def crank_feats(fargs):
rss, ccs, lv, installed_in, dfile, nfeatures = fargs
noaa_init(installed_in)
wat = pd.read_csv(dfile).set_index('station')
es = ['e' + str(x) for x in range(0, nfeatures)]
#ccs = [3, 4, 6, 7, 8, 9, 10, 11, 12, 15, 20, 30, 40]
#rss=[0, 1]
prefix='eigen' + str(nfeatures)
#let's do some clustering with the six eigenvectors and see how they hold together
flatnew, nmeans, nstds = flatten(wat[es]) #strictly speaking not necessary since
flatold, omeans, ostds = flatten(wat[lv])
#note: this method flattens wat internally
produce_kmeans_climates(wat, es, ccs, rss, prefix)
for rs in rss:
kf = pd.read_csv(noaafile('climates/' + prefix + '_rs_' + str(rs) + '.csv'))
for cc in ccs:
#this silhouettes thing gobbles memory, I'm guessing because each worker
#creates an entire new metric matrix.
kf['sil_eigen_' + str(cc)] = silhouette_samples(flatnew, kf['vtx'+str(cc)].values)
#pull out silhouette scores on the old metric too, just for fun...
kf['sil_old_' + str(cc)] = silhouette_samples(flatold, kf['vtx'+str(cc)].values)
kf.to_csv(noaafile('climates/' + prefix + '_sil_rs_' + str(rs) + '.csv'), index=False)
def bestRep(dat,labels,outName):
bestExample = []
silSamp = metrics.silhouette_samples(dat, labels)
for num in np.unique(labels):
clusterMask = labels==num
bestExample.append(outName[clusterMask][np.argmax(silSamp[clusterMask])])
return bestExample
def cluster_driver(a_driver):
# print a_driver['DStats']
# print "#############################DStats Above#################################ValueError: zero-size array to reduction operation minimum which has no identity#################"
X = StandardScaler().fit_transform(a_driver['DStats'])
# print X
# print "DStats are.....::" , a_driver['DStats']
# print "X is...........::" ,['AvgDistDel', 'AvgACosDel', 'SDevDistDel', 'SDevACosDel','TotalTime','SkewDistDel','SkewACosDel'] X
# print "############################Scaled X Above###################################################"
# db = KMeans(n_clusters=20,n_jobs = -1).fit(X)
db = DBSCAN(eps=0.45).fit(X)
# core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
# core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
# n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
print "###############################################################################"
# print('Estimated number of clusters: %d' % n_clusters_)
# print 'Count of Predicts::', len(X)
print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, labels,metric="mahalanobis"))
# print "##############################DBSCAN X Below#################################################"
# print X G:/Continuing Education/Research & Presentations/Self - Machine Learning/Kaggle/DriverTelemetricAnalysis-AXA/'
# try:
return (metrics.silhouette_samples(X, labels,metric="mahalanobis")+1)/2
def test_silhouette_samples(self):
result = self.df.metrics.silhouette_samples()
expected = metrics.silhouette_samples(self.data, self.pred)
self.assertTrue(isinstance(result, pdml.ModelSeries))
self.assert_index_equal(result.index, self.df.index)
self.assert_numpy_array_almost_equal(result.values, expected)
def silhouette_analysis(clustering, labels=None):
distance_df = clustering['distance_df']
if labels is None:
labels = clustering['labels']
sample_scores = silhouette_samples(distance_df, metric='precomputed', labels=labels)
score = np.mean(sample_scores)
return sample_scores, score
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 visualize_silhouette_score(X,y_km):
cluster_labels = np.unique(y_km)
n_clusters = cluster_labels.shape[0]
silhouette_vals = metrics.silhouette_samples(X,
y_km,
metric='euclidean')
y_ax_lower, y_ax_upper = 0, 0
yticks = []
for i, c in enumerate(cluster_labels):
c_silhouette_vals = silhouette_vals[y_km == c]
c_silhouette_vals.sort()
y_ax_upper += len(c_silhouette_vals)
color = cm.jet(i / n_clusters)
plt.barh(range(y_ax_lower, y_ax_upper),
c_silhouette_vals,
height=1.0,
edgecolor='none',
color=color)
yticks.append((y_ax_lower + y_ax_upper) / 2)
y_ax_lower += len(c_silhouette_vals)
silhouette_avg = np.mean(silhouette_vals)
plt.axvline(silhouette_avg,
color="red",
linestyle="--")
plt.yticks(yticks, cluster_labels + 1)
plt.ylabel('Cluster')
plt.xlabel('Silhouette coefficient')
plt.show()
def silhouette_original_clusterings(dataset='CB1', neuropil='Antennal_lobe', clusterer_or_k=60):
"""Returns a pandas dataframe with the silhouette index of each cluster member.
The dataframe have columns (cluster_id, member_id, silhouette).
"""
# Read the expression matrix
print('Reading expression matrix')
Xdf = ExpressionDataset.dataset(dset=dataset, neuropil=neuropil).Xdf(index_type='string')
# Generate a flat map cluster_id -> members
print('Finding cluster assignments')
clusters_df, _ = get_original_clustering(dataset=dataset, neuropil=neuropil,
clusterer_or_k=clusterer_or_k)
dfs = []
for cluster_id, members in zip(clusters_df.cluster_id,
clusters_df.original_voxels_in_cluster):
dfs.append(pd.DataFrame({'cluster_id': cluster_id, 'member_id': members}))
members_df = pd.concat(dfs).set_index('member_id').loc[Xdf.index]
# Compute the distance matrix - this must be parameterised
print('Computing distance')
import mkl
mkl.set_num_threads(6)
D = dicedist_metric(Xdf)
# Compute silhouette
# Here we could go for the faster implementation in third_party, if needed
print('Computing silhouette index')
members_df['silhouette'] = silhouette_samples(D.values,
members_df.cluster_id.values,
metric='precomputed')
return (members_df.
reset_index().
rename(columns=lambda col: {'index': 'member_id'}.get(col, col))
[['cluster_id', 'member_id', 'silhouette']])
def cluster_driver(a_driver):
# print a_driver['DStats']
# print "#############################DStats Above##################################################"
X = StandardScaler().fit_transform(a_driver['DStats'])
# print X
# print "DStats are.....::" , a_driver['DStats']
# print "X is...........::" , X
# print "############################Scaled X Above###################################################"
db = DBSCAN(eps=0.6, min_samples=5).fit(X)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
print "###############################################################################"
# print('Estimated number of clusters: %d' % n_clusters_)
# print 'Count of Predicts::', len(X)
# print("Silhouette Coefficient: %0.3f" % metrics.silhouette_score(X, labels))
# print "##############################DBSCAN X Below#################################################"
# print X G:/Continuing Education/Research & Presentations/Self - Machine Learning/Kaggle/DriverTelemetricAnalysis-AXA/'
# try:
return (metrics.silhouette_samples(X, labels)+1)/2
def fit(self, X, y=None, **kwargs):
"""
Fits the model and generates the silhouette visualization.
"""
