for filling...
for (int c=0;c<Nmean[0];c++)
{
mix[c] = 0.0;
for (int i=0;i<Nmean[1];i++) MEAN2(c,i) = 0.0;
sd[c] = 0.0;
}
// m-step - update the mixing vector, means and sd...
// *Calculate mean and mixing vector incrimentally...
for (int f=0;f<Nfeats[0];f++)
{
for (int c=0;c<Nmean[0];c++)
{
mix[c] += WV2(f,c);
if (WV2(f,c)>1e-6) // Msut not update if value is too low due to division in update - NaN avoidance.
{
for (int i=0;i<Nmean[1];i++)
{
MEAN2(c,i) += WV2(f,c) * (FEATS2(f,i) - MEAN2(c,i)) / mix[c];
}
}
}
}
// prevent the mix of any given component getting too low - will cause the algorithm to NaN...
for (int c=0;c<Nmean[0];c++)
{
if (mix[c]<1e-6) mix[c] = 1e-6;
}
// *Calculate the sd simply, initial calculation is sum of squared differences...
for (int f=0;f<Nfeats[0];f++)
{
for (int c=0;c<Nmean[0];c++)
{
float distSqr = 0.0;
for (int i=0;i<Nmean[1];i++)
{
float delta = FEATS2(f,i) - MEAN2(c,i);
distSqr += delta*delta;
}
sd[c] += WV2(f,c) * distSqr;
}
}
// *Final adjustments for the new state...
float mixSum = 0.0;
for (int c=0;c<Nmean[0];c++)
{
sd[c] = sqrt(sd[c]/(mix[c]*float(Nfeats[1])));
mixSum += mix[c];
}
for (int c=0;c<Nmean[0];c++) mix[c] /= mixSum;
}
"""
# Weave it...
weave.inline(code,['feats', 'maxIters', 'epsilon', 'mix', 'mean', 'sd', 'wv', 'pwv', 'norms', 'sqrt2pi'])
# Store result...
self.mix = mix
self.mean = mean
self.sd = sd
def fit(self, X):
self.X = X
self.N = X.shape[0]
self.ndim = X.shape[1]
np.random.seed(self.random_seed)
matX = np.asmatrix(X)
# initialization schemes
if self.init_method == 'random':
if self.init_means is not None:
mu = self.init_means
else:
mu = X[np.random.choice(range(0, len(X)), self.num_gaussians), :] # sample from the data
if self.init_cov is not None:
sigma = self.init_cov
else:
sigma = list()
for k in range(self.num_gaussians):
sigma.append(np.identity(self.ndim, dtype=np.float64))
sigma[k] += np.random.rand(self.ndim, self.ndim) # purely synthetic
sigma[k] = np.dot(sigma[k], sigma[k].T) # making it positive semi-definite and symmetric
sigma[k] /= sigma[k].sum()
# lowerbound = k * self.N / self.num_gaussians # sample from data
# upperbound = lowerbound + 20
# sigma[k] = np.cov(X[lowerbound:upperbound, :].T)
if self.init_weights is not None:
lmbda = self.init_weights
else:
lmbda = np.random.rand(self.num_gaussians)
lmbda /= lmbda.sum()
elif self.init_method == 'kmeans': # use means of kmeans as initial means, and calculate cov from the clusters
model = KMeans(K=self.num_gaussians, max_iter=5)
model.fit(X)
labels = model.pred(X)
mu = np.zeros((self.num_gaussians, self.ndim))
sigma = [np.zeros((self.ndim, self.ndim))] * self.num_gaussians
for k in range(self.num_gaussians):
cluster = X[labels == k]
mu[k] = cluster.mean(axis=0)
sigma[k] = np.cov(cluster.T)
if self.init_weights is not None:
lmbda = self.init_weights
else:
lmbda = np.random.rand(self.num_gaussians)
lmbda /= lmbda.sum()
######## BEGIN ACTUAL ALGORITHM ###################
for iter in range(self.max_iter):
