def test_KMeans_scores(self):
digits = datasets.load_digits()
df = pdml.ModelFrame(digits)
scaled = pp.scale(digits.data)
df.data = df.data.pp.scale()
self.assert_numpy_array_almost_equal(df.data.values, scaled)
clf1 = cluster.KMeans(init='k-means++', n_clusters=10,
n_init=10, random_state=self.random_state)
clf2 = df.cluster.KMeans(init='k-means++', n_clusters=10,
n_init=10, random_state=self.random_state)
clf1.fit(scaled)
df.fit_predict(clf2)
expected = m.homogeneity_score(digits.target, clf1.labels_)
self.assertEqual(df.metrics.homogeneity_score(), expected)
expected = m.completeness_score(digits.target, clf1.labels_)
self.assertEqual(df.metrics.completeness_score(), expected)
expected = m.v_measure_score(digits.target, clf1.labels_)
self.assertEqual(df.metrics.v_measure_score(), expected)
expected = m.adjusted_rand_score(digits.target, clf1.labels_)
self.assertEqual(df.metrics.adjusted_rand_score(), expected)
expected = m.homogeneity_score(digits.target, clf1.labels_)
self.assertEqual(df.metrics.homogeneity_score(), expected)
expected = m.silhouette_score(scaled, clf1.labels_, metric='euclidean',
sample_size=300, random_state=self.random_state)
result = df.metrics.silhouette_score(metric='euclidean', sample_size=300,
random_state=self.random_state)
self.assertAlmostEqual(result, expected)
def main():
digits = datasets.load_digits()
#print_digit_data(digits) # tok
#plot_training_data(digits) # tok
#plot_target_data(digits) # tok
#show_PCA_training(digits) # tok
data = preprocess_data(digits) # tok
#print(data) # tok
X_train, X_test, y_train, y_test = split_data_into_training_and_test(data, digits) # tok
clf = cluser_digits(X_train) # tok
# show_cluster_digits(clf) # TOK
y_pred = predict_labels(clf, X_test, y_test, X_train, y_train) # tok
show_prediction_confusion_matrix(y_test, y_pred) # tok
homogeneity_score(clf, X_test, y_test, X_train, y_train, y_pred) # tok
##########################################
# try a different model
svc_model, X_train, X_test, y_train, y_test, images_train, images_test = model_SVC(digits) # tok
# grid_search - use this to tune parameters
grid_search(digits) # tok
apply_grid_search(clf, X_test, y_test, X_train, y_train)
predicted = classify_rbf(svc_model, X_test, y_test, images_test)
check_model_performance(y_test, predicted)
show_model2_results(svc_model, X_train, y_train)
def aggregate_stats(infiles, outfile):
"""
Combine all the aggstats into a single file
Compute summary statistics
"""
res = []
for infile in infiles:
d = pickle.load(open(infile, 'r'))
print "The file is", infile
assigndf = d['df']
meta = d['meta']
neurons = meta['neurons']
m = extract_metadata(infile)
if len(m) == 0:
# skip the stupid non-replicated ones
continue
for k, v in m.iteritems():
assigndf[k] = v
assigndf['true_assign_role'] = [np.array(neurons['role']) for _ in range(len(assigndf))]
# compute the statistics
assigndf['ari'] = assigndf.apply(lambda x : metrics.adjusted_rand_score(x['true_assign'], irm.util.canonicalize_assignment(x['assign'])), axis=1)
assigndf['homogeneity'] = assigndf.apply(lambda x : metrics.homogeneity_score(x['true_assign'], irm.util.canonicalize_assignment(x['assign'])), axis=1)
assigndf['completeness'] = assigndf.apply(lambda x : metrics.completeness_score(x['true_assign'], irm.util.canonicalize_assignment(x['assign'])), axis=1)
# don't consider the ones where the role is "none" as these are multi-role ones
neurons.ix[neurons['role'].isnull(), 'role'] = 'I'
assigndf['role_ari'] = assigndf.apply(lambda x : metrics.adjusted_rand_score(neurons['role'],
irm.util.canonicalize_assignment(x['assign'])), axis=1)
assigndf['role_homogeneity'] = assigndf.apply(lambda x : metrics.homogeneity_score(neurons['role'],
irm.util.canonicalize_assignment(x['assign'])), axis=1)
assigndf['role_completeness'] = assigndf.apply(lambda x : metrics.completeness_score(neurons['role'],
irm.util.canonicalize_assignment(x['assign'])), axis=1)
assigndf['type_n_true'] = assigndf.apply(lambda x : len(np.unique(x['true_assign'])), axis=1)
assigndf['type_n_learned'] = assigndf.apply(lambda x : len(np.unique(x['assign'])), axis=1)
assigndf['auc'] = assigndf.apply(lambda x: metrics.roc_auc_score(x['heldout_link_truth'], x['heldout_link_predprob']), axis=1)
#assigndf['f1'] = assigndf.apply(lambda x: metrics.f1_score(x['heldout_link_truth'], x['heldout_link_predprob']), axis=1)
#
# fraction of mass in top N types
res.append(assigndf)
alldf = pandas.concat(res)
pickle.dump(alldf, open(outfile, 'w'), -1)
def kmeans(input_file, n_clusters, Output):
lvltrace.lvltrace("LVLEntree dans kmeans unsupervised")
ncol=tools.file_col_coma(input_file)
data = np.loadtxt(input_file, delimiter=',', usecols=range(ncol-1))
X = data[:,1:]
y = data[:,0]
sample_size, n_features = X.shape
k_means=cluster.KMeans(init='k-means++', n_clusters=n_clusters, n_init=10)
k_means.fit(X)
reduced_data = k_means.transform(X)
values = k_means.cluster_centers_.squeeze()
labels = k_means.labels_
k_means_cluster_centers = k_means.cluster_centers_
print "#########################################################################################################\n"
#print y
#print labels
print "K-MEANS\n"
print('homogeneity_score: %f'%metrics.homogeneity_score(y, labels))
print('completeness_score: %f'%metrics.completeness_score(y, labels))
print('v_measure_score: %f'%metrics.v_measure_score(y, labels))
print('adjusted_rand_score: %f'%metrics.adjusted_rand_score(y, labels))
print('adjusted_mutual_info_score: %f'%metrics.adjusted_mutual_info_score(y, labels))
print('silhouette_score: %f'%metrics.silhouette_score(X, labels, metric='euclidean', sample_size=sample_size))
print('\n')
print "#########################################################################################################\n"
results = Output+"kmeans_scores.txt"
file = open(results, "w")
file.write("K-Means Scores\n")
file.write("Homogeneity Score: %f\n"%metrics.homogeneity_score(y, labels))
file.write("Completeness Score: %f\n"%metrics.completeness_score(y, labels))
file.write("V-Measure: %f\n"%metrics.v_measure_score(y, labels))
file.write("The adjusted Rand index: %f\n"%metrics.adjusted_rand_score(y, labels))
file.write("Adjusted Mutual Information: %f\n"%metrics.adjusted_mutual_info_score(y, labels))
file.write("Silhouette Score: %f\n"%metrics.silhouette_score(X, labels, metric='euclidean', sample_size=sample_size))
file.write("\n")
file.write("True Value, Cluster numbers, Iteration\n")
for n in xrange(len(y)):
file.write("%f, %f, %i\n"%(y[n],labels[n],(n+1)))
file.close()
import pylab as pl
from itertools import cycle
# plot the results along with the labels
k_means_cluster_centers = k_means.cluster_centers_
fig, ax = plt.subplots()
im=ax.scatter(X[:, 0], X[:, 1], c=labels, marker='.')