# TODO: decide to use this method or the score method to draw.
# NOTE: Probably this would be better in score, but the standard score
# is a little different and I'm not sure how it's used.
# Fit the wrapped estimator
self.estimator.fit(X, y, **kwargs)
# Get the properties of the dataset
self.n_samples_ = X.shape[0]
self.n_clusters_ = self.estimator.n_clusters
# Compute the scores of the cluster
labels = self.estimator.predict(X)
self.silhouette_score_ = silhouette_score(X, labels)
self.silhouette_samples_ = silhouette_samples(X, labels)
# Draw the silhouette figure
self.draw(labels)
# Return the estimator
return self
def run_clutering(n_sites,order_dict,sim_mat):
n_clusters = 6
name_file = 'clustering_sil' + str(n_clusters)
output_file = open(name_file,'w')
name_file1 = 'clustering_labels' + str(n_clusters)
output_file1 = open(name_file1,'w')
spectral = cluster.SpectralClustering(n_clusters=n_clusters, \
eigen_solver='arpack',affinity='precomputed')
labels = spectral.fit_predict(sim_mat)
silhouette_avg = metrics.silhouette_score(sim_mat,labels)
output_file.write(" ".join(["aver silhouette_score:",str(silhouette_avg)]))
# Compute the silhouette scores for each sample
sample_silhouette_values = metrics.silhouette_samples(sim_mat, labels)
for siteid in order_dict:
stringa = ' '.join( \
[siteid,
str(sample_silhouette_values[order_dict[siteid]])])
output_file.write(stringa +'\n')
for siteid in order_dict:
stringa = ' '.join( \
[str(siteid),str(labels[order_dict[siteid]])
])
output_file1.write(stringa +'\n')
def calculateNumberOfIdealClusters(maxAmount, corpus):
print "Initializing silhouette analysis"
range_n_clusters = range(2, maxAmount) # max amount of clusters equal to amount of jobs
silhouette_high = 0;
silhouette_high_n_clusters = 2;
for n_clusters in range_n_clusters:
# Initialize the clusterer with n_clusters value
cluster = AgglomerativeClustering(n_clusters=n_clusters, linkage="ward", affinity="euclidean")
cluster_labels = cluster.fit_predict(corpus)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed clusters
silhouette_avg = silhouette_score(corpus, cluster_labels)
print "For n_clusters = %d, the average silhouette_score is: %.5f" % (n_clusters, silhouette_avg)
if (silhouette_avg > silhouette_high):
silhouette_high = silhouette_avg
silhouette_high_n_clusters = n_clusters
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(corpus, cluster_labels)
print ("Highest score = %f for n_clusters = %d" % (silhouette_high, silhouette_high_n_clusters))
return silhouette_high_n_clusters
def get_silhouette(df):
df=df[(df.AB!=".")].copy()
df.loc[:,'AB']=pd.to_numeric(df.loc[:,'AB'])
df.loc[:,'CN']=pd.to_numeric(df.loc[:,'CN'])
tp=df.iloc[0,:].loc['svtype']
[mn_CN, mn_AB]=df.loc[:, ['CN', 'AB']].mean(skipna=True)
[sd_CN, sd_AB]=df.loc[:, ['CN', 'AB']].std(skipna=True)
if df.loc[:,'GT'].unique().size==1:
df.loc[:,'sil_gt_avg']=1
df.loc[:, 'sil_gt']=1
df=df[ ['var_id', 'sample', 'svtype', 'AF', 'GT', 'CN', 'AB', 'sil_gt_avg', 'sil_gt']]
return df
#standardize the 2 dims
if sd_AB>0.01:
df.loc[:, 'AB1']=(df.loc[:,'AB']-mn_AB)/sd_AB
else:
df.loc[:, 'AB1']=df.loc[:, 'AB']
if tp in ['DEL', 'DUP', 'MEI'] or sd_CN>0.01:
df.loc[:, 'CN1']=(df.loc[:,'CN']-mn_CN)/sd_CN
else:
df.loc[:, 'CN1']=df.loc[:, 'CN']
gt_code={'0/0':1, '0/1':2, '1/1':3}
df.loc[:,'gtn']=df.loc[:, 'GT'].map(gt_code)
dist_2d_sq=spatial.distance.squareform(spatial.distance.pdist(df[['AB1', 'CN1']], metric='cityblock'))
df.loc[:, 'sil_gt_avg']=metrics.silhouette_score(dist_2d_sq, df.loc[:, 'gtn'].values, metric='precomputed')
df.loc[:, 'sil_gt']=metrics.silhouette_samples(dist_2d_sq, df.loc[:, 'gtn'].values, metric='precomputed')
df=df[ ['var_id', 'sample', 'svtype', 'AF', 'GT', 'CN', 'AB', 'sil_gt_avg', 'sil_gt']]
return df
def find_clusters(df, k_vals=[4, 9, 16, 25], how='hierarchical'):
'''Find clusters, and if method is k-means run silhouette analysis
to determine the value of k.
Args:
df (data frame): A data frame with normalised expression data.
k_vals (list or range): The range over which to test k.
how ('hierarchical' or 'kmeans'): Clustering method.
Returns:
A list of cluster numbers.
'''
## Don't run the silhouette analysis for hierarchical clustering,
## just calculate the clusters using estimate of k.
if how == 'hierarchical':
k = int(np.sqrt((len(df) / 2.0)))
hc = hac.linkage(df, method='average')
optimal_clusters = hac.fcluster(hc, t=k, criterion='maxclust')
## If method is k-means, run silhouette analysis.
elif how == 'kmeans':
best_combined_score = 0
optimal_k = 2
## Try values of k from range and keep track of optimal k according
## to silhouette score.
for k in k_vals:
km = KMeans(n_clusters=k, random_state=10)
clusters = km.fit_predict(df)
silhouette_avg = silhouette_score(df, clusters)
sample_silhouette_values = silhouette_samples(df, clusters)
above_mean = 0
silhouette_sizes = []
for i in range(k):
ith_cluster_silhouette_values = sample_silhouette_values[clusters == i]
size_cluster_i = ith_cluster_silhouette_values.shape[0]
silhouette_sizes.append(size_cluster_i)
if max(ith_cluster_silhouette_values) > silhouette_avg:
above_mean += 1
## This combined score should pick the best value of k
above_mean_score = float(above_mean) / k
std_score = 1.0/np.std(silhouette_sizes) if np.std(silhouette_sizes) > 1.0 else 1.0
combined_score = (silhouette_avg + above_mean_score + std_score) / 3
## Put the clusters in the new column in the data frame.
if combined_score > best_combined_score:
best_combined_score = combined_score
optimal_k = k
optimal_clusters = clusters
optimal_clusters = [cluster + 1 for cluster in optimal_clusters]
return optimal_clusters
def test_gmm():
sil = pyclust.validate.Silhouette()
sil_score = sil.score(X, ypred, sample_size=None)
print(sil_score[0])
print(sil.sample_scores[:10])
print(silhouette_score(X, ypred, sample_size=None))
print(silhouette_samples(X, ypred)[:10])
def compute_sil_score_vector(filelist): """returns dictionary indexed by num_clusters and values which are vectors of silscore for all samples """ silscore = dict() for f in filelist: y, X = get_labels_features(f) num_clusters = np.unique(y).shape[0] silscore[num_clusters]= sklm.silhouette_samples(X,y) return silscore
def silhouette_samples(clusters, word2vec_model):
labels = []
matrix = []
for i in range(len(clusters)):
words = clusters[i][-1]
_, mat = get_words_matrix(words, word2vec_model)
for j in range(len(mat)):
matrix.append(list(mat[j]))
labels.append(i)
matrix = np.array(matrix)
labels = np.array(labels)
samples_score = metrics.silhouette_samples(matrix, labels)
return labels, samples_score
def grind_kmeans(fargs):
rss, ccs, mus, lv, installed_in, mdat, prefix = fargs
noaa_init(installed_in)
produce_kmeans_climates(mdat, lv, ccs, rss, prefix)
for rs in rss:
kf = pd.read_csv(noaafile('climates/' + prefix + '_rs_' + str(rs) + '.csv'))
for cc in ccs:
#this silhouettes thing gobbles memory, I'm guessing because each worker
#creates an entire new metric matrix.
kf['sil' + str(cc)] = silhouette_samples(mus, kf['vtx'+str(cc)].values, metric='precomputed')
kf.to_csv(noaafile('climates/' + prefix + '_sil_rs_' + str(rs) + '.csv'), index=False)
def plotter_3d(pit, day, clusters, files):
data = pickle.load(open("/usr/local/bee/beemon/beeW/Chris/" + pit + "/" + day + "/clusterdata_" + str(clusters) + "_" + str(files) + "_reduced.p", 'rb'), encoding = 'bytes')
labels = pickle.load(open("/usr/local/bee/beemon/beeW/Chris/" + pit + "/" + day + "/clusterdata_" + str(clusters) + "_" + str(files) + ".pkl", 'rb'), encoding = 'bytes')
try:
if len(labels[0]) < 400:
silhouettes = silhouette_samples(data, labels[0])
print(silhouettes)
print(np.mean(silhouettes))
except Exception:
print("Silhouette scoring cannot be done.")