phat = np.zeros((self.N, self.num_gaussians))
N = np.zeros(self.num_gaussians)
# E step
for k in range(0, self.num_gaussians):
normal_var = normal(mean=mu[k], cov=sigma[k])
phat[:, k] = lmbda[k] * normal_var.pdf(X)
phat /= phat.sum(axis=1)[:, None]
# faster to do it all with numpy than use loops
# for n in range(0, self.N): # loop over each data point
# for k in range(0, self.num_gaussians):
# normalx = normal(mean=mu[k], cov=sigma[k]).pdf(X[n, :])
# phat[n, k] = lmbda[k] * normalx
# phat[n, :] /= phat[n, :].sum()
# M step
for k in range(self.num_gaussians):
N[k] = phat[:, k].sum()
mu[k] = np.dot(phat[:, k], X) / N[k]
intermed = np.multiply(phat[:, k], (matX - mu[k]).T).T
sigma[k] = np.dot(intermed.T, (matX - mu[k])) / N[k]
lmbda[k] = N[k] / self.N
pass # end of this iteration
self.mu = mu
self.sigma = sigma
self.lmbda = lmbda
dimensions = 3
for tests in range(0, 4):
precisions = []
times = []
for executions in range(0, 100):
print(str(executions) + "%")
start_time = time.time()
particles = []
k_means = KMeans()
# Particles Initialization
for i in range(population_size):
p = Particle()
num_clusters = random.randint(2, 7)
plist = [num_clusters, ]
plist.extend([random.uniform(0, 10) for i in range(0, k_means.dimens * 7)])
p.current_position = array(plist)
p.best_position = p.current_position
p.fitness = 0.0
p.velocity = 0.0
particles.append(p)
import cPickle
import matplotlib.pyplot as plt
import numpy as np
from kmeans import KMeans,biKMeans
if __name__ == "__main__":
#加载数据
X,y = cPickle.load(open('data.pkl','r'))
#依次画出迭代1次、2次、3次...的图
for max_iter in range(6):
#设置参数
n_clusters = 10
initCent = X[50:60] #将初始质心初始化为X[50:60]
#训练模型
clf = KMeans(n_clusters,initCent,max_iter)
clf.fit(X)
cents = clf.centroids
labels = clf.labels
sse = clf.sse
#画出聚类结果，每一类用一种颜色
colors = ['b','g','r','k','c','m','y','#e24fff','#524C90','#845868']
for i in range(n_clusters):
index = np.nonzero(labels==i)[0]
x0 = X[index,0]
x1 = X[index,1]
y_i = y[index]
for j in range(len(x0)):
plt.text(x0[j],x1[j],str(int(y_i[j])),color=colors[i],\
fontdict={'weight': 'bold', 'size': 9})
plt.scatter(cents[i,0],cents[i,1],marker='x',color=colors[i],linewidths=12)
import numpy as np
import matplotlib.pyplot as plt
from scipy.misc import *
import scipy.io as sio
from kmeans import KMeans
plt.close('all')
X = sio.loadmat('ex7data2.mat')['X']
classifier = KMeans(X)
initial_centroids = np.asarray([[3, 3], [6, 2], [8, 5]])
idx = classifier.find_closest_centroids(initial_centroids)
print("Closest centroids for the first 3 examples:")
print(np.str(idx[0:3]))
print("(the closest centroids should be 0, 2, 1 respectively)")
centroids = classifier.compute_centroids(idx)
print("Centroids computed after initial finding of closest centroids: \n")
print(np.str(centroids))
print('(the centroids should be');
print(' [ 2.428301 3.157924 ]');
print(' [ 5.813503 2.633656 ]');
print(' [ 7.119387 3.616684 ]\n');
centroids, idx = classifier.run(plot_progress=True)
plt.show()
print("K-Means Done.")