for k in xrange(n_clusters):
my_members = labels == k
cluster_center = k_means_cluster_centers[k]
ax.plot(cluster_center[0], cluster_center[1], 'w', color='b',
marker='x', markersize=6)
fig.colorbar(im)
plt.title("Number of clusters: %i"%n_clusters)
save = Output + "kmeans.png"
plt.savefig(save)
lvltrace.lvltrace("LVLsortie dans kmeans unsupervised")
def clustering(dataset):
vectorizer = dataset.vectorizer
X = dataset.X
true_k = dataset.n_classes
labels = dataset.target
km = cluster.KMeans(n_clusters=true_k, max_iter=100, n_init=1)
print("Clustering sparse data with %s" % km)
t0 = time()
km.fit(X)
print("done in %0.3fs" % (time() - t0))
print()
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels, km.labels_))
print("Completeness: %0.3f" % metrics.completeness_score(labels, km.labels_))
print("V-measure: %0.3f" % metrics.v_measure_score(labels, km.labels_))
print("Adjusted Rand-Index: %.3f"
% metrics.adjusted_rand_score(labels, km.labels_))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(X, labels, sample_size=1000))
print()
print("Top terms per cluster:")
order_centroids = km.cluster_centers_.argsort()[:, ::-1]
terms = vectorizer.get_feature_names()
sizes = np.sum(km.labels_[:, np.newaxis] == np.arange(true_k), axis=0)
for i in range(true_k):
print("Cluster %d (%d):" % (i, sizes[i]), end='')
for ind in order_centroids[i, :10]:
print(' %s' % terms[ind], end='')
print()
def kmeans_setup(data):
if pca_f == 1:
pca = PCA(n_components = num_clusters).fit(data)
initializer = pca.components_
name = 'PCA'
else:
initializer = 'k-means++'
name = 'k-means++'
t0 = time()
estimator = KMeans(init=initializer, n_clusters=num_clusters, n_init = num_init, max_iter = num_iterations)
estimator.fit(data)
if debug == True:
sample_size = 300
print('% 9s %.2fs %i %.3f %.3f %.3f %.3f %.3f %.3f'
% (name, (time() - t0), estimator.inertia_,
metrics.homogeneity_score(labels, estimator.labels_),
metrics.completeness_score(labels, estimator.labels_),
metrics.v_measure_score(labels, estimator.labels_),
metrics.adjusted_rand_score(labels, estimator.labels_),
metrics.adjusted_mutual_info_score(labels, estimator.labels_),
metrics.silhouette_score(data, estimator.labels_,
metric='euclidean',
sample_size=sample_size)))
return estimator
def affin_test():
savefile = open('traindata.pkl', 'rb')
(x_train, y_train, t1) = cPickle.load(savefile)
savefile.close()
x_train, X_valid, y_train, y_valid = cross_validation.train_test_split(
x_train, y_train, test_size=0.9, random_state=42)
labels_true = y_train
x_train = StandardScaler().fit_transform(x_train)
af = AffinityPropagation(preference=-50).fit(x_train)
cluster_centers_indices = af.cluster_centers_indices_
labels = af.labels_
n_clusters_ = len(cluster_centers_indices)
print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f"
% metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f"
% metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(x_train, labels, metric='sqeuclidean'))
def run(self):
meandist=[]
homogeneity_scores=[]
completeness_scores=[]
rand_scores=[]
silhouettes=[]
for k in self.clusters:
model = KMeans(n_clusters=k, max_iter=5000, init='k-means++')
labels = model.fit_predict(self.X)
if k == self.targetcluster and self.stats:
nd_data = np.concatenate((self.X, np.expand_dims(labels, axis=1),np.expand_dims(self.y, axis=1)), axis=1)
pd_data = pd.DataFrame(nd_data)
pd_data.to_csv("cluster.csv", index=False, index_label=False, header=False)
print model.cluster_centers_
for i in range (0,3):
print "Cluster {}".format(i)
cluster = pd_data.loc[pd_data.iloc[:,-2]==i].iloc[:,-2:]
print cluster.shape[0]
print float(cluster.loc[cluster.iloc[:,-1]==0].shape[0])/cluster.shape[0]
print float(cluster.loc[cluster.iloc[:,-1]==1].shape[0])/cluster.shape[0]
meandist.append(sum(np.min(cdist(self.X, model.cluster_centers_, 'euclidean'), axis=1))/ self.X.shape[0])
homogeneity_scores.append(metrics.homogeneity_score(self.y, labels))
completeness_scores.append(metrics.completeness_score(self.y, labels))
rand_scores.append(metrics.adjusted_rand_score(self.y, labels))
if self.gen_plot:
#self.visualize()
self.plot(meandist, homogeneity_scores, completeness_scores, rand_scores, silhouettes)
def bench_k_means(estimator, name, data, target_labels, sample_size):
"""For benchmarking K-Means estimators. Prints different clustering metrics and train accuracy
ARGS
estimator: K-Means clustering algorithm <sklearn.cluster.KMeans>
name: estimator name <str>
data: array-like or sparse matrix, shape=(n_samples, n_features)
target_labels: labels of data points <number array>
sample_size: size of the sample to use when computing the Silhouette Coefficient <int>
"""
t0 = time()
estimator.fit(data)
_, _, train_accuracy = compute_residuals_and_rsquared(estimator.labels_, target_labels)
print('% 9s\t%.2fs\t%i\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f'
% (name, (time() - t0), estimator.inertia_,
metrics.homogeneity_score(target_labels, estimator.labels_),
metrics.completeness_score(target_labels, estimator.labels_),
metrics.v_measure_score(target_labels, estimator.labels_),
metrics.adjusted_rand_score(target_labels, estimator.labels_),
metrics.adjusted_mutual_info_score(target_labels, estimator.labels_),
metrics.silhouette_score(data, estimator.labels_,metric='euclidean',sample_size=sample_size),
train_accuracy
)
)
def bench_k_means(estimator, name, data, sample_size, labels,postIds):
data=sparse.csr_matrix(data)
t0 = time()
print("Performing dimensionality reduction using LSA")
t0 = time()
lsa = TruncatedSVD(500)
data = lsa.fit_transform(data)
data = Normalizer(copy=False).fit_transform(data)
print("done in %fs" % (time() - t0))
print()
#sData=sparse.csr_matrix(data)
val=estimator.fit(data)
print('% 9s %.2fs %i %.3f %.3f %.3f %.3f %.3f '
% (name, (time() - t0), estimator.inertia_,
metrics.homogeneity_score(labels, estimator.labels_),
metrics.completeness_score(labels, estimator.labels_),
metrics.v_measure_score(labels, estimator.labels_),
metrics.adjusted_rand_score(labels, estimator.labels_),
metrics.adjusted_mutual_info_score(labels, estimator.labels_)))
print("Parsing USer File:")
parseUserFile()
print("extracting User File:")
clusterDict=extractCluster(postIds,estimator.labels_)
print("writing Cluster Data to File")
writeCluterToFile(clusterDict)
def main(argv):
file_vectors,clust_type, clusters, distance, cluster_param, std = get_arguments(argv)
fname='.'.join(map(str,[file_vectors.split('/')[-1],clust_type, clusters, distance, cluster_param, std]))
writer=open(fname,'w') ## better to put in EX1, EX2, .. folders
print 'clustering:',clust_type
print 'clusters:',clusters
print 'cluster_param:',cluster_param
print 'std:',std
X,words,truth=load_data(file_vectors,True)
X=np.array(X)
if clust_type=='affin':
labels=affin_sclustering(X, n_clust=int(clusters), distance=distance, gamma=float(cluster_param), std=bool(std))
else:
labels=knn_sclustering(X, n_clust=int(clusters), k=int(cluster_param))
writer.write('\nVMeas:'+ str(v_measure_score(truth,labels)))
writer.write('\nRand:'+str(adjusted_rand_score(truth,labels)))
writer.write('\nHomogen:'+str(homogeneity_score(truth,labels))+'\n')
i=0
for word in words:
writer.write(word+' : '+str(labels[i])+'\n')
i+=1
writer.close()
def bench_k_means(estimator, data, labels):
t0 = time()
estimator.fit(data)
print("time to fit: {:.5}".format(time() - t0))
homogenity = metrics.homogeneity_score(labels, estimator.labels_)
completeness = metrics.completeness_score(labels, estimator.labels_)
v_measure = metrics.v_measure_score(labels, estimator.labels_)
print("homogenity {:.5}, completeness {:.5}, v_measure_score {:.5}".format(
homogenity, completeness, v_measure)
)
adj_rand_score = metrics.adjusted_rand_score(
labels, estimator.labels_
)
print("adjusted_rand_score {:.5}".format(adj_rand_score))
adj_mutual_info_score = metrics.adjusted_mutual_info_score(
labels, estimator.labels_
)
print("adjusted_mutual_info_score {:.5}".format(
adj_mutual_info_score)
)
silhouette_score = metrics.silhouette_score(
data, estimator.labels_, metric='euclidean'
)
print("silhouette_score {:.5}".format(
metrics.silhouette_score(data, estimator.labels_,
metric='euclidean'))
)
return [
homogenity, completeness, v_measure, adj_rand_score,
adj_mutual_info_score, silhouette_score
]
def cluster(Z, K=4, algo='kmeans'):
descr = Z.columns
X = Imputer().fit_transform(Z)
##############################################################################
if algo == 'dbscan':
# Compute DBSCAN
db = DBSCAN(eps=0.3, min_samples=10).fit(X)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f" % metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f" % metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, labels))
elif algo == 'kmeans':
km = KMeans(n_clusters=K)
km.fit(X)
print(km.labels_)
return km
def cluster_evaluation(D, y_true, n_clusters, eps=0.8, min_samples=10):
##############################################################################
# Extract Y true
labels_true = y_true
##############################################################################
# transform distance matrix into a similarity matrix
S = 1 - D
##############################################################################
# compute DBSCAN
#db = DBSCAN(eps=eps, min_samples=min_samples).fit(S)
db = Ward(n_clusters=n_clusters).fit(S)
#core_samples = db.core_sample_indices_
labels = db.labels_
# number of clusters in labels, ignoring noise if present
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
print 'Number of clusters: %d' % n_clusters_
print 'Homogeneity: %0.3f' % metrics.homogeneity_score(labels_true, labels)
print 'Completeness: %0.3f' % metrics.completeness_score(labels_true, labels)
print 'V-meassure: %0.3f' % metrics.v_measure_score(labels_true, labels)
print 'Adjusted Rand Index: %0.3f' % metrics.adjusted_rand_score(labels_true, labels)
print 'Adjusted Mutual Information: %0.3f' % metrics.adjusted_mutual_info_score(labels_true, labels)
print 'Silhouette Coefficient: %0.3f' % metrics.silhouette_score(D, labels, metric='precomputed')
def predictAffinityPropagation(X, labels_true):
#ranX, ranY = shuffle(X, y, random_state=0)
af = AffinityPropagation(preference=-50).fit(X)
cluster_centers_indices = af.cluster_centers_indices_
labels = af.labels_
n_clusters_ = len(cluster_centers_indices)
print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f"
% metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f"
% metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(X, labels, metric='sqeuclidean'))
plt.close('all')
plt.figure(1)
plt.clf()
colors = cycle('bgrcmykbgrcmykbgrcmykbgrcmyk')
for k, col in zip(range(n_clusters_), colors):
class_members = labels == k
cluster_center = X[cluster_centers_indices[k]]
plt.plot(X[class_members, 0], X[class_members, 1], col + '.')
plt.plot(cluster_center[0], cluster_center[1], 'o', markerfacecolor=col,
markeredgecolor='k', markersize=14)
for x in X[class_members]:
plt.plot([cluster_center[0], x[0]], [cluster_center[1], x[1]], col)
plt.title('Estimated number of clusters: %d' % n_clusters_)
plt.show()
def compare(method1, method2, fig=False):
X1 = np.load('{0}_{1}_X_2d.npy'.format(species, method1))
X2 = np.load('{0}_{1}_X_2d.npy'.format(species, method2))
print 'n_cluster\tHomo\tCompl\tNMI\tARI'
for i in range(2, 6):
clust1 = Clustering(species, method1, X1, None, n_clusters=i)
clust2 = Clustering(species, method2, X2, None, n_clusters=i)
clust1.agglomerative(linkage='ward')
clust2.agglomerative(linkage='ward')
label1 = clust1.pred_labels('ward')
label2 = clust2.pred_labels('ward')
if i == 3 and fig:
names = np.unique(label1)
figName = '{0}_{1}_on_{2}'.format(species, method1, method2)
plot2d(X2, label1, names, figName, figName)
names = np.unique(label2)
figName = '{0}_{1}_on_{2}'.format(species, method2, method1)
plot2d(X1, label2, names, figName, figName)
print '{0}\t{1}\t{2}\t{3}\t{4}\n'.format(i, metrics.homogeneity_score(label1, label2),
metrics.completeness_score(label1, label2),
metrics.normalized_mutual_info_score(label1, label2),
metrics.adjusted_rand_score(label1, label2))
def clustering_by_kmeans(vectorizer, X, true_k):
print "Clustering in " + str(true_k) + " groups by K-means..."