num1 = int(clusters)
path1 = "Pit:" + pit + " Day:" + day + " Clusters:" + str(clusters) + " Files:" + str(files)
graph_3d(data, num1, path1, labels)
plt.close()
def Silhouette(D,labels,k):
"""
Taken from SKlearn's plot kmeans example
D = matriz de distancia
k = numero de clusters
"""
plt.ion()
fig, ax1 = plt.subplots()
fig.set_size_inches(18, 7)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(D) + (k + 1) * 10])
sample_silhouette_values = metrics.silhouette_samples(D , labels, metric='precomputed')
y_lower = 10
for i in range(k):
ith_cluster_silhouette_values = \
sample_silhouette_values[labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / k)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
y_lower = y_upper + 10
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
silhouette_avg = metrics.silhouette_score(D , labels, metric='precomputed')
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([])
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
plt.suptitle(("Silhouette analysis with n_clusters =",k," and average = ",silhouette_avg),
fontsize=14, fontweight='bold')
plt.show()
def get_silhouette_scores(X, km, nc):
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
cluster_labels = km.labels_
silhouette_avg = silhouette_score(X, cluster_labels)
#print ("For n_clusters =" + str(nc) + "The average silhouette_score is :"
# + str(silhouette_avg))
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
return silhouette_avg, sample_silhouette_values
def identify_accurate_number_of_clusters(self, model, compounds, max_range=3):
silhouette_avg_scores = []
for n_cluster in range(2, max_range):
assigned_cluster = cluster.KMeans(n_clusters=n_cluster,
n_init=20).fit_predict(model)
silhouette_avg = silhouette_score(model, assigned_cluster)
silhouette_avg_scores.append(silhouette_avg)
max_silhouette_score = max(silhouette_avg_scores)
index_max_score = silhouette_avg_scores.index(max_silhouette_score)
final_cluster_num = range(2, max_range)[index_max_score]
final_assigned_cluster = cluster.KMeans(n_init=20,
n_clusters=final_cluster_num).fit_predict(model)
final_sample_sil_vals = silhouette_samples(model, final_assigned_cluster)
return final_assigned_cluster, final_cluster_num, final_sample_sil_vals
def kmeans(cluster_data):
# Data pre-processing
scaler = preprocessing.StandardScaler()
km = KMeans(n_clust, init='random')#random_state=10)
km.fit(cluster_data) #change variable - data with labels
#clf.fit(clusterdata)
#cluster_number = km.predict(scaler.fit_transform(clusterdata))
#cluster_number = clf.predict(clusterdata)
centers = km.cluster_centers_
# Compute the silhouette score
labels = km.labels_
score = metrics.silhouette_score(cluster_data, labels)
sample_score = metrics.silhouette_samples(cluster_data, labels)
sum_of_squares = km.inertia_
return(labels, score, sample_score, centers, sum_of_squares)
def fit_plot_save(k, smoothExprs, day, probeID, geneSymbol, organ, strain, path):
"""
Fit k-means, plot and save results
Arguments
=========
k - no. of clusters
smoothExprs - gene expression rows = genes, columns = day
day - day
probeID - probeID
geneSymbol - geneSymbol
path - path
Returns
=========
None - results are plotted and saved
"""
model = KMeans(n_clusters=k)
model.fit(smoothExprs)
clustCentre = model.cluster_centers_
# Plot results
plot_silhouette(silhouette_samples(smoothExprs, model.labels_), model.labels_)
clust.multi_plot(smoothExprs, clustCentre, day, model.labels_)
# Hierarchical clustering
# Ward + Euclidean
header = ["Cluster%i" % label for label in np.unique(model.labels_)]
hclust = hc.linkage(clustCentre, method='ward', metric='euclidean')
plt.figure(); plt.title("Hclust() Ward + Euclidean")
hc.dendrogram(hclust, color_threshold=0.0, labels=header)
#seed=101
#embedding = tsne.tsne(smoothExprs, no_dims = 3, initial_dims = 20, perplexity = 30.0, seed=seed) # low dimensional embedding
#tsne.plot(embedding, model.labels_)
# Save model
io.save_pickle(os.path.join(path['Clust']['Model'], organ + strain + ".pickle"), model)
# Save Gene/Probe List
geneList = clust.get_gene_list(model.labels_, geneSymbol)
probeList = clust.get_gene_list(model.labels_, probeID)
io.write_list_to_csv(os.path.join(path['Clust']['GeneList'], organ + strain + ".csv"), header, geneList) # Gene list
io.write_list_to_csv(os.path.join(path['Clust']['ProbeList'], organ + strain + ".csv"), header, probeList) # Probe list
# Save Cluster "centres"
dataMatrix = np.hstack((np.array(header)[:, None], clustCentre))
header = list(itertools.chain.from_iterable([["Cluster"], list(day)]))
io.write_to_csv(os.path.join(path['Clust']['Centres'], organ + strain + ".csv"), header, dataMatrix) # Cluster "centres"
# Save Alternate plot
hFig = clust.multi_plot(smoothExprs, clustCentre, day, model.labels_)
io.save_pdf(os.path.join(path['Clust']['Plot'], organ + strain + "2.pdf"), hFig) # Plot
def _internal(cluster_list, affinity_matrix, dist_matrix,
idx, n_jobs, n, queue_y):
for i in range(idx, n, n_jobs):
sp = SpectralClustering(n_clusters=cluster_list[i],
affinity='precomputed',
norm_laplacian=True,
n_init=1000)
sp.fit(affinity_matrix)
save_results_clusters("res_spectral_{:03d}_clust.csv"
.format(cluster_list[i]),
sample_names, sp.labels_)
silhouette_list = silhouette_samples(dist_matrix, sp.labels_,
metric="precomputed")
queue_y[i] = np.mean(silhouette_list)
def main():
X, y = make_blobs(n_samples=150,
n_features=2,
centers=3,
cluster_std=0.5,
shuffle=True,
random_state=0)
km = KMeans(n_clusters=2,
init='k-means++',
n_init=10,
max_iter=300,
tol=1e-04,
random_state=0)
y_km = km.fit_predict(X)
cluster_labels = np.unique(y_km)
n_clusters = cluster_labels.shape[0]
silhouette_vals = silhouette_samples(X,
y_km, metric='euclidean')
y_ax_lower, y_ax_upper = 0, 0
yticks = []
for i, c in enumerate(cluster_labels):
c_silhouette_vals = silhouette_vals[y_km == c]
c_silhouette_vals.sort()
y_ax_upper += len(c_silhouette_vals)
color = cm.jet(i / n_clusters)
plt.barh(range(y_ax_lower, y_ax_upper),
c_silhouette_vals,
height=1.0,
edgecolor='none',
color=color)
yticks.append((y_ax_lower + y_ax_upper) / 2)
y_ax_lower += len(c_silhouette_vals)
silhouette_avg = np.mean(silhouette_vals)
plt.axvline(silhouette_avg,
color='red',
linestyle='--')
plt.yticks(yticks, cluster_labels + 1)
plt.ylabel('Cluster')
plt.xlabel('Silhouette Coefficient')
plt.show()
return
def eval_silhouette(self, verbose=True):
"""Evaluate each estimator via silhouette score."""