s1[i] = (x1, y1)
r2, theta2 = np.random.normal(5, 0.25), np.random.uniform(0, 2*np.pi)
x2, y2 = r2 * np.cos(theta2), r2 * np.sin(theta2)
s2[i] = (x2, y2, r2, theta2)
plt.scatter(x1, y1)
plt.scatter(x2, y2)
data.append((x1, y1))
data.append((x2, y2))
plt.show()
# TODO 5: K-means nad ovim podacima
kmeans = KMeans(n_clusters=2, max_iter=100)
kmeans.fit(data)
colors = {0: 'red', 1: 'green'}
plt.figure()
for idx, cluster in enumerate(kmeans.clusters):
plt.scatter(cluster.center[0], cluster.center[1], c=colors[idx], marker='x', s=200) # iscrtavanje centara
for datum in cluster.data: # iscrtavanje tacaka
plt.scatter(datum[0], datum[1], c=colors[idx])
plt.show()
# TODO 7: DBSCAN nad ovim podacima
dbscan = DBScan(epsilon=1.2, min_points=3)
dbscan.fit(data)
from em import calculate_em, _calculate_normal
from em import calculate_log_likelihood
from kmeans import KMeans
n_clusters = 4
X = utils.load_data('EMGaussienne.data')
Xtest = utils.load_data('EMGaussienne.test')
max_iterations = 150
ridge = 1e-6
verbose = True
n_samples, n_features = X.shape
# Initialise the data using kmeans
k_means = KMeans(k=n_clusters)
k_means_labels, _ = k_means.fit(X.copy())
k_means_cluster_centers = k_means.centers_
mu, sigma, tpi = calculate_em(X, n_clusters)
print 'Log likelihood %d' % calculate_log_likelihood(X, mu, sigma, tpi)
print 'Log likelihood %d' % calculate_log_likelihood(Xtest, mu, sigma, tpi)
p = np.zeros((n_clusters, n_samples))
for i in range(n_clusters):
p[i, :] = _calculate_normal(X, mu[i, :], sigma[i, :])
em_labels = p.argmax(axis=0)
p = np.zeros((n_clusters, n_samples))
for i in range(n_clusters):
def preConfigureModel(self):
configureStart = time.time() # the pre-configuration starting time
# get the previous trading day
yesterday = self.dateOfTrade
while True:
yesterday -= datetime.timedelta(days = 1)
datasetPath = 'dataset/' + yesterday.strftime('%d-%h-%G')
if isdir(datasetPath):
break
else:
continue
try:
remove('data/all_features.pkl')
except:
pass
print 'Pre-Configuration stage, on date :', yesterday
# the last day best features and last day points are saved
featureObject = GetFeatures(datasetPath + '/corpora')
extractionStart = time.time()
featureObject.extractFeatures(parameters.ourFeatureType) # 2-word combinations fe method
extractionEnd = time.time()
print '\nFeature Extraction time : %.2f minutes' %((extractionEnd - extractionStart)/60)
selectionStart = time.time()
featureObject.selectFeatures(parameters.ourSelectionType, parameters.initialNumberOfFeatures) # bns fs method, no of features
selectionEnd = time.time()
print 'Feature Selection time : %.2f minutes' %((selectionEnd - selectionStart)/60)
numberOfVectors = featureObject.representFeatures()
print 'Document vectors formed .. '
copy('data/best_features.pkl', 'data/all_best_features.pkl')
#------------------------------------ K-means Running ---------------------------------------
print '\nRunning K-means ..'
kmeansStart = time.time()
kmeansObject = KMeans()
kmeansObject.getDataPoints()
kmeansObject.getInitialCenters()
iterationNumber = 1
notConverged = True
while notConverged == True and iterationNumber < parameters.maximumIterations :
timeNow = time.time()
if iterationNumber % 20 == 0:
print '..Iteration Number : %3d Time Elapsed till now : %.2f minutes' %(iterationNumber, (timeNow - kmeans_start) / 60.0)
else:
pass
kmeansObject.assignToCluster()
notConverged = kmeansObject.recalculateCentroids()
iterationNumber += 1
kmeansObject.saveClusters()
kmeansEnd = time.time()
print 'Kmeans running time : %.2f minutes' %((kmeansEnd - kmeansStart)/60)
#-------------------------------------------------------------------------------------------------------
# cluster info
fileReader = open('data/cluster_info.pkl', 'r')
clusterInfo = pickle.load(fileReader)
fileReader.close()
# for projected clustering
print '\nPreparing the initial fading clusters ..'
projectedClusteringStart = time.time()
self.projectedClusteringObject = ProjectedClustering()
self.projectedClusteringObject.prepareFadingClusters(clusterInfo)
projectedClusteringEnd = time.time()
print 'Fading clusters preparation time : %.2f minutes' %((projectedClusteringEnd - projectedClusteringStart) / 60)
# take the last 10 files of 'yesterday' and store in the 'last' folder
lastFileNames = []
fileReader = open(datasetPath + '/log_file.txt', 'r')
for line in fileReader:
lastFileNames.append(line.split(' ')[0])
fileReader.close()
fileWriter = open('last/log.txt', 'w') # write the names of files
lastFileNames = lastFileNames[-10:]
for fileName in lastFileNames:
try:
copy(datasetPath + '/corpora/' + fileName, 'last/' + fileName)
except:
pass
fileWriter.write(fileName + '\n')
fileWriter.close()
# get the ann ready
self.annObject.loadAnnWeights()
print '\nANN locked and loaded ..'
configureEnd = time.time()
print "Total time taken to pre-configure : %.2f minutes" %((configureEnd - configureStart)/60)