km = KMeans(n_clusters=true_k, init='k-means++', max_iter=500, n_init=1)
km.fit_predict(X)
print "Measuring..."
print("Homogeneity: %0.3f" % metrics.homogeneity_score(documents, km.labels_))
print("Completeness: %0.3f" % metrics.completeness_score(documents, km.labels_))
print("V-measure: %0.3f" % metrics.v_measure_score(documents, km.labels_)) #V-measure is an entropy-based measure which explicitly measures how successfully the criteria of homogeneity and completeness have been satisfied.
print("Adjusted Rand-Index: %.3f" % metrics.adjusted_rand_score(documents, km.labels_))
print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, km.labels_, sample_size=1000))
#print top terms per cluster clusters
clusters = km.labels_.tolist() # 0 iff term is in cluster0, 1 iff term is in cluster1 ... (lista de termos)
#print "Lista de termos pertencentes aos clusters " + str(clusters)
print "Total de " + str(len(km.labels_)) + " documents"
#Example to get all documents in cluster 0
#cluster_0 = np.where(clusters==0) # don't forget import numpy as np
#print cluster_0
#cluster_0 now contains all indices of the documents in this cluster, to get the actual documents you'd do:
#X_cluster_0 = documents[cluster_0]
terms = vectorizer.get_feature_names()
#print terms
measuring_kmeans(true_k,clusters)
def cluster(algorithm, data, topics, make_silhouette=False):
print str(algorithm)
clusters = algorithm.fit_predict(data)
labels = algorithm.labels_
print 'Homogeneity: %0.3f' % metrics.homogeneity_score(topics, labels)
print 'Completeness: %0.3f' % metrics.completeness_score(topics, labels)
print 'V-measure: %0.3f' % metrics.v_measure_score(topics, labels)
print 'Adjusted Rand index: %0.3f' % metrics.adjusted_rand_score(topics, labels)
print 'Silhouette test: %0.3f' % metrics.silhouette_score(data, labels)
print ' ***************** '
silhouettes = metrics.silhouette_samples(data, labels)
num_clusters = len(set(clusters))
print 'num clusters: %d' % num_clusters
print 'num fitted: %d' % len(clusters)
# Make a silhouette plot if the flag is set
if make_silhouette:
order = numpy.lexsort((-silhouettes, clusters))
indices = [numpy.flatnonzero(clusters[order] == num_clusters) for k in range(num_clusters)]
ytick = [(numpy.max(ind)+numpy.min(ind))/2 for ind in indices]
ytickLabels = ["%d" % x for x in range(num_clusters)]
cmap = cm.jet( numpy.linspace(0,1,num_clusters) ).tolist()
clr = [cmap[i] for i in clusters[order]]
fig = plt.figure()
ax = fig.add_subplot(111)
ax.barh(range(data.shape[0]), silhouettes[order], height=1.0,
edgecolor='none', color=clr)
ax.set_ylim(ax.get_ylim()[::-1])
plt.yticks(ytick, ytickLabels)
plt.xlabel('Silhouette Value')
plt.ylabel('Cluster')
plt.savefig('cluster.png')
def cluster(model, uids):
##############################################################################
# Generate sample data
X = []
for uid in uids:
X.append(model.docvecs[uid])
labels_true = uids
##############################################################################
# Compute Affinity Propagation
af = AffinityPropagation(preference=-50).fit(X)
pickle.dump(af, open('data/af.pick', 'w'))
cluster_centers_indices = af.cluster_centers_indices_
labels = af.labels_
n_clusters_ = len(cluster_centers_indices)
print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f"
% metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f"
% metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(X, labels, metric='sqeuclidean'))
def bestClassify(X,Y):
"Best classifier function"
tfidf = True
if tfidf:
vec = TfidfVectorizer(preprocessor = identity,
tokenizer = identity, sublinear_tf = True)
else:
vec = CountVectorizer(preprocessor = identity,
tokenizer = identity)
km = KMeans(n_clusters=2, n_init=100, verbose=1)
clusterer = Pipeline( [('vec', vec),
('cls', km)] )
prediction = clusterer.fit_predict(X,Y)
checker = defaultdict(list)
for pred,truth in zip(prediction,Y):
checker[pred].append(truth)
labeldict = {}
for pred, label in checker.items():
labeldict[pred] = Counter(label).most_common(1)[0][0]
#print(pred, Counter(label).most_common(1)[0][0])
prediction = [labeldict[p] for p in prediction]
labels = list(labeldict.values())
print(labels)
print(confusion_matrix(Y, prediction, labels=labels))
print("Homogeneity:", homogeneity_score(Y,prediction))
print("Completeness:", completeness_score(Y,prediction))
print("V-measure:", v_measure_score(Y,prediction))
print("Rand-Index:", adjusted_rand_score(Y,prediction))
def get_result(km, labels):
homo_score = metrics.homogeneity_score(labels, km.labels_)
complete_score = metrics.completeness_score(labels, km.labels_)
v_score = metrics.v_measure_score(labels, km.labels_)
rand_score = metrics.adjusted_rand_score(labels, km.labels_)
mutual_info = metrics.adjusted_mutual_info_score(labels, km.labels_)
return homo_score, complete_score, v_score, rand_score, mutual_info
def run_clustering( clusterer, data, labels ):
"""
Cluster: Using a predefined and parameterized clustering algorithm, fit
some dataset and perform metrics given a set of ground-truth labels.
clusterer: the clustering algorithm, from sklearn
data: array-like dataset input
labels: vector of ground-truth labels
"""
# Time the operation
t0 = time()
clusterer.fit(data)
t1 = time()
# Perform metrics
runtime = (t1 - t0)
homogeneity = metrics.homogeneity_score( labels, clusterer.labels_ )
completeness = metrics.completeness_score( labels, clusterer.labels_ )
v_measure = metrics.v_measure_score( labels, clusterer.labels_ )
adjusted_rand = metrics.adjusted_rand_score( labels, clusterer.labels_ )
adjusted_mutual = metrics.adjusted_mutual_info_score( labels,
clusterer.labels_ )
# Output to logs
logging.info(" |- Execution time: %fs" % runtime)
logging.info(" |- Homogeneity: %0.3f" % homogeneity)
logging.info(" |- Completeness: %0.3f" % completeness)
logging.info(" |- V-measure: %0.3f" % v_measure)
logging.info(" |- Adjusted Rand-Index: %.3f" % adjusted_rand)
logging.info(" |- Adjusted Mutual Info: %.3f" % adjusted_mutual)
def cluseval(label, truth):
rand = metrics.adjusted_rand_score(truth, label)
mutual = metrics.adjusted_mutual_info_score(truth, label)
h**o = metrics.homogeneity_score(truth, label)
complete = metrics.completeness_score(truth, label)
v = metrics.v_measure_score(truth, label)
result = [rand, mutual, h**o, complete, v]
return result
def print_cluster(clusterTrainClass, labels, clusterTestStory):
print("Homogeneity: %0.3f" % metrics.homogeneity_score(clusterTrainClass, labels))
print("Completeness: %0.3f" % metrics.completeness_score(clusterTrainClass, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(clusterTrainClass, labels))
print("Adjusted Rand Index: %0.3f" % metrics.adjusted_rand_score(clusterTrainClass, labels))
print("Adjusted Mutual Information: %0.3f" % metrics.adjusted_mutual_info_score(clusterTrainClass, labels))
print "Silhouette Coefficient:"
print metrics.silhouette_score(clusterTestStory, labels, metric='euclidean')
def evaluate(labels_true, labels):
homogeneity = metrics.homogeneity_score(labels_true, labels)
completeness = metrics.completeness_score(labels_true, labels)
v_measure = metrics.v_measure_score(labels_true, labels)
adjusted_rand = metrics.adjusted_rand_score(labels_true, labels)
adjusted_mutual_info = metrics.adjusted_mutual_info_score(labels_true, labels)
#silhouette = metrics.silhouette_score(data, labels, metric='sqeuclidean')
return homogeneity, completeness, v_measure, adjusted_rand, adjusted_mutual_info#, silhouette
def cluster_metrics(labels_1, labels_2):
print("\n".join(
[
"Normalized Mutual Information: %f" % (normalized_mutual_info_score(labels_1, labels_2)),
"Adjusted Rand Score: %f" % (adjusted_rand_score(labels_1, labels_2)),
"Homogeneity: %f" % (homogeneity_score(labels_1, labels_2)),
"Completeness: %f" % (completeness_score(labels_1, labels_2))
]
))
def main():
# Parse command line arguments
parser = argparse.ArgumentParser(usage=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='Perform spectral clustering.')
parser.add_argument("--clusters", "-c", type=int, help='Number of clusters.')
parser.add_argument("--knn", "-k", type=int, default=0,
help='Number of nearest neighbors, 0 means all.')
parser.add_argument("--sm", "-s",
help='File containing similarity matrix')
parser.add_argument("--iterations", "-i", type=int, default=10,
help='Number of KMeans iterations.')
parser.add_argument("--true_labels", "-t",
help='File containing the true labels.')
parser.add_argument("--output", "-o", help='Name of the file to write' +
' the labels to.')
parser.add_argument("--normalize", "-n", action='store_true',
help='Normalize each row so that the max value is one.')