for k in self.n_clusters:
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
cluster_labels = self.estimators[k].labels_
results = munch.Munch()
results.silhouette_avg = silhouette_score(self.X, cluster_labels)
if verbose:
print("For n_clusters = {k} The average silhouette_score is : {avg_sil}".format(k=k, avg_sil=results.silhouette_avg))
# Compute the silhouette scores for each sample
results.sample_silhouette_values = silhouette_samples(self.X, cluster_labels)
self.silhouette_results[k] = results
def silhouette_clusters(data, clusters):
"""
:param data: n*d where n is the number of observations and d the dimensions of
each observation
:param clusters: an array of length n
compute silhoutte score for every cluster
"""
silhouette_samples_score = metrics.silhouette_samples(data, clusters, metric='euclidean')
values_possible = np.unique(clusters)
silhouette_mean_clusters = np.zeros((1, len(values_possible)))
k = 0
for i in values_possible:
index = np.where(clusters == i)
silhouette_mean_clusters[k] = np.mean(silhouette_samples_score[index])
k += 1
return silhouette_mean_clusters
def optimum_clusters(range_n_clusters,y):
logger.info('Start deciding Optimum Number of Clusters')
dic = {}
for n_clusters in range_n_clusters:
s_cluster = []
cluster = KMeans(n_clusters=n_clusters, random_state=10) # # Create a subplot with 1 row and 2 columns
cluster_labels = cluster.fit_predict(y)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
#silhouette_avg = silhouette_score(y, cluster_labels)
#print("For n_clusters =", n_clusters, "The average silhouette_score is :", silhouette_avg)
# centers = cluster.cluster_centers_
# print (centers)
sample_silhouette_values = silhouette_samples(y, cluster_labels)
for i in range(n_clusters):
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
s_cluster.append(size_cluster_i)
mean_s = np.mean(s_cluster)
mse = 0
for j in s_cluster:
mse = mse+(s_cluster[j] - mean_s)**2
dic[n_clusters] = mse
#print (dic)
min_d = min(dic, key=dic.get)
logger.info('Optimum number of Clusters Decided')
return (min_d)
def silhouette_analysis(self):
if not self.pca_reduced:
self.pc_analysis()
range_n_clusters = range(2, 10)
for n_clusters in range_n_clusters:
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(self.pca_reduced) + (n_clusters + 1) * 10])
clusterer = KMeans(n_clusters=n_clusters, random_state=10)
cluster_labels = clusterer.fit_predict(self.pca_reduced)
silhouette_avg = silhouette_score(self.pca_reduced, cluster_labels)
print("For n_clusters =", n_clusters, "the average silhouette_score is :", silhouette_avg)
sample_silhouette_values = silhouette_samples(self.pca_reduced, cluster_labels)
y_lower = 10
for i in range(n_clusters):
ith_cluster_silhouette_values = sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper), 0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
y_lower = y_upper + 10
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([])
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
colors = cm.spectral(cluster_labels.astype(float) / n_clusters)
ax2.scatter(self.pca_reduced[:, 0], self.pca_reduced[:, 1], marker='.', s=30, lw=0, alpha=0.7, c=colors)
centers = clusterer.cluster_centers_
ax2.scatter(centers[:, 0], centers[:, 1], marker='o', c="white", alpha=1, s=200)
for i, c in enumerate(centers):
ax2.scatter(c[0], c[1], marker='$%d$' % i, alpha=1, s=50)
ax2.set_title("The visualization of the clustered data.")
ax2.set_xlabel("Feature space for the 1st feature")
ax2.set_ylabel("Feature space for the 2nd feature")
plt.suptitle(("Silhouette analysis for KMeans clustering on sample data "
"with n_clusters = %d" % n_clusters),
fontsize=14, fontweight='bold')
def k_medoids_over_instances(self,
dataset,
cols,
k,
distance_metric,
max_iters,
n_inits=5,
p=1):
# If we set it to default we use the pyclust package...
temp_dataset = dataset[cols]
if distance_metric == 'default':
km = pyclust.KMedoids(n_clusters=k, n_trials=n_inits)
km.fit(temp_dataset.as_matrix())
cluster_assignment = km.labels_
else:
self.p = p
cluster_assignment = []
best_silhouette = -1
# Compute all distances
D = self.compute_distance_matrix_instances(temp_dataset,
distance_metric)
for it in range(0, n_inits):
# First select k random points as centers:
centers = random.sample(range(0, len(dataset.index)), k)
prev_centers = []
points_to_cluster = []
n_iter = 0
while (n_iter < max_iters) and not (centers == prev_centers):
n_iter += 1
prev_centers = centers
# Assign points to clusters.
points_to_centroid = D[centers].idxmin(axis=1)
new_centers = []
for i in range(0, k):
# And find the new center that minimized the sum of the differences.
best_center = D.ix[points_to_centroid == centers[i],
points_to_centroid ==
centers[i]].sum().idxmin(axis=1)
new_centers.append(best_center)
centers = new_centers
# Convert centroids to cluster numbers:
points_to_centroid = D[centers].idxmin(axis=1)
current_cluster_assignment = []
for i in range(0, len(dataset.index)):
current_cluster_assignment.append(
centers.index(points_to_centroid.ix[i, :]))
silhouette_avg = silhouette_score(
temp_dataset, np.array(current_cluster_assignment))
if silhouette_avg > best_silhouette:
cluster_assignment = current_cluster_assignment
best_silhouette = silhouette_avg
# And add the clusters and silhouette scores to the dataset.
dataset['cluster'] = cluster_assignment
silhouette_avg = silhouette_score(temp_dataset,
np.array(cluster_assignment))
silhouette_per_inst = silhouette_samples(temp_dataset,
np.array(cluster_assignment))
dataset['silhouette'] = silhouette_per_inst
return dataset
def kmeans_base_clustering(corr: Union[np.ndarray, pd.DataFrame],
names_features: list = None,
max_num_clusters: int = 10,
**kwargs: Any) -> (pd.DataFrame, dict, pd.Series):
"""
Perform base clustering with Kmeans.
Arguments
---------
corr: numpy.array or pd.DataFrame
Correlation matrix.
names_features : list of str
List of names for features.
max_num_clusters: int
Maximum number of clusters.
**kwargs
Arbitrary keyword arguments for sklearn.cluster.KMeans().
Returns
-------
pd.DataFrame
Clustered correlation matrix.
dictionary
List of clusters and their content.
pd.Series
Silhouette scores.
Notes
-----
Function adapted from "Machine Learning for Asset Managers",
Marcos López de Prado (2020).
To learn more about sklearn.cluster.KMeans():
https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html#sklearn.cluster.KMeans
"""
# Initializations
corr = pd.DataFrame(data=corr,
index=names_features,
columns=names_features)
silh_score = pd.Series()
# Define the observations matrix
Xobs = (((1 - corr.fillna(0)) / 2.)**.5).values
# Modify it to get an Euclidean distance matrix
X = np.zeros(shape=Xobs.shape)
for i, j in itertools.product(range(X.shape[0]), range(X.shape[1])):
X[i, j] = np.sqrt(sum((Xobs[i, :] - Xobs[j, :])**2))
X = pd.DataFrame(data=X, index=names_features, columns=names_features)
# Loop to generate different numbers of clusters
for i in range(2, max_num_clusters + 1):
# Define model and fit
kmeans_current = cluster.KMeans(n_clusters=i, **kwargs).fit(X)
# Compute silhouette score
silh_current = silhouette_samples(X, kmeans_current.labels_)
# Compute clustering quality q (t-statistic of silhouette score)
quality_current = silh_current.mean() / silh_current.std()
quality = silh_score.mean() / silh_score.std()
# Keep best quality scores and clustering
if np.isnan(quality) or (quality_current > quality):
silh_score = silh_current
kmeans = kmeans_current
# Extract index according to sorted labels
new_idx = np.argsort(kmeans.labels_)
# Reorder rows and columns
clustered_corr = corr.iloc[new_idx]
clustered_corr = clustered_corr.iloc[:, new_idx]
# Form clusters
clusters = {
i: clustered_corr.columns[np.where(kmeans.labels_ == i)[0]].tolist()
for i in np.unique(kmeans.labels_)
}
# Define a series with the silhouette score
silh_score = pd.Series(silh_score, index=X.index)
return clustered_corr, clusters, silh_score
def cluster_observation_matrix(X: pd.DataFrame,
n_clust_range: range,
model: cluster,
verbose: bool = True,
**kwargs: Any) -> (dict, dict):
"""
Apply clustering for an arbitrary model as long as the model has an argument 'n_clusters'.
Parameters
----------
X : pd.DataFrame
The Observation matrix on which the clustering is based.
n_clust_range: range
Range of integer values for the number of clusters to be tested.
model : sklearn.cluster
The clustering model to be used from sklearn.
verbose : bool
Verbose option.
**kwargs :
Arguments for the clustering model.
Returns
-------
dict
Labels corresponding to the different clusters.
dict
Quality corresponding to the different clusters.
Notes
-----
To learn more about sklearn.cluster:
https://scikit-learn.org/stable/modules/classes.html?highlight=cluster#module-sklearn.cluster
"""
# Checks
if min(n_clust_range) < 2:
raise AssertionError(
"Argument n_clust_range must have values starting at values >= 2.")