args = parser.parse_args()
sm = np.load(args.sm)
if args.normalize:
sm /= sm.max(axis=1)[:, np.newaxis]
# Ensure symmetric
sm = (sm + sm.T) / 2
labels = []
if args.knn > 0:
labels = SpectralClustering(n_clusters=args.clusters,
affinity='nearest_neighbors', n_neighbors=args.knn,
n_init=args.iterations).fit(sm).labels_
else:
labels = SpectralClustering(n_clusters=args.clusters,
affinity='precomputed',
n_init=args.iterations).fit(sm).labels_
with open(args.output, 'w') as fout:
for l in labels:
fout.write(str(l) + '\n')
# Load the true labels.
if args.true_labels:
true_labels = []
with open(args.true_labels, 'r') as fin:
for line in fin:
true_labels.append(int(line.strip()))
# Run the metrics.
print("Homogeneity: %0.3f" % metrics.homogeneity_score(true_labels, labels))
print("Completeness: %0.3f" % metrics.completeness_score(true_labels, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(true_labels, labels))
print("Adjusted Rand Index: %0.3f"
% metrics.adjusted_rand_score(true_labels, labels))
print("Adjusted Mutual Information: %0.3f"
% metrics.adjusted_mutual_info_score(true_labels, labels))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(sm, labels))
def eval_clusters(self):
"""calculates the adjusted rand index of the clustering
based on the label of the points
"""
_, labels_true, labels_pred = self.get_labels()
ari = metrics.adjusted_rand_score(labels_true, labels_pred)
hom = metrics.homogeneity_score(labels_true, labels_pred)
comp = metrics.completeness_score(labels_true, labels_pred)
return ari, hom, comp
def get_cluster_metrics(X, labels, labels_true=None):
metrics_dict = dict()
metrics_dict['Silhouette coefficient'] = metrics.silhouette_score(X,
labels,
metric='precomputed')
if labels_true:
metrics_dict['Completeness score'] = metrics.completeness_score(labels_true, labels)
metrics_dict['Homogeneity score'] = metrics.homogeneity_score(labels_true, labels)
return metrics_dict
def evaluateAllAlgorithms(self):
algs = [self.labels_db,self.labels_ap]
t**s =['DBASE','AP']
for i in range(2):
print 'Algorithm:',t**s[i]
print("\tHomogeneity: %0.3f" % metrics.homogeneity_score(self.labels_gt, algs[i]))
print("\tCompleteness: %0.3f" % metrics.completeness_score(self.labels_gt, algs[i]))
print("\tV-measure: %0.3f" % metrics.v_measure_score(self.labels_gt, algs[i]))
print("\tAdjusted Rand Index: %0.3f"% metrics.adjusted_rand_score(self.labels_gt, algs[i]))
print("\tAdjusted Mutual Information: %0.3f"% metrics.adjusted_mutual_info_score(self.labels_gt, algs[i]))
gmmClusterer = GaussianMixture(n_components=2)
t0 = time()
gmmTrainedLabels = gmmClusterer.fit(Train_Matrix)
gmmTestLabels = gmmClusterer.predict(Test_Matrix)
print(82 * '*')
print("Cluster Means: ", str(gmmClusterer.means_))
print(82 * '-')
print("Cluster Covariance: ", gmmClusterer.covariances_)
print(82 * '-')
print("Precisions: ", str(gmmClusterer.precisions_))
print(82 * '-')
print('Model\t\ttime\thomo\tcompl\tv-meas\tARI \tAMI')
print('%-9s\t%.2fs\t%.3f\t%.3f\t%.3f\t%.3f\t%.3f' %
('GMM', (time() - t0),
metrics.homogeneity_score(Test_Target_Matrix, gmmTestLabels),
metrics.completeness_score(Test_Target_Matrix, gmmTestLabels),
metrics.v_measure_score(Test_Target_Matrix, gmmTestLabels),
metrics.adjusted_rand_score(Test_Target_Matrix, gmmTestLabels),
metrics.adjusted_mutual_info_score(Test_Target_Matrix, gmmTestLabels)))
# plt.scatter(Test_Matrix.iloc[0,:], Test_Matrix.iloc[1,:], color='black')
# # Prediction and draw the diagram
# #plt.plot(range(len(testData)), y_testDataPrediction_tuned, color='red', linewidth=1)
# #plt.legend(["predict", "true"], loc='upper right')
# plt.title('GMM Clustering')
# plt.show()
print '---'
print 'true kappas {}'.format(kappas)
print 'vmf-soft kappas {}'.format(
vmf_soft.concentrations_[[vmf_soft_mu_0_idx, vmf_soft_mu_1_idx]])
print 'vmf-hard kappas {}'.format(
vmf_hard.concentrations_[[vmf_hard_mu_0_idx, vmf_hard_mu_1_idx]])
print '---'
print 'vmf-soft weights {}'.format(
vmf_soft.weights_[[vmf_soft_mu_0_idx, vmf_soft_mu_1_idx]])
print 'vmf-hard weights {}'.format(
vmf_hard.weights_[[vmf_hard_mu_0_idx, vmf_hard_mu_1_idx]])
print '---'
print("Homogeneity: %0.3f (k-means)" %
metrics.homogeneity_score(labels, km.labels_))
print("Homogeneity: %0.3f (spherical k-means)" %
metrics.homogeneity_score(labels, skm.labels_))
print("Homogeneity: %0.3f (vmf-soft)" %
metrics.homogeneity_score(labels, vmf_soft.labels_))
print("Homogeneity: %0.3f (vmf-hard)" %
metrics.homogeneity_score(labels, vmf_hard.labels_))
print '---'
print("Completeness: %0.3f (k-means)" %
metrics.completeness_score(labels, km.labels_))
print("Completeness: %0.3f (spherical k-means)" %
metrics.completeness_score(labels, skm.labels_))
print("Completeness: %0.3f" %
metrics.completeness_score(labels, vmf_soft.labels_))
print("Completeness: %0.3f" %
class_list = []
data_test = np.array(data_test)
index = 0
print (shape(centers))
for i in range (shape(centers)[0]):
best_dist = 9999999
for j in range (shape(data_test)[0]):
dist=0
for k in range(shape(centers)[1]):
dist = dist+((centers[i][k]-data_test[j][k])**2)
dist = (dist)**0.5
if dist<best_dist:
best_dist=dist
index=j
class_list.append(label_test[index])
pred=clusters
for i in range (len(clusters)):
pred[i]=class_list[clusters [i]]
print('Homogeneity score :\n', metrics.homogeneity_score(label_test, pred))
print('F1 score :\n', f1_score(label_test, pred, average=None))
print ('ACCURACY :\n', metrics.classification_report(label_test, pred))
print('Confusion matrix:\n', confusion_matrix(label_test, pred))
def kmeans(principalDf, NbCluster, finalDf):
kmeans = KMeans(n_clusters=3, init='k-means++').fit(principalDf)
KM_clustered = principalDf.copy()
KM_clustered = pd.DataFrame(KM_clustered)
KM_clustered.loc[:, 'Cluster'] = kmeans.labels_ # append labels to points
frames = [finalDf['Analysis'], KM_clustered['Cluster']]
result = pd.concat(frames, axis=1)
print('-' * 60)
print("Kmeans résultat")
print('-' * 60)
print("Shape: {}".format(result.shape))
print(result.sample(5))
# =============================================================================
# Assigning a label to each cluster
# As there's no relation between a cluster number and the true label we need to map a cluster to the one label which appears most in that cluster
#
# These corrected predicted labels are needed below to calculate model performance vs the the true labels
# =============================================================================
print('\n')
for ClusterNum in range(3):
OneCluster = pd.DataFrame(
result[result['Cluster'] == ClusterNum].groupby('Analysis').size())
OneCluster.columns = ['Size']
NewDigit = OneCluster.index[OneCluster['Size'] ==
OneCluster['Size'].max()].tolist()
NewDigit[0]
rowIndex = result.index[result['Cluster'] == ClusterNum]
result.loc[rowIndex, 'TransLabel'] = NewDigit[0]
print(ClusterNum, NewDigit[0])
# =============================================================================
# # Check performance of classification to 3 clusters
# =============================================================================
print('-' * 60)
print('K-Means performance')
print('-' * 60)
Correct = (finalDf['Analysis'] == result['TransLabel']).sum()
Accuracy = round(Correct / finalDf.shape[0], 3)
print('Accuracy ', Accuracy)
# =============================================================================
# # METRICS for clustering algorithms
# =============================================================================
print(
'homogeneity_score: ',
round(
metrics.homogeneity_score(finalDf['Analysis'],
result['TransLabel']), 3))
print(
'completeness_score: ',
round(
metrics.completeness_score(finalDf['Analysis'],
result['TransLabel']), 3))
print(
'v_measure_score: ',
round(
metrics.v_measure_score(finalDf['Analysis'], result['TransLabel']),
3))
print(
'adjusted_rand_score: ',
round(
metrics.adjusted_rand_score(finalDf['Analysis'],
result['TransLabel']), 3))
print(
'adjusted_mutual_info_score: ',
round(
metrics.adjusted_mutual_info_score(finalDf['Analysis'],
result['TransLabel']), 3))
# Step size of the mesh. Decrease to increase the quality of the VQ.
h = .02 # point in the mesh [x_min, x_max]x[y_min, y_max].
# Plot the decision boundary. For that, we will assign a color to each
x_min, x_max = principalDf.to_numpy()[:, 0].min(
) - 1, principalDf.to_numpy()[:, 0].max() + 1
y_min, y_max = principalDf.to_numpy()[:, 1].min(
) - 1, principalDf.to_numpy()[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
np.arange(y_min, y_max, h))
# Obtain labels for each point in mesh. Use last trained model.
Z = kmeans.predict(np.c_[xx.ravel(), yy.ravel()])
# Put the result into a color plot
Z = Z.reshape(xx.shape)
plt.figure(1)
plt.clf()
plt.imshow(Z,
interpolation='nearest',
extent=(xx.min(), xx.max(), yy.min(), yy.max()),
cmap=plt.cm.Paired,
aspect='auto',
origin='lower')
plt.plot(principalDf.to_numpy()[:, 0],
principalDf.to_numpy()[:, 1],
'k.',
markersize=2)
# Plot the centroids as a white X
centroids = kmeans.cluster_centers_
plt.scatter(centroids[:, 0],
centroids[:, 1],
marker='x',
s=169,
linewidths=3,
color='w',
zorder=10)
plt.title('K-means clustering on the digits dataset (PCA-reduced data)\n'
'Centroids are marked with white cross')
plt.xlim(x_min, x_max)
plt.ylim(y_min, y_max)
plt.xticks(())
plt.yticks(())
plt.show()
from sklearn.cluster import KMeans
km3 = KMeans(n_clusters=3, init='k-means++', max_iter=100, n_init=1)
get_ipython().magic('time km3.fit(X_lsa)')
# In[11]:
# How do we know the clustering result is good or not?
# If we have labels available, we can use this to derive how coherent the clusters are.
# Homogeneity: each cluster contains only members of a single class
from sklearn import metrics
labels = subnews['Class']
print("Homogeneity for 3 clusters: %0.3f" %
metrics.homogeneity_score(labels, km3.labels_))
# In[12]:
# Let's try some other K values to compare their metrics
km2 = KMeans(n_clusters=2, init='k-means++', max_iter=100, n_init=1)
get_ipython().magic('time km2.fit(X_lsa)')
km4 = KMeans(n_clusters=4, init='k-means++', max_iter=100, n_init=1)
get_ipython().magic('time km4.fit(X_lsa)')
km5 = KMeans(n_clusters=5, init='k-means++', max_iter=100, n_init=1)
get_ipython().magic('time km5.fit(X_lsa)')
# In[13]:
Score = defaultdict(list)
adjMI = defaultdict(list)
S_homog = defaultdict(list)
S_adjMI = defaultdict(list)
S_vm = defaultdict(list)
for k in clusters:
km.set_params(n_clusters=k)
gmm.set_params(n_components=k)
km.fit(X_scaled)
gmm.fit(X_scaled)
Score['km'].append(km.score(X_scaled))
Score['gmm'].append(gmm.score(X_scaled))
S_homog['km'].append(
metrics.homogeneity_score(labels, km.predict(X_scaled)))
S_homog['gmm'].append(
metrics.homogeneity_score(labels, gmm.predict(X_scaled)))
S_adjMI['km'].append(
metrics.adjusted_mutual_info_score(labels, km.predict(X_scaled)))
S_adjMI['gmm'].append(
metrics.adjusted_mutual_info_score(labels, gmm.predict(X_scaled)))
S_vm['km'].append(metrics.v_measure_score(labels, km.predict(X_scaled)))
S_vm['gmm'].append(metrics.v_measure_score(labels, gmm.predict(X_scaled)))
plt.figure(figsize=(9.6, 7.2))
plt.xlabel('Number of clusters')
plt.ylabel('Score value')
plt.title('Score vs. Cluster number for K-mean and Gaussian Mixture (species)')
plt.grid(True)
#plt.legend(['Train', 'Test'], loc='lower right')
df.max()
df.min()
type(predictors)
#==============================================================================
# Clustering using Kmeans
#==============================================================================
#defining the object that will carry out the kmeans clustering part.
KMeans_object = KMeans(init = 'k-means++', n_clusters = 17, n_init= 10)
#doing the kmeans clustering
KMeans_object.fit(predictors)
#printing the inertia
print('The Inertia is:', KMeans_object.inertia_)
#Calculating the Homogenity score
print('Homogenity Score is:', metrics.homogeneity_score(outcomes, KMeans_object.labels_))
#Calculating the Completeness Score
print('Completeness Score is:', metrics.completeness_score(outcomes, KMeans_object.labels_))
#calculating the V-measure score
print('V-Measure Score is:', metrics.v_measure_score(outcomes, KMeans_object.labels_))
#calculating the adjusted rand score
print('Adjusted Rand Score is:', metrics.adjusted_rand_score(outcomes, KMeans_object.labels_))
#calculating the adjusted mutual information score
print('Adjusted Mututal Info Score is:', metrics.adjusted_mutual_info_score(outcomes, KMeans_object.labels_))
#Calculating the SIlhoutte Score. We are not sampling the dataset to calculate it.
print('Silhoutte Score is:', metrics.silhouette_score(predictors2, KMeans_object.labels_, metric='euclidean'))
def predict_and_cluster(opts,mode):
n_digits = 3
n_samples, n_features = (25,1927)
labels = array([0,1,2,1,1,2,2,1,2,0,0,0,1,1,2,1,1,1,1,1,1,1,1,2,1])
true_k = np.unique(labels).shape[0]
corpus, news = jieba_tokenizer()
print("Extracting features from the training dataset using a sparse vectorizer")
t0 = time()
if opts.use_hashing:
if opts.use_idf:
# Perform an IDF normalization on the output of HashingVectorizer
hasher = HashingVectorizer(n_features=opts.n_features,
stop_words='english', non_negative=True,
norm=None, binary=False)
vectorizer = make_pipeline(hasher, TfidfTransformer())
else:
vectorizer = HashingVectorizer(n_features=opts.n_features,
stop_words='english',
non_negative=False, norm='l2',
binary=False)
else:
vectorizer = TfidfVectorizer(max_df=0.5, max_features=opts.n_features,
min_df=2, stop_words='english',
use_idf=opts.use_idf)
X = vectorizer.fit_transform(corpus)
print("done in %fs" % (time() - t0))
# n_samples: how many articles are there
# n_features: how many different words in all articles are there
print("n_samples: %d, n_features: %d" % X.shape)
print()
if opts.n_components:
print("Performing dimensionality reduction using LSA")
t0 = time()
# Vectorizer results are normalized, which makes KMeans behave as
# spherical k-means for better results. Since LSA/SVD results are
# not normalized, we have to redo the normalization.
svd = TruncatedSVD(opts.n_components)
lsa = make_pipeline(svd, Normalizer(copy=False))
X = lsa.fit_transform(X)
print("done in %fs" % (time() - t0))
svd = TruncatedSVD().fit(X)
X_proj = svd.transform(X)
explained_variances = np.var(X_proj, axis=0) / np.var(X, axis=0).sum()
print("Explained variance of the SVD step: {}%".format(
int(explained_variances[0] * 100)))
print()
# =================================================
# clustering
# if opts.minibatch:
# km = MiniBatchKMeans(n_clusters=true_k, init='k-means++', n_init=1,
# init_size=1000, batch_size=1000, verbose=True)
# else:
km = KMeans(n_clusters=true_k, init='k-means++', max_iter=100, n_init=1,
verbose=True) # always better
print("Clustering sparse data with %s" % km)
t0 = time()
km.fit(X)
print("done in %0.3fs" % (time() - t0))
print()
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels, km.labels_))
print("Completeness: %0.3f" % metrics.completeness_score(labels, km.labels_))
print("V-measure: %0.3f" % metrics.v_measure_score(labels, km.labels_))
print("Adjusted Rand-Index: %.3f"
% metrics.adjusted_rand_score(labels, km.labels_))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(X, labels, sample_size=None))
print()
if not (opts.n_components or opts.use_hashing):
print("Top terms per cluster:")
order_centroids = km.cluster_centers_.argsort()[:, ::-1]
terms = vectorizer.get_feature_names()
for i in range(true_k):
print("Cluster %d:" % i, end='')
for ind in order_centroids[i, :10]:
print(' %s' % terms[ind], end='')
print()
for i in range(len(news)):
news[i].category = labels[i]
from sklearn.metrics.pairwise import cosine_similarity
FG=nx.Graph()
for i in range(len(news)):
news[i].similarity = cosine_similarity(X[i:i+1], X)[0]
cs = news[i].similarity
# print (cs)
for j in range(len(news)):
if i != j:
FG.add_weighted_edges_from([(i,j,cs[j])])
# for i in range(len(news)):
# print(news[i].number, news[i].title, news[i].time, news[i].category, news[i].url, news[i].similarity)
bestpart(FG,labels,km.labels_)
titles = u'原始数据', u'KMeans++聚类', u'旋转后数据', u'旋转后KMeans++聚类',\
u'方差不相等数据', u'方差不相等KMeans++聚类', u'数量不相等数据', u'数量不相等KMeans++聚类'
model = KMeans(n_clusters=4, init='k-means++', n_init=5)
plt.figure(figsize=(9, 10), facecolor='w')
for i, (x, y, title) in enumerate(zip(data_list, y_list, titles), start=1):
plt.subplot(4, 2, i)
plt.title(title)
if i % 2 == 1:
y_pred = y
else:
y_pred = model.fit_predict(x)
model.cluster_centers_
print i
print 'Homogeneity：', homogeneity_score(y, y_pred)
print 'completeness：', completeness_score(y, y_pred)
print 'V measure：', v_measure_score(y, y_pred)
print 'AMI：', adjusted_mutual_info_score(y, y_pred)
print 'ARI：', adjusted_rand_score(y, y_pred)
print 'Silhouette：', silhouette_score(x, y_pred), '\n'
plt.scatter(x[:, 0],
x[:, 1],
c=y_pred,
s=30,
cmap=cm,
edgecolors='none')
x1_min, x2_min = np.min(x, axis=0)
x1_max, x2_max = np.max(x, axis=0)
x1_min, x1_max = expand(x1_min, x1_max)
x2_min, x2_max = expand(x2_min, x2_max)
# use: https://scikit-learn.org/stable/modules/clustering.html#clustering-performance-evaluation
# ADJUSTED RAND SCORE
# https://scikit-learn.org/stable/modules/clustering.html#adjusted-rand-index
print('--> adjusted rand score')
#print('adjusted rand score on training set: {}'.format(metrics.adjusted_rand_score(y_train, y_train_pred)))
#print('adjusted rand score on testing set: {}'.format(metrics.adjusted_rand_score(y_test, y_test_pred)))
print('adjusted rand score: {}'.format(metrics.adjusted_rand_score(y, y_pred)))
# HOMOGENEITY
# https://scikit-learn.org/stable/modules/clustering.html#homogeneity-completeness-and-v-measure
# homogeneity: each cluster contains only members of a single class.
print('--> homogeneity: each cluster contains only members of a single class.')
# print('homogeneity score on training set: {}'.format(metrics.homogeneity_score(y_train, y_train_pred)))
# print('homogeneity score on testing set: {}'.format(metrics.homogeneity_score(y_test, y_test_pred)))
print('homogeneity score: {}'.format(metrics.homogeneity_score(y, y_pred)))
# COMPLETENESS
# https://scikit-learn.org/stable/modules/clustering.html#homogeneity-completeness-and-v-measure
# completeness: all members of a given class are assigned to the same cluster.
print('--> completeness: all members of a given class are assigned to the same cluster.')
# print('completeness score on training set: {}'.format(metrics.completeness_score(y_train, y_train_pred)))
# print('completeness score on testing set: {}'.format(metrics.completeness_score(y_test, y_test_pred)))
print('completeness score: {}'.format(metrics.completeness_score(y, y_pred)))
# FOWLKES MALLOWS SCORES
# https://scikit-learn.org/stable/modules/clustering.html#fowlkes-mallows-scores
print('--> fowlkes mallows score: The Fowlkes-Mallows score FMI is defined as the geometric mean of the pairwise precision and recall.')