# Initialization
save_labels = {}
save_quality = {}
n_clust_range_min = n_clust_range[0]
n_clust_range_max = n_clust_range[-1]
n_clust_range_step = int(n_clust_range[-1] - n_clust_range[-2])
# Looping
for k in n_clust_range:
# Build clusters
fitted_model = model(n_clusters=k, **kwargs).fit(X)
save_labels[k] = fitted_model.labels_.tolist()
# Compute scores
silh = silhouette_samples(X, fitted_model.labels_)
save_quality[k] = silh.mean() / silh.std()
# Plot qualities
if verbose:
plt.xticks(ticks=n_clust_range)
plt.plot(n_clust_range, list(save_quality.values()))
# Make it cute
plt.title("Normalized Silhouette Score")
plt.xlabel("Number of clusters")
plt.ylabel("Score")
# Make bars containing the clusters composition
m = len(save_labels)
assert (m == len(n_clust_range))
bars = np.zeros(shape=(m, n_clust_range_max))
# Loop over max number of clusters
for k in n_clust_range:
# Count appearing values
count_vals = []
for j in range(n_clust_range_max):
count_vals.append(int(save_labels[k].count(j)))
# Distribute these values to build bars
for i in range(n_clust_range_max):
bars[(k - n_clust_range_min) // n_clust_range_step,
i] = count_vals[i]
# Plot clusters compositions with bar plot
if verbose:
plt.figure(figsize=(10, 5))
m = bars.shape[0]
sum_bars = [0] * m
for i in range(n_clust_range_max):
if i > 0:
sum_bars += bars[:, i - 1]
plt.bar(n_clust_range, bars[:, i], width=0.8, bottom=sum_bars)
# Make it cute
plt.xticks(ticks=n_clust_range)
plt.title("Composition of clusters")
plt.xlabel("Number of clusters")
plt.ylabel("Composition")
# Return labels
return save_labels, save_quality
def sample_silhouette_score(self, x, cluster_clients):
self.sample_silh_score = silhouette_samples(x, cluster_clients)
def SilhouetteScores(vectors, mode, cluster_range, view, output):
"""
Compute silhouette and elbow method (nltk/sklearn) for range of clusters
param1: array of vecotors (3 dimensions)
param2: mode ('nltk'/'sklearn'/'agglomerative')
param3: list/range of number of clusters
param4: output path of figure (needs {} to format number of clusters)
output: tupel of two dicts with elbow and silhouette scores (nltk/sklearn),
dict with silhouette scores (agglomerative)
"""
if mode.lower() == "nltk":
rng = random.Random()
rng.seed(123)
wcss = {} # for elbow method
s_scores = {} # for silhouette scores
for NUM_CLUSTERS in tqdm(cluster_range):
kclusterer = KMeansClusterer(
NUM_CLUSTERS,
distance=nltk.cluster.util.cosine_distance,
repeats=25,
rng=rng,
avoid_empty_clusters=True)
labels = kclusterer.cluster(vectors, assign_clusters=True)
# elbow method
# the centroids: kclusterer.means()
centroid_array = np.vstack(
[kclusterer.means()[label] for label in labels])
wcss[NUM_CLUSTERS] = nltk_inertia(vectors, centroid_array)
# silhouette scores
if 1 < NUM_CLUSTERS:
silhouette_s = metrics.silhouette_samples(vectors,
labels,
metric='cosine')
ss_max = max(silhouette_s)
ss_min = min(silhouette_s)
ss_mean = float(sum(silhouette_s) / len(silhouette_s))
s_scores[NUM_CLUSTERS] = (ss_max, ss_min, ss_mean)
# plotting
scatterplot3D(vectors,
color=labels,
view=view,
output=output.format(NUM_CLUSTERS))
return (wcss, s_scores)
elif mode.lower() == "sklearn":
wcss = {} # for elbow method
s_scores = {} # for silhouette scores
for NUM_CLUSTERS in tqdm(cluster_range):
kmeans = cluster.KMeans(n_clusters=NUM_CLUSTERS,
n_init=25,
random_state=42)
kmeans.fit(vectors) # compute k-means clustering
labels = kmeans.labels_
# elbow method
wcss[NUM_CLUSTERS] = kmeans.inertia_
# silhouette scores
if 1 < NUM_CLUSTERS:
silhouette_s = metrics.silhouette_samples(vectors,
labels,
metric='euclidean')
ss_max = max(silhouette_s)
ss_min = min(silhouette_s)
ss_mean = float(sum(silhouette_s) / len(silhouette_s))
s_scores[NUM_CLUSTERS] = (ss_max, ss_min, ss_mean)
# plotting
scatterplot3D(vectors,
color=labels,
view=view,
output=output.format(NUM_CLUSTERS))
return (wcss, s_scores)
elif mode.lower() == "agglomerative":
s_scores = {}
for NUM_CLUSTERS in tqdm(cluster_range):
agglo = cluster.AgglomerativeClustering(n_clusters=NUM_CLUSTERS)
agglo.fit(vectors) # compute k-means clustering
labels = agglo.labels_
# silhouette scores
if 1 < NUM_CLUSTERS:
silhouette_s = metrics.silhouette_samples(vectors,
labels,
metric='euclidean')
ss_max = max(silhouette_s)
ss_min = min(silhouette_s)
ss_mean = float(sum(silhouette_s) / len(silhouette_s))
s_scores[NUM_CLUSTERS] = (ss_max, ss_min, ss_mean)
# plotting
scatterplot3D(vectors,
color=labels,
view=view,
output=output.format(NUM_CLUSTERS))
return s_scores
ax1.set_ylim([0, len(X) + (n_clusters + 1) * 10])
# Initialize the clusterer with n_clusters value and a random generator
# seed of 10 for reproducibility.
clusterer = KMeans(n_clusters=n_clusters, random_state=10)
cluster_labels = clusterer.fit_predict(X)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters =", n_clusters, "The average silhouette_score is :",
silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
def calculateSilhouetteScore(self, dataFile):
"""Calculate the silhouette score for different numbers of clusters.
:param self: An instance of the class SilhouetteScore.
:param dataFile: An array with the input data points.
:return: A list with the names of the image files created.
"""
instanceKmeans = KmeansRunner()
X = instanceKmeans.retrieveData(dataFile)
if (X.shape[0] > 10000):
size = round(X.shape[0] * 0.001)
idx = np.random.randint(X.shape[0], size=size)
subset = X[idx, :]
X = subset
range_n_clusters = [2, 3, 4, 5, 6]
list_images = []
for n_clusters in range_n_clusters:
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(X) + (n_clusters + 1) * 10])
clusterer = KMeans(n_clusters=n_clusters, random_state=10)
cluster_labels = clusterer.fit_predict(np.array(X))
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(n_clusters):
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
y_lower = y_upper + 10
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([])
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
colors = cm.spectral(cluster_labels.astype(float) / n_clusters)
ax2.scatter(X[:, 0], X[:, 1], marker=".", s=30, lw=0, alpha=0.7,
c=colors)
centers = clusterer.cluster_centers_
ax2.scatter(centers[:, 0], centers[:, 1],
marker="o", c="white", alpha=1, s=200)
for i, c in enumerate(centers):
ax2.scatter(c[0], c[1], marker="$%d$" % i, alpha=1, s=50)
ax2.set_title("The visualization of the clustered data.")
ax2.set_xlabel("Feature space for the 1st feature")
ax2.set_ylabel("Feature space for the 2nd feature")
plt.suptitle(("Silhouette analysis for k-means"
"clustering on sample data "
"with n_clusters = %d" % n_clusters),
fontsize=14, fontweight="bold")
fig.savefig("cluster_" + str(n_clusters) + ".png")
list_images.append("cluster_" + str(n_clusters) + ".png")
return list_images
def silhouette(dataset, n):
range_n_clusters = [2, 3, 4, 5, 6, 7, 8, 9, 10]
if n < 5:
range_n_clusters = [2, 3, 4, 5, 6, 7]
for n_clusters in range_n_clusters:
# Create a subplot with 1 row and 2 columns
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
# The 1st subplot is the silhouette plot
# The silhouette coefficient can range from -1, 1 but in this example all
# lie within [-0.1, 1]
ax1.set_xlim([-0.1, 1])
# The (n_clusters+1)*10 is for inserting blank space between silhouette
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(dataset) + (n_clusters + 1) * 10])
# Initialize the clusterer with n_clusters value and a random generator
# seed of 10 for reproducibility.
clusterer = KMeans(n_clusters=n_clusters, random_state=10)
cluster_labels = clusterer.fit_predict(dataset)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(dataset, cluster_labels)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(dataset, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
# The vertical line for average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([]) # Clear the yaxis labels / ticks
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
# 2nd Plot showing the actual clusters formed
colors = cm.nipy_spectral(cluster_labels.astype(float) / n_clusters)
ax2.scatter(dataset[:, 0],
dataset[:, 1],
marker='.',
s=30,
lw=0,
alpha=0.7,
c=colors,
edgecolor='k')
# Labeling the clusters
centers = clusterer.cluster_centers_
# Draw white circles at cluster centers
ax2.scatter(centers[:, 0],
centers[:, 1],
marker='o',
c="white",
alpha=1,
s=200,
edgecolor='k')
for i, c in enumerate(centers):
ax2.scatter(c[0],
c[1],
marker='$%d$' % i,
alpha=1,
s=50,
edgecolor='k')
ax2.set_title("The visualization of the clustered data.")