# print('fowlkes mallows score on training set: {}'.format(metrics.fowlkes_mallows_score(y_train, y_train_pred)))
# print('fowlkes mallows score on testing set: {}'.format(metrics.fowlkes_mallows_score(y_test, y_test_pred)))
print('fowlkes mallows score: {}'.format(metrics.fowlkes_mallows_score(y, y_pred)))
# -*- coding: utf-8 -*- """ Created on Wed May 2 21:53:10 2018 meanshift with iris data @author: shifuddin """ from load_data import load_csv from sklearn.cluster import MeanShift, estimate_bandwidth from sklearn.metrics import homogeneity_score ''' Load X, y from uri ''' uri = 'https://archive.ics.uci.edu/ml/machine-learning-databases/spect/SPECTF.test' X, y = load_csv(uri, ',', 1, 45, 0, 1, True) ''' Calculate bandwidth / radius of each cluster centroid from data ''' bandwidth = estimate_bandwidth(X, quantile=.1, n_samples=100) ms = MeanShift(bandwidth=bandwidth, bin_seeding=True) ms.fit(X) labels = ms.labels_ centroids = ms.cluster_centers_ homogeneity = homogeneity_score(y.ravel(), labels)
def show_db(label_data,
db,
corpus,
corpus_embeddings,
corpus_file=None,
label_file=None):
if label_file is not None:
# 读取真实标签数据
label_data = pd.read_csv(label_file)
labels_true = label_data.flag.to_list()
labels = db.labels_
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
n_noise_ = list(labels).count(-1)
clustered_sentences = [[] for i in range(n_clusters_)]
if corpus_file is not None:
# 读取原始文本
corpus = pd.read_csv(corpus_file).content.to_list()
for sentence_id, cluster_id in enumerate(labels):
clustered_sentences[cluster_id].append(corpus[sentence_id])
for i, cluster in enumerate(clustered_sentences):
print("Cluster ", i + 1)
print(cluster)
print("")
print('Estimated number of clusters: %d' % n_clusters_)
print('Estimated number of noise points: %d' % n_noise_)
print("Homogeneity: %0.3f" %
metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" %
metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f" %
metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f" %
metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f" %
metrics.silhouette_score(corpus_embeddings, labels))
# #############################################################################
# Plot result
import matplotlib.pyplot as plt
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
# Black removed and is used for noise instead.
unique_labels = set(labels)
colors = [
plt.cm.Spectral(each) for each in np.linspace(0, 1, len(unique_labels))
]
for k, col in zip(unique_labels, colors):
if k == -1:
# Black used for noise.
col = [0, 0, 0, 1]
class_member_mask = (labels == k)
xy = corpus_embeddings[class_member_mask & core_samples_mask]
plt.plot(xy[:, 0],
xy[:, 1],
'o',
markerfacecolor=tuple(col),
markeredgecolor='k',
markersize=14)
xy = corpus_embeddings[class_member_mask & ~core_samples_mask]
plt.plot(xy[:, 0],
xy[:, 1],
'o',
markerfacecolor=tuple(col),
markeredgecolor='k',
markersize=6)
plt.title('Estimated number of clusters: %d' % n_clusters_)
plt.show()
def main():
# initialization
retval = os.getcwd()
corpus_path = retval + "/../vector_model_w_stem/corpus3/"
word_set = {}
term_list = []
num_dimensionality = 25
num_clusters = 5
# get word list for each document
for file_name in os.listdir(corpus_path):
vector = {}
file_path = corpus_path + file_name
for line in open(file_path).read().split("\n"):
word = line.split("\t")[0]
if word:
value = float(line.split("\t")[1])
term_list.append(word)
vector[word] = value
word_set[file_name] = vector
# get term list (vocabulary) based on documents
print("------------------ Parameters Detail ---------------------")
print("The length of total word list: " + str(len(term_list)))
# remove duplicate
term_list = list(set(term_list))
print("Remove duplicate the length of vocabulary: " + str(len(term_list)))
# generate term-document matrix and document list
term_document_matrix = []
doc_list = []
ground_truth = []
for doc_name in word_set.keys():
vector = word_set[doc_name]
ground_truth.append(doc_name.split("-")[0])
term_document_vector = []
for word_voc in term_list:
if word_voc in vector.keys():
value = vector[word_voc]
term_document_vector.append(value)
else:
term_document_vector.append(0)
term_document_matrix.append(term_document_vector)
doc_list.append(doc_name)
print("The number of document: " + str(len(doc_list)))
print("The number of clusters: " + str(num_clusters))
print("The dimensionality: " + str(num_dimensionality))
term_document_matrix = np.array(term_document_matrix).transpose()
# SVD
U, Sigma, V = np.linalg.svd(term_document_matrix)
# dimensionality reduction for each document
doc_matrix_reduced = dimensionality_reduction(Sigma, V, num_dimensionality)
# k-means clustering
km = KMeans(n_clusters=num_clusters)
km.fit(doc_matrix_reduced.transpose())
# evaluate the quality of k-means clustering
print("------------------ Clustering Result ---------------------")
for label in range(0, num_clusters):
for idx in range(0, len(doc_list)):
if km.labels_[idx] == label:
print doc_list[idx] + "\t" + str(km.labels_[idx])
print("------------------- Evaluation Score ---------------------")
print("Homogeneity: %0.3f" %
metrics.homogeneity_score(ground_truth, km.labels_))
print("Completeness: %0.3f" %
metrics.completeness_score(ground_truth, km.labels_))
print("V-measure: %0.3f" %
metrics.v_measure_score(ground_truth, km.labels_))
print("Adjusted Rand-Index: %.3f" %
metrics.adjusted_rand_score(ground_truth, km.labels_))
# visualization the result of clustering
visualization_clustering(doc_matrix_reduced, ground_truth)
print("----------------------- All Set -------------------------")
def ClusterByHDbScan(listtuple_pred_true_text, avgItemsInCluster_in_a_batch):
print("\nClusterByHDbScan")
printClusterEvaluation_list(listtuple_pred_true_text)
print(len(listtuple_pred_true_text), avgItemsInCluster_in_a_batch)
dic_tupple_class_predicted = groupTxtByClass(listtuple_pred_true_text,
False)
numberOfClusters_predicted = len(dic_tupple_class_predicted)
dic_tupple_class_true = groupTxtByClass(listtuple_pred_true_text, True)
numberOfClusters_true = len(dic_tupple_class_true)
print("numberOfClusters_true=" + str(numberOfClusters_true) +
", numberOfClusters_predicted=" + str(numberOfClusters_predicted))
train_data = []
train_predlabels = []
train_trueLabels = []
for pred_true_text in listtuple_pred_true_text:
train_predlabels.append(pred_true_text[0])
train_trueLabels.append(pred_true_text[1])
train_data.append(pred_true_text[2])
vectorizer = TfidfVectorizer(max_df=1.0,
min_df=1,
stop_words='english',
use_idf=True,
smooth_idf=True,
norm='l2')
X = vectorizer.fit_transform(train_data)
svd = TruncatedSVD(2)
normalizer = Normalizer(copy=False)
lsa = make_pipeline(svd, normalizer)
X_svd = lsa.fit_transform(X)
min_cluster_size_in_a_batch = int(math.ceil(avgItemsInCluster_in_a_batch))
min_cluster_size_in_a_batch = 2
clusterer = hdbscan.HDBSCAN(min_cluster_size=min_cluster_size_in_a_batch)
clusterer.fit(X)
X_hdbscan_labels = clusterer.labels_
print("X-total-clusters=" + str(X_hdbscan_labels.max()))
print("Homogeneity: %0.4f" %
metrics.homogeneity_score(train_trueLabels, X_hdbscan_labels))
print("Completeness: %0.4f" %
metrics.completeness_score(train_trueLabels, X_hdbscan_labels))
print("V-measure: %0.4f" %
metrics.v_measure_score(train_trueLabels, X_hdbscan_labels))
print("Adjusted Rand-Index: %.4f" %
metrics.adjusted_rand_score(train_trueLabels, X_hdbscan_labels))
print("nmi_score-whole-data: %0.4f" %
metrics.normalized_mutual_info_score(
train_trueLabels, X_hdbscan_labels, average_method='arithmetic'))
clusterer_svd = hdbscan.HDBSCAN(
min_cluster_size=min_cluster_size_in_a_batch)
clusterer_svd.fit(X_svd)
X_svd_hdbscan_labels = clusterer_svd.labels_
db = DBSCAN().fit(X_svd)
X_svd_dbscan_labels = db.labels_
print("X-svd-total-clusters=" + str(X_svd_hdbscan_labels.max()))
print("Homogeneity: %0.4f" %
metrics.homogeneity_score(train_trueLabels, X_svd_hdbscan_labels))
print("Completeness: %0.4f" %
metrics.completeness_score(train_trueLabels, X_svd_hdbscan_labels))
print("V-measure: %0.4f" %
metrics.v_measure_score(train_trueLabels, X_svd_hdbscan_labels))
print("Adjusted Rand-Index: %.4f" %
metrics.adjusted_rand_score(train_trueLabels, X_svd_hdbscan_labels))
print("nmi_score-whole-data: %0.4f" %
metrics.normalized_mutual_info_score(train_trueLabels,
X_svd_hdbscan_labels,
average_method='arithmetic'))
print("X-svd-dbscan-total-clusters=" + str(X_svd_dbscan_labels.max()))
print("Homogeneity: %0.4f" %
metrics.homogeneity_score(train_trueLabels, X_svd_dbscan_labels))
print("Completeness: %0.4f" %
metrics.completeness_score(train_trueLabels, X_svd_dbscan_labels))
print("V-measure: %0.4f" %
metrics.v_measure_score(train_trueLabels, X_svd_dbscan_labels))
print("Adjusted Rand-Index: %.4f" %
metrics.adjusted_rand_score(train_trueLabels, X_svd_dbscan_labels))
print("nmi_score-whole-data: %0.4f" %
metrics.normalized_mutual_info_score(train_trueLabels,
X_svd_dbscan_labels,
average_method='arithmetic'))
print float(clus.loc[clus.iloc[:,
-1] == 1].shape[0]) / clus.shape[0]
h**o = []
comp = []
v_mea = []
sil = []
man = []
numPoints = 8
for i in range(2, numPoints):
rp = SparseRandomProjection(n_components=6)
projected_data = rp.fit_transform(X)
gm = mixture.GMM(n_components=i, covariance_type='diag')
gm.fit(projected_data)
y_pred = gm.predict(projected_data)
h**o.append(metrics.homogeneity_score(y, y_pred))
comp.append(metrics.completeness_score(y, y_pred))
v_mea.append(metrics.v_measure_score(y, y_pred))
sil.append(
metrics.silhouette_score(projected_data,
gm.predict(projected_data),
metric='euclidean'))
man.append(
metrics.silhouette_score(projected_data,
gm.predict(projected_data),
metric='manhattan'))
x = xrange(2, numPoints)
fig = plt.figure()
plt.plot(x, h**o, label='homogeneity score')
plt.plot(x, comp, label='completeness score')
from sklearn import metrics labels_true = [0, 0, 0, 1, 1, 1] labels_pred = [0, 0, 1, 1, 2, 2] # labels_pred = [1, 1, 0, 0, 3, 3] labels_pred = labels_true[:] # metrics.adjusted_rand_score(labels_true, labels_pred) print metrics.adjusted_rand_score(labels_true, labels_pred) print metrics.adjusted_mutual_info_score(labels_true, labels_pred) print metrics.homogeneity_score(labels_true, labels_pred) print metrics.completeness_score(labels_true, labels_pred)
def analyze_k_means(estimator, name, data):
t0 = time()
estimator.fit(data)
print(" %9s %.2fs %i %.3f %.3f %.3f %.3f %.3f %.3f"%( name, time()-t0, estimator.inertia_, metrics.homogeneity_score(labels, estimator.labels_), metrics.completeness_score(labels, estimator.labels_), metrics.v_measure_score(labels, estimator.labels_), metrics.adjusted_rand_score(labels, estimator.labels_), metrics.adjusted_mutual_info_score(labels, estimator.labels_), metrics.silhouette_score(data, estimator.labels_, metric='euclidean', sample_size = samples) ))
# contrast train data
X_contrast = np.zeros(np.shape(X_train))
for i in range(len(X_contrast)):
image = X_train[i, :]
image = image.astype(np.uint8)
X_contrast[i] = cv2.equalizeHist(image).reshape(1, NUMBER_OF_PIXELS)
# normalize train data
X_contrast = X_contrast.astype('float32') / MAX_BRIGHTNESS - MEAN
X_train = X_train.astype('float32') / MAX_BRIGHTNESS - MEAN
# run kmeans with 19 clusters, as there are 19 letters left in the data
kmeans = KMeans(init="k-means++", n_clusters=19, n_init=4)
# run k-means on full dataset train
kmeans_full = kmeans.fit(X_contrast)
labels = kmeans.predict(X_contrast)
# print number of iterations train data
print('Number of iterations Full Kmeans train data {}'.format(
kmeans_full.n_iter_))
# Print scores full train dataset
print('Homogeneity Score Full Train Dataset: {}'.format(
homogeneity_score(y_train, labels)))
print('Completeness Score Full Train Dataset: {}'.format(
completeness_score(y_train, labels)))
print('V-score Score Full train Dataset: {}'.format(
v_measure_score(y_train, labels)))
def Evaluate_old(listtuple_pred_true_text, ignoreMinusOne=False):
preds = []
trues = []
new_listtuple_pred_true_text = []
totalwords = 0
for pred_true_text in listtuple_pred_true_text:
if str(pred_true_text[1]) == '-1' and ignoreMinusOne == True:
continue
preds.append(pred_true_text[0])
trues.append(pred_true_text[1])
new_listtuple_pred_true_text.append(
[pred_true_text[0], pred_true_text[1], pred_true_text[2]])
totalwords += len(pred_true_text[2])
#print(pred_true_text[2], totalwords)
print("evaluate total texts=" + str(len(new_listtuple_pred_true_text)))
score = metrics.homogeneity_score(trues, preds)
print("homogeneity_score-whole-data: %0.8f" % score)
score = metrics.completeness_score(trues, preds)
print("completeness_score-whole-data: %0.8f" % score)
score = metrics.v_measure_score(trues, preds)
print("v_measure_score-whole-data: %0.8f" % score)
score = metrics.normalized_mutual_info_score(trues,
preds,
average_method='arithmetic')
print("nmi_score-whole-data: %0.8f" % score)
#score=metrics.adjusted_mutual_info_score(trues, preds)
#print ("adjusted_mutual_info_score-whole-data: %0.4f" % score)
#score=metrics.adjusted_rand_score(trues, preds)
#print ("adjusted_rand_score-whole-data: %0.4f" % score)
dic_tupple_class = groupItemsBySingleKeyIndex(new_listtuple_pred_true_text,
0) #before 0
dic_tupple_class_true = groupItemsBySingleKeyIndex(
new_listtuple_pred_true_text, 1) #before 1
print("pred clusters=" + str(len(dic_tupple_class)) + ", true clusters=" +
str(len(dic_tupple_class_true)))
ComputePurity(dic_tupple_class)
li = [
len(dic_tupple_class_true[x]) for x in dic_tupple_class_true
if isinstance(dic_tupple_class_true[x], list)
]
print('min', min(li), 'max', max(li), 'median', statistics.median(li),
'avg', statistics.mean(li), 'std', statistics.stdev(li), 'sum of li',
sum(li))
print('avg words per text', totalwords / len(new_listtuple_pred_true_text),
'totalwords', totalwords, '#texts',
len(new_listtuple_pred_true_text))
'''print("---Pred distribution")
###################################################################
Kclusters = range(2,50,2)
km_sil_scores = []
km_homo_scores = []
km_inertia_scores = []
km_fitness_times = []
for k in Kclusters:
t1 = time.time()
km = KMeans(n_clusters=k, n_init=10,random_state=100,n_jobs=-1).fit(X1)
t2 = time.time()
km_fitness_times.append(t2 - t1)
km_sil_scores.append(silhouette_score(X1, km.labels_))
km_homo_scores.append(homogeneity_score(Y1, km.labels_))
km_inertia_scores.append(km.inertia_)
em_sil_scores = []
em_homo_scores = []
em_aic_scores = []
em_bic_scores = []
em_fitness_times = []
for k in Kclusters:
t1 = time.time()
em = GaussianMixture(n_components=k,covariance_type='diag',n_init=1,warm_start=True,random_state=100).fit(X1)
t2 = time.time()
em_fitness_times.append(t2 - t1)
6: "total sulfur dioxide (mg/dm^3)",
7: "density(g/cm^3)",
8: "pH",
9: "sulphates (g/dm^3)",
10: "alcohol (vol.%)",
11: "quality"
}
wine_2 = wine_2.rename(columns=mapping_2)
wine_2 = wine_2.drop(['quality'], axis=1)
kmeans = KMeans(n_clusters=7, random_state=0).fit(wine_2)
print("For 7 clusters, comparing them to the wine quality:")
print("Silhouette score", metrics.silhouette_score(wine_2, kmeans.labels_))
print("Completeness score",
metrics.completeness_score(wine["quality"], kmeans.labels_))
print("Homogeneity score",
metrics.homogeneity_score(wine["quality"], kmeans.labels_))
#testing cluster sizes
store = []
for i in range(3, 10):
kmeans = KMeans(n_clusters=i, random_state=0).fit(wine_2)
store.append((metrics.silhouette_score(wine_2, kmeans.labels_), i))
plt.scatter([s[1] for s in store], [s[0] for s in store])
plt.xlabel("Clusters")
plt.ylabel("Silhouette score")
plt.savefig("clusters.png")
plt.close()
#graphs showing the groupings obtained
batch_size=1000,
verbose=opts.verbose)
else:
km = KMeans(n_clusters=true_k,
init='k-means++',
max_iter=100,
n_init=1,
verbose=opts.verbose)
print("Clustering sparse data with %s" % km)
t0 = time()
km.fit(X)
print("done in %0.3fs" % (time() - t0))
print()
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels, km.labels_))
print("Completeness: %0.3f" % metrics.completeness_score(labels, km.labels_))
print("V-measure: %0.3f" % metrics.v_measure_score(labels, km.labels_))
print("Adjusted Rand-Index: %.3f" %
metrics.adjusted_rand_score(labels, km.labels_))
print("Silhouette Coefficient: %0.3f" %
metrics.silhouette_score(X, km.labels_, sample_size=1000))
print()
if not opts.use_hashing:
print("Top terms per cluster:")
if opts.n_components:
original_space_centroids = svd.inverse_transform(km.cluster_centers_)
order_centroids = original_space_centroids.argsort()[:, ::-1]
np.sum(evidenceList[allClusters[i] == lowClusterNo[i]] == "N")) # TN
allResults[i][3] = float(
np.sum(evidenceList[allClusters[i] == lowClusterNo[i]] == "Y")) # FN
# Evaluating cluster validation scores
# Each valList element contains [Adjusted Rand, Mutual Info, Adjusted Mutual Info, Normalized Mutual Info, Homogeneity, Completeness, V Measure]
valList = []
for i in range(0, len(allClusters)):
valItem = []
valItem.append(metrics.adjusted_rand_score(evidenceList, allClusters[i]))
valItem.append(metrics.mutual_info_score(evidenceList, allClusters[i]))
valItem.append(
metrics.adjusted_mutual_info_score(evidenceList, allClusters[i]))
valItem.append(
metrics.normalized_mutual_info_score(evidenceList, allClusters[i]))
valItem.append(metrics.homogeneity_score(evidenceList, allClusters[i]))
valItem.append(metrics.completeness_score(evidenceList, allClusters[i]))
valItem.append(metrics.v_measure_score(evidenceList, allClusters[i]))
valList.append(valItem)
# Writing results
statFile = open(
outputLocationStat + inputFileName.split("/")[-1].split(".")[0] + "_" +
algorithm + "_" + method + "_" + distance + "_" + str(noClust) + ".stat",
"w")
for i in range(0, len(allResults)):
statFile.write("# " + allLabels[i] + "\n")
tp = allResults[i][0]
fp = allResults[i][1]
tn = allResults[i][2]
fn = allResults[i][3]
#for each k, calculate the silhouette_coefficient by using: silhouette_score(X_training, kmeans.labels_)
#find which k maximizes the silhouette_coefficient
silhouette_coeff = silhouette_score(X_training, kmeans.labels_)
silhouette_scores[k] = (silhouette_coeff)
#plot the value of the silhouette_coefficient for each k value of kmeans so that we can see the best k
k_value = [x for x in range(2,21)]
plt.plot(silhouette_scores.keys(),silhouette_scores.values(),)
# plt.show()
best_k = dict(sorted(silhouette_scores.items(), key = itemgetter(1), reverse = True)[:1])
#reading the validation data (clusters) by using Pandas library
df1 = pd.read_csv('testing.csv', header=None)
#assign your data labels to vector labels (you might need to reshape the row vector to a column vector)
# do this: np.array(df.values).reshape(1,<number of samples>)[0]
labels = np.array(df1.values).reshape(1,-1)[0]
#Calculate and print the Homogeneity of this kmeans clustering
print("K-Means Homogeneity Score = " + metrics.homogeneity_score(labels, kmeans.labels_).__str__())
#rung agglomerative clustering now by using the best value o k calculated before by kmeans
#Do it:
agg = AgglomerativeClustering(n_clusters=best_k.keys()[0], linkage='ward')
agg.fit(X_training)
# Calculate and print the Homogeneity of this agglomerative clustering
print("Agglomerative Clustering Homogeneity Score = " + metrics.homogeneity_score(labels, agg.labels_).__str__())
# In[ ]:
x = data[['0', '1']].values
x.shape
# In[ ]:
#printing results
print('labels:')
# print(labelsPred)
# tEnd = datetime.datetime.now()
# print('Time: ' + str(tEnd - tStart))
print('Measures:')
print('HS: ' + str(metrics.homogeneity_score(y, labelsPred)))
print('CS: ' + str(metrics.completeness_score(y, labelsPred)))
print('VM: ' + str(metrics.v_measure_score(y, labelsPred)))
print('AMI: ' + str(metrics.adjusted_mutual_info_score(y, labelsPred)))
print('ARI: ' + str(metrics.adjusted_rand_score(y, labelsPred)))
# In[ ]:
import matplotlib.pyplot as plt
from itertools import cycle, islice
fig = plt.figure()
colors = np.array(
list(
islice(
cycle([
X = X.toarray()
#y = np.array(labels)
print "Affinity Clustering..."