ax2.set_xlabel("Feature space for the 1st feature")
ax2.set_ylabel("Feature space for the 2nd feature")
plt.suptitle(
("Silhouette analysis for KMeans clustering on sample data "
"with n_clusters = %d" % n_clusters),
fontsize=14,
fontweight='bold')
plt.show()
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(peopleMatrixPcaTransform) + (n_clusters + 1) * 10])
# Initialize the clusterer with n_clusters value and a random generator
# seed of 10 for reproducibility.
clusterer = KMeans(n_clusters=n_clusters, random_state=10)
cluster_labels = clusterer.fit_predict(peopleMatrixPcaTransform)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = metrics.silhouette_score(peopleMatrixPcaTransform,
cluster_labels)
# Compute the silhouette scores for each sample
sample_silhouette_values = metrics.silhouette_samples(
peopleMatrixPcaTransform, cluster_labels)
# The score is bounded between -1 for incorrect clustering and +1 for highly dense clustering.
# Scores around zero indicate overlapping clusters.
# The score is higher when clusters are dense and well separated, which relates to a standard concept of a cluster.
print(
"\n\n\nFor n_clusters =", n_clusters,
"\n\nThe average silhouette_score is :", silhouette_avg,
"\n\n* The silhouette score is bounded between -1 for incorrect clustering and +1 for highly dense clustering.",
"\n* Scores around zero indicate overlapping clusters.",
"\n* The score is higher when clusters are dense and well separated, which relates to a standard concept of a cluster",
"\n\nThe individual silhouette scores were :",
sample_silhouette_values, "\n\nAnd their assigned clusters were :",
cluster_labels,
"\n\nWhich correspond to : 'Jane', 'Bob', 'Mary', 'Mike', 'Alice', 'Skip', 'Kira', 'Moe', 'Sara', and 'Tom'"
def __plot_clusters_onto_2D(self,
clusterer,
X,
dim_reduction_method,
perplexity,
plot=False):
"""
For high dimensional data, use t-SNE to reduce the dimensionality and plot result
on a 2D plane.
Args:
perplexity: The perplexity is related to the number of nearest neighbors that is used
in other manifold learning algorithms. Larger datasets usually require a
larger perplexity. Consider selecting a value between 5 and 50. The choice
is not extremely critical since t-SNE is quite insensitive to this parameter.
"""
if hasattr(clusterer, 'predict'):
cluster_labels = clusterer.predict(X)
else:
cluster_labels = clusterer.labels_
if len(set(cluster_labels)) == 1:
print(
"clustering failed. unable to group data into two more clusters."
)
return
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(X, cluster_labels)
n_clusters = clusterUtilities.get_n_clusters(clusterer)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
if plot is True:
cmap = cm.get_cmap("CMRmap")
# Create a subplot with 1 row and 2 columns
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
# The 1st subplot is the silhouette plot
# The silhouette coefficient can range from -1, 1 but in this example all
# lie within [-0.1, 1]
ax1.set_xlim([-0.1, 1])
# The (n_clusters+1)*10 is for inserting blank space between silhouette
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(X) + (n_clusters + 1) * 10])
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
# cm.spectral has been removed since matplotlib 2.2
#color = cm.spectral(float(i) / n_clusters)
color = cmap(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
# The vertical line for average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([]) # Clear the yaxis labels / ticks
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
# map X (high dimensional) to 2D
if X.shape[1] > 2:
# reduce the dimensionality of input data to 2D
if dim_reduction_method == DIM_REDUCTION_METHOD_KERNEL_PCA:
kpca = KernelPCA(n_components=2,
kernel="rbf",
gamma=10,
random_state=0)
X = kpca.fit_transform(X)
else:
tsne = manifold.TSNE(n_components=2,
perplexity=perplexity,
init='pca',
random_state=0)
X = tsne.fit_transform(X)
# 2nd Plot showing the actual clusters formed
colors = cmap(cluster_labels.astype(float) / n_clusters)
ax2.scatter(X[:, 0],
X[:, 1],
marker='.',
s=100,
lw=0,
alpha=0.7,
c=colors,
edgecolor='k')
ax2.set_title(
"The visualization of the clustered data({}).".format(
dim_reduction_method))
ax2.set_xlabel("reduced feature space of 1st dimension")
ax2.set_ylabel("reduced feature space of 2nd dimension")
plt.suptitle(("Silhouette analysis for clustering methods "
"with n_clusters = %d" % n_clusters),
fontsize=14,
fontweight='bold')
plt.show()
def plot_silhouette(clf, X, title='Silhouette Analysis', metric='euclidean', copy=True, ax=None,
figsize=None, title_fontsize="large", text_fontsize="medium"):
"""Plots silhouette analysis of clusters using fit_predict.
Args:
clf: Clusterer instance that implements ``fit`` and ``fit_predict`` methods.
X (array-like, shape (n_samples, n_features)):
Data to cluster, where n_samples is the number of samples and
n_features is the number of features.
title (string, optional): Title of the generated plot. Defaults to "Silhouette Analysis"
metric (string or callable, optional): The metric to use when calculating distance
between instances in a feature array. If metric is a string, it must be one of
the options allowed by sklearn.metrics.pairwise.pairwise_distances. If X is
the distance array itself, use "precomputed" as the metric.
copy (boolean, optional): Determines whether ``fit`` is used on **clf** or on a
copy of **clf**.
ax (:class:`matplotlib.axes.Axes`, optional): The axes upon which to plot
the learning curve. If None, the plot is drawn on a new set of axes.
figsize (2-tuple, optional): Tuple denoting figure size of the plot e.g. (6, 6).
Defaults to ``None``.
title_fontsize (string or int, optional): Matplotlib-style fontsizes.
Use e.g. "small", "medium", "large" or integer-values. Defaults to "large".
text_fontsize (string or int, optional): Matplotlib-style fontsizes.
Use e.g. "small", "medium", "large" or integer-values. Defaults to "medium".
Returns:
ax (:class:`matplotlib.axes.Axes`): The axes on which the plot was drawn.
Example:
>>> import scikitplot.plotters as skplt
>>> kmeans = KMeans(n_clusters=4, random_state=1)
>>> skplt.plot_silhouette(kmeans, X)
<matplotlib.axes._subplots.AxesSubplot object at 0x7fe967d64490>
>>> plt.show()
.. image:: _static/examples/plot_silhouette.png
:align: center
:alt: Silhouette Plot
"""
if copy:
clf = clone(clf)
cluster_labels = clf.fit_predict(X)
n_clusters = len(set(cluster_labels))
silhouette_avg = silhouette_score(X, cluster_labels, metric=metric)
sample_silhouette_values = silhouette_samples(X, cluster_labels, metric=metric)
if ax is None:
fig, ax = plt.subplots(1, 1, figsize=figsize)
ax.set_title(title, fontsize=title_fontsize)
ax.set_xlim([-0.1, 1])
ax.set_ylim([0, len(X) + (n_clusters + 1) * 10 + 10])
ax.set_xlabel('Silhouette coefficient values', fontsize=text_fontsize)
ax.set_ylabel('Cluster label', fontsize=text_fontsize)
y_lower = 10
for i in range(n_clusters):
ith_cluster_silhouette_values = sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax.fill_betweenx(np.arange(y_lower, y_upper),
0, ith_cluster_silhouette_values,
facecolor=color, edgecolor=color, alpha=0.7)
ax.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i), fontsize=text_fontsize)
y_lower = y_upper + 10
ax.axvline(x=silhouette_avg, color="red", linestyle="--",
label='Silhouette score: {0:0.3f}'.format(silhouette_avg))
ax.set_yticks([]) # Clear the y-axis labels / ticks
ax.set_xticks(np.arange(-0.1, 1.0, 0.2))
ax.tick_params(labelsize=text_fontsize)
ax.legend(loc='best', fontsize=text_fontsize)
return ax
def perform_silhouette_analysis(path, segment_lengths, range_nclusters,
plot_silhouette):
for iseg_length in segment_lengths:
print("Segment Length = " + str(iseg_length))
if plot_silhouette:
fig = plt.figure(1)
df_features = pd.read_csv(
os.path.join(
path,
"Data/length" + str(iseg_length) + "/segment_features.csv"))
#df_xys = pd.read_csv(os.path.join(path, "Data/length" + str(iseg_length) + "/segment_xys.csv"))
numpy_features = df_features.iloc[:, 4:12].values
#fit kmeans
features_scaled = preprocessing.scale(numpy_features)
plot_index = 0
for n_clusters in range_nclusters:
if plot_silhouette:
plot_index = plot_index + 1
ax1 = plt.subplot(len(range_nclusters), 1, plot_index)
fig.set_size_inches(7, 18)
# The 1st subplot is the silhouette plot
# The silhouette coefficient can range from -1, 1 but in this example all
# lie within [-0.1, 1]
ax1.set_xlim([-0.1, 1])
plt.axes
# The (n_clusters+1)*10 is for inserting blank space between silhouette
# plots of individual clusters, to demarcate them clearly.
ax1.set_ylim([0, len(features_scaled) + (n_clusters + 1) * 10])
# perform kmeans
clusterer = KMeans(n_clusters=n_clusters,
random_state=0,
max_iter=1000)
cluster_labels = clusterer.fit_predict(features_scaled)
# Calculate the average silhouette value for all segments and print to screen
#pdb.set_trace()
silhouette_avg = silhouette_score(features_scaled, cluster_labels)
print("n_clusters = " + str(n_clusters) +
" Avg silhouette_score = " + str(silhouette_avg))
if plot_silhouette:
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(
features_scaled, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
#ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
# The vertical line for average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([]) # Clear the yaxis labels / ticks
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
# # 2nd Plot showing the actual clusters formed
# colors = cm.spectral(cluster_labels.astype(float) / n_clusters)
# ax2.scatter(features_scaled[:, 0], features_scaled[:, 1], marker='.', s=30, lw=0, alpha=0.7,
# c=colors, edgecolor='k')
#
# # Labeling the clusters
# centers = clusterer.cluster_centers_
# # Draw white circles at cluster centers
# ax2.scatter(centers[:, 0], centers[:, 1], marker='o',
# c="white", alpha=1, s=200, edgecolor='k')
#
# for i, c in enumerate(centers):
# ax2.scatter(c[0], c[1], marker='$%d$' % i, alpha=1,
# s=50, edgecolor='k')
#
# ax2.set_title("The visualization of the clustered data.")
# ax2.set_xlabel("Feature space for the 1st feature")
# ax2.set_ylabel("Feature space for the 2nd feature")
plt.suptitle((
"Silhouette analysis for KMeans clustering on sample data "
"with n_clusters = %d" % n_clusters),
fontsize=14,
fontweight='bold')
plt.show()
if plot_silhouette:
plt.savefig(
os.path.join("figs/",
"silhouette_length" + str(iseg_length) + ".pdf"))
plt.close(fig)
#perform_silhouette_analysis(path = "../../",
# segment_lengths = [100,150,200,250,300],
# range_nclusters = range(2,11),
# plot_silhouette = False)
def test_clustering3(_x, _y, _data, _xLab, _yLab, N_CLUSTERS, _latLon_params,
_basemp, **kwargs):
pred_dict = {}
np.random.seed(0)
colors = np.array([x for x in 'bgrcmykbgrcmykbgrcmykbgrcmyk'])
colors = np.hstack([colors] * 20)
plot_num = 1
X = _data
print(_data[:10])
# normalize dataset for easier parameter selection
X = StandardScaler().fit_transform(X)
# Compute distances
# create clustering estimators
print(kwargs['models'])
alg_list = []
for model in kwargs['models']:
# estimate bandwidth for mean shift
bandwidth = cluster.estimate_bandwidth(X, quantile=0.3)
ms = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
if model in ['Ward', 'AgglomerativeClustering']:
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(X, n_neighbors=10)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
if model == 'Ward':
ward = cluster.AgglomerativeClustering(
n_clusters=N_CLUSTERS,
linkage='ward',
connectivity=connectivity)
alg_list.append(('Ward', ward))
if model == 'AgglomerativeClustering':
average_linkage = cluster.AgglomerativeClustering(
linkage="average",
affinity="cityblock",
n_clusters=N_CLUSTERS,
connectivity=connectivity)
alg_list.append(('AgglomerativeClustering', average_linkage))
if model == 'MiniBatchKMeans':
two_means = cluster.MiniBatchKMeans(n_clusters=N_CLUSTERS)
alg_list.append(('MiniBatchKMeans', two_means))
if model == 'SpectralClustering':
spectral = cluster.SpectralClustering(n_clusters=N_CLUSTERS,
eigen_solver='arpack',
affinity="nearest_neighbors")
alg_list.append(('SpectralClustering', spectral))
if model == 'DBSCAN':
dbscan = cluster.DBSCAN(eps=.2)
alg_list.append(('DBSCAN', dbscan))
if model == 'AffinityPropagation':
affinity_propagation = cluster.AffinityPropagation(damping=.9,
preference=-200)
alg_list.append(('AffinityPropagation', affinity_propagation))
print(alg_list)
models = {}
for name, algorithm in alg_list:
models[name] = {}
# predict cluster memberships
models[name]['start'] = time.time()
algorithm.fit(X)
models[name]['end'] = time.time()
if hasattr(algorithm, 'labels_'):
y_pred = algorithm.labels_.astype(np.int)
models[name]['y_pred'] = y_pred
else:
y_pred = algorithm.predict(X)
models[name]['y_pred'] = y_pred
models[name]['sil_score'] = metrics.silhouette_score(
X, y_pred, metric='euclidean')
models[name]['sample_sil_vals'] = silhouette_samples(X, y_pred)
models[name]['model'] = algorithm
models[name]['N_CLUSTERS'] = N_CLUSTERS
return models
ax1.set_ylim([0, len(data_vectorized) + (n_clusters + 1) * 10])
# Initialize the clusterer with n_clusters value and a random generator
# seed of 1 for reproducibility.
clusterer = KMeans(n_clusters=n_clusters, random_state=1)
cluster_labels = clusterer.fit_predict(data_vectorized)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(data_vectorized, cluster_labels)
print("For n_clusters =", n_clusters,
"The average silhouette_score is :", silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(data_vectorized,
cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
def silhouette(name, n_clusters, x):
averages = []
for n_cluster in n_clusters:
plot.style.use('seaborn-darkgrid')
plot.title(
f'Silhouette on the {name} dataset, using {n_cluster}-means')
ax = plot.gca()
ax.set_xlim([-0.1, 1])
ax.set_ylim([0, len(x) + (n_cluster + 1) * 10])
clusterer = KMeans(n_clusters=n_cluster, random_state=0)
cluster_labels = clusterer.fit_predict(x)
silhouette_avg = silhouette_score(x, cluster_labels)
averages.append(silhouette_avg)
sample_silhouette_values = silhouette_samples(x, cluster_labels)
y_lower = 10
for i in range(n_cluster):
ith_cluster_silhouette_values = sample_silhouette_values[
cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / n_cluster)
ax.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
ax.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
y_lower = y_upper + 10
ax.set_xlabel("The silhouette coefficient values")
ax.set_ylabel("Cluster labels")
ax.axvline(x=silhouette_avg, color="red", linestyle="--")
ax.set_yticks([])
ax.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
plot.show()
lb = np.min(averages)
ub = np.max(averages)
amplitude = ub - lb
lb -= 0.2 * amplitude
ub += 0.2 * amplitude
plot.style.use('seaborn-darkgrid')
plot.title(f'Silhouette averages on the {name} dataset using k-means')
plot.bar(n_clusters, averages)
plot.xticks(n_clusters)
plot.xlabel('Number of clusters')
plot.ylabel('Silhouette averages')
plot.ylim([lb, ub])
plot.show()
print(f'{name}: {averages}')
def K_Means_silhouette_analysis(X, y):
cluster_range = [3, 5, 7, 9, 11, 13, 15]
for num_cluster in cluster_range:
figure_to_show, (ax1, ax2) = plt.subplots(1, 2)
figure_to_show.set_size_inches(20, 8)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(X) + (num_cluster + 1) * 10])
clusterer = KMeans(n_clusters=num_cluster, random_state=10)
cluster_labels = clusterer.fit_predict(X)
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters = ", num_cluster,
"The average silhouette_score is :", silhouette_avg)
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(num_cluster):
ith_cluster_silhouette_values = sample_silhouette_values[
cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / num_cluster)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
y_lower = y_upper + 10
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
ax1.set_ylabel("Cluster label")
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([])
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
colors = cm.nipy_spectral(cluster_labels.astype(float) / num_cluster)
ax2.scatter(X[:, 0],
X[:, 1],
marker='.',
s=30,
lw=0,
alpha=0.7,
c=colors,
edgecolor='k')
centers = clusterer.cluster_centers_
ax2.scatter(centers[:, 0],
centers[:, 1],
marker='o',
c="white",
alpha=1,
s=200,
edgecolor='k')
for i, c in enumerate(centers):
ax2.scatter(c[0],
c[1],
marker='$%d$' % i,
alpha=1,
s=50,
edgecolor='k')
ax2.set_title("The visualization of the clustered data.")
ax2.set_xlabel("Feature space for the 1st feature")
ax2.set_ylabel("Feature space for the 2nd feature")
plt.suptitle((
"Silhouette analysis for KMeans clustering on sample data with num_cluster = %d"
% num_cluster),
fontsize=14,
fontweight='bold')
plt.show()
# Initialize the clusterer with n_clusters value and a random generator
# seed of 10 for reproducibility.
clusterer = KMeans(n_clusters=n_clusters, random_state=6, n_jobs=-1)
cluster_labels = clusterer.fit_predict(sample_descriptors)
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(sample_descriptors,
cluster_labels,
sample_size=100)
print("For n_clusters =", n_clusters, "The average silhouette_score is :",
silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(sample_descriptors,
cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = sample_silhouette_values[cluster_labels
== i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
import pandas as pd
from sklearn import cluster
from sklearn import metrics
votes = pd.read_csv("/home/algo/Downloads/congress.csv")
votes.shape
cluster_model = cluster.AgglomerativeClustering(n_clusters=2,
affinity='euclidean',
linkage='ward')
cluster_model.fit(votes.iloc[:, 3:])
labels = cluster_model.labels_
silhouette_avg = metrics.silhouette_score(votes.iloc[:, 3:],
labels,
metric='euclidean')
silhouette_samples = metrics.silhouette_samples(votes.iloc[:, 3:],
labels,
metric='euclidean')
ch_score = metrics.calinski_harabaz_score(votes.iloc[:, 3:], labels)
for n_clusters in range(2, 6):
cluster_model = cluster.AgglomerativeClustering(n_clusters=n_clusters,
random_state=10)
cluster_labels = cluster_model.fit_predict(votes.iloc[:, 3:])
silhouette_avg = metrics.silhouette_score(votes.iloc[:, 3:],
cluster_labels,
metric='euclidean')
print("For n_clusters =", n_clusters, "The average silhouette_score is:",
silhouette_avg)
for i in range(100):
print('Trial number ', i)
start_time = time.time()
for k in n_clusters:
data = init_data.copy()
# QUALITY CHECK DATA
for j in range(1000):
X = data.values
kmeans = KMeans(n_clusters=k)
cluster_labels = kmeans.fit_predict(X)
sample_sil_coefficients = metrics.silhouette_samples(
X, cluster_labels)
data, count_negative = qualityCheck(data, sample_sil_coefficients)
print('Number of data retained after quality check', len(data))
if count_negative == 0:
X = data.values
kmeans = KMeans(n_clusters=k)
cluster_labels = kmeans.fit_predict(X)
sil_score = metrics.silhouette_score(X, cluster_labels)
ssd_center = kmeans.inertia_
scores[counter] = {
'trial': i + 1,
'cluster_number': k,
'silhouette_score': sil_score,
def vis(X, y, nameappendix, k):
scaler = MinMaxScaler(feature_range=[0,100])
scaler.fit(X)
X = pd.DataFrame(scaler.transform(X))
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(15, 6)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(X) + (k + 1) * 10])
print("Num of clusters: ", k)
clusters = KMeans(n_clusters = k, random_state = 10).fit(X)
labels = clusters.labels_
print("NMI score: %.5f" % normalized_mutual_info_score(y, labels))
silhouette_avg = sil_score(X, labels)
print("Silhouette score: ", silhouette_avg)
sample_silhouette_values = silhouette_samples(X, labels)
y_lower = 10
for i in range(k):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = sample_silhouette_values[labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
# color = plt.spectral(float(i) / numOfCluster)
color = plt.get_cmap('Spectral')(float(i) / k)
ax1.fill_betweenx(np.arange(y_lower, y_upper), 0, ith_cluster_silhouette_values, facecolor=color, edgecolor=color, alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("Silhouette Coefficients for Clusters.")
ax1.set_xlabel("Silhouette Coefficient Values")
ax1.set_ylabel("Cluster Labels")
# The vertical line for average silhouette score of all the values
ax1.axvline(x=silhouette_avg, color="red", linestyle="--")
ax1.set_yticks([]) # Clear the yaxis labels / ticks
ax1.set_xticks([-0.1, 0, 0.2, 0.4, 0.6, 0.8, 1])
# 2nd Plot showing the actual clusters formed
# colors = plt.spectral(labels.astype(float) / numOfCluster)
colors = plt.get_cmap('Spectral')(labels.astype(float) / k)
# print(X.values[:, 10])
# colors = ["b","g","r","c","m","y","k"]
ax2.scatter(X.values[:, 3], X.values[:,5], marker='.', s=30, lw=0, alpha=0.7, c=colors, edgecolor='k')
# Labeling the clusters
centers = clusters.cluster_centers_
# Draw white circles at cluster centers
ax2.scatter(centers[:, 3], centers[:, 5], marker='o', c="white", alpha=1, s=200, edgecolor='k')
for i, c in enumerate(centers):
ax2.scatter(c[3], c[5], marker='$%d$' % i, alpha=1, s=50, edgecolor='k')
ax2.set_title("Clustering Visualization")
ax2.set_xlabel("1st feature: Pressure X4")
ax2.set_ylabel("2nd feature: Pressure X5")
plt.suptitle("Analysis for KMeans for " + str(k) + " Clusters", fontsize=14, fontweight='bold')
# plt.savefig('img/kmeans_vis' + str(k) + '.png')
plt.show()
def make_new_outputs(corr: Union[np.array, pd.DataFrame], clusters: dict,
clusters2: dict) -> (pd.DataFrame, dict, pd.Series):
"""
Makes new outputs for kmeans_advanced_clustering() by recombining two sets of clusters
together, recomputing their correlation matrix, distance matrix, kmeans labels and silhouette scores.
Arguments
---------
corr : numpy.array or pd.DataFrame
Correlation matrix.
clusters : dict
First set of clusters.
clusters2 : dict
Second set of clusters.
Returns
-------
pd.DataFrame
Clustered correlation matrix.
dictionary
List of clusters and their content.
pd.Series
Silhouette scores.
Notes
-----
Function adapted from "Machine Learning for Asset Managers",
Marcos López de Prado (2020).
"""
# Initializations
# Add clusters keys to the new cluster
clusters_new = {}
for i in clusters.keys():
clusters_new[len(clusters_new.keys())] = list(clusters[i])
for i in clusters2.keys():
clusters_new[len(clusters_new.keys())] = list(clusters2[i])
# Compute new correlation matrix
new_idx = [j for i in clusters_new for j in clusters_new[i]]
corr_new = corr.loc[new_idx, new_idx]
# Compute the observation matrix
Xobs = (((1 - corr.fillna(0)) / 2.)**.5).values
# Compute the Euclidean distance matrix
X = np.zeros(shape=Xobs.shape)
for i, j in itertools.product(range(X.shape[0]), range(X.shape[1])):
X[i, j] = np.sqrt(sum((Xobs[i, :] - Xobs[j, :])**2))
new_names_features = corr_new.columns.tolist()
X = pd.DataFrame(data=X,
index=new_names_features,
columns=new_names_features)
# Add labels together
kmeans_labels = np.zeros(len(X.columns))
for i in clusters_new.keys():
idxs = [X.index.get_loc(k) for k in clusters_new[i]]
kmeans_labels[idxs] = i
# Compute the silhouette scores
silh_new = pd.Series(silhouette_samples(