print X
##############################################################################
# Compute Affinity Propagation
af = AffinityPropagation().fit(X)
cluster_centers_indices = af.cluster_centers_indices_
labels = af.labels_
n_clusters_ = len(cluster_centers_indices)
print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f"
% metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f"
% metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f"
% metrics.silhouette_score(X, labels, metric='sqeuclidean'))
##############################################################################
# Plot result
import pylab as pl
from itertools import cycle
def calc_measures_avg(measures, n_imgs, ignore_classes, for_final_result):
measures_result = {}
# these measures can just be averaged
for measure in [
Constants.ERRORS, Constants.IOU, Constants.BINARY_IOU,
Constants.AP, Constants.MOTA, Constants.MOTP,
Constants.AP_INTERPOLATED, Constants.FALSE_POSITIVES,
Constants.FALSE_NEGATIVES, Constants.ID_SWITCHES
]:
if measure in measures:
measures_result[measure] = numpy.sum(measures[measure]) / n_imgs
# TODO: This has to be added as IOU instead of conf matrix.
if Constants.CONFUSION_MATRIX in measures:
measures_result[Constants.IOU] = calc_iou(measures, n_imgs,
ignore_classes)
if Constants.CLICKS in measures:
clicks = [
int(x.rsplit(':', 1)[-1]) for x in measures[Constants.CLICKS]
]
measures_result[Constants.CLICKS] = float(numpy.sum(clicks)) / n_imgs
if for_final_result and Constants.DETECTION_AP in measures:
from object_detection.utils.object_detection_evaluation import ObjectDetectionEvaluation
if isinstance(measures[Constants.DETECTION_AP],
ObjectDetectionEvaluation):
evaluator = measures[Constants.DETECTION_AP]
else:
n_classes = measures[Constants.DETECTION_AP][-2]
evaluator = ObjectDetectionEvaluation(n_classes,
matching_iou_threshold=0.5)
evaluator.next_image_key = 0 # add a new field which we will use
_add_aps(evaluator, measures[Constants.DETECTION_AP])
aps, mAP, _, _, _, _ = evaluator.evaluate()
measures_result[Constants.DETECTION_APS] = aps
measures_result[Constants.DETECTION_AP] = mAP
if for_final_result and Constants.CLUSTER_IDS in measures and Constants.ORIGINAL_LABELS in measures:
from sklearn.metrics import adjusted_mutual_info_score, homogeneity_score, completeness_score
labels_true = numpy.reshape(
numpy.array(measures[Constants.ORIGINAL_LABELS],
dtype=numpy.int32), [-1])
labels_pred = numpy.reshape(
numpy.array(measures[Constants.CLUSTER_IDS], dtype=numpy.int32),
[-1])
ami = adjusted_mutual_info_score(labels_true, labels_pred)
measures_result[Constants.ADJUSTED_MUTUAL_INFORMATION] = ami
homogeneity = homogeneity_score(labels_true, labels_pred)
measures_result[Constants.HOMOGENEITY] = homogeneity
completeness = completeness_score(labels_true, labels_pred)
measures_result[Constants.COMPLETENESS] = completeness
NO_EVAL = False
if not NO_EVAL:
if for_final_result and Constants.ORIGINAL_LABELS in measures and Constants.EMBEDDING in measures:
from sklearn import mixture
from sklearn.cluster import KMeans
from sklearn.metrics import adjusted_mutual_info_score, homogeneity_score, completeness_score
embeddings = numpy.array(measures[Constants.EMBEDDING],
dtype=numpy.int32)
embeddings = numpy.reshape(embeddings, [-1, embeddings.shape[-1]])
labels_true = numpy.reshape(
numpy.array(measures[Constants.ORIGINAL_LABELS],
dtype=numpy.int32), [-1])
# n_components = 80
# n_components = 400
# n_components = 1000
n_components = 3000
import time
# start = time.time()
# gmm = mixture.GaussianMixture(n_components=n_components, covariance_type='full')
# gmm.fit(embeddings)
# labels_pred= gmm.predict(embeddings)
# print "gmm took ", time.time()-start
start = time.time()
kmeans = KMeans(n_clusters=n_components, n_jobs=-1)
labels_pred = kmeans.fit_predict(embeddings)
print("km took ", time.time() - start)
ami = adjusted_mutual_info_score(labels_true, labels_pred)
measures_result[Constants.ADJUSTED_MUTUAL_INFORMATION] = ami
homogeneity = homogeneity_score(labels_true, labels_pred)
measures_result[Constants.HOMOGENEITY] = homogeneity
completeness = completeness_score(labels_true, labels_pred)
measures_result[Constants.COMPLETENESS] = completeness
return measures_result
shuffle(shuffleind)
zipper = sorted((zip(shuffleind, reads, read_parent_id)))
z, reads, read_parent_id = (list(t) for t in zip(*zipper))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#HOMOGENEITY AND COMPLETENESS FOR FULL DATASET WITH PREVIOUSLY CALCULATED GOOD_THRESH!
#Find suitable threshold
print("\n\nThreshold approximation:")
good_thresh = find_threshold(50, 15, 40, 1)
print("\n\nFull clustering:")
clus_N, cluster_sizes, read_labels = simplesim_cluster(good_thresh)
print('\n\n~~~~~~~INFO~~~~~~~')
hom = metrics.homogeneity_score(read_parent_id, read_labels)
comp = metrics.completeness_score(read_parent_id, read_labels)
print("Homogeneity: %0f" % hom)
print("Completeness: %0f" % comp)
homogeneity_lst.append(hom)
completeness_lst.append(comp)
print("\nDONE TRIPLICATES LOOP\n")
cluster_eff_lst_lst.append(cluster_eff_lst)
homogeneity_lst_lst.append(homogeneity_lst)
completeness_lst_lst.append(completeness_lst)
#PANDAS DATAFRAME FROM THIS?!
max_features=10000,
min_df=2,
stop_words='english',
use_idf=True)
matrix = vectorizer.fit_transform(dataset.data)
print("n_samples: %d, n_features: %d" % matrix.shape)
print()
#降维
print("Performing dimensionality reduction using LSA")
t0 = time()
svd = TruncatedSVD(2) #维度
normalizer = Normalizer(copy=False)
lsa = make_pipeline(svd, normalizer)
matrix_l = lsa.fit_transform(matrix)
# #############################################################################
# Do the actual clustering
gmm = mixture.GaussianMixture(n_components=50, covariance_type='full')
labels = gmm.fit(matrix_l).predict(matrix_l)
labels_pred = labels
print("Homogeneity: %0.3f" %
metrics.homogeneity_score(labels_ture, labels_pred))
print("Completeness: %0.3f" %
metrics.completeness_score(labels_ture, labels_pred))
print("NMI: %0.3f" % metrics.normalized_mutual_info_score(
labels_ture, labels_pred, average_method='arithmetic'))
ax[1].set_title('Actual Training Labels')
# Show the plots
plt.show()
# Evaluation of Clustering Model
# Import `metrics` from `sklearn`
from sklearn import metrics
# Print out the confusion matrix with `confusion_matrix()`
print(metrics.confusion_matrix(y_test, y_pred))
from sklearn.metrics import homogeneity_score, completeness_score, v_measure_score, adjusted_rand_score, adjusted_mutual_info_score, silhouette_score
print('% 9s' % 'inertia h**o compl v-meas ARI AMI silhouette')
print('%i %.3f %.3f %.3f %.3f %.3f %.3f' %
(clf.inertia_, homogeneity_score(y_test, y_pred),
completeness_score(y_test, y_pred), v_measure_score(
y_test, y_pred), adjusted_rand_score(
y_test, y_pred), adjusted_mutual_info_score(y_test, y_pred),
silhouette_score(X_test, y_pred, metric='euclidean')))
# try out Support Vector Machines
# Import `train_test_split`
from sklearn.cross_validation import train_test_split
# Split the data into training and test sets
X_train, X_test, y_train, y_test, images_train, images_test = train_test_split(
digits.data, digits.target, digits.images, test_size=0.25, random_state=42)
# Import the `svm` model
from sklearn import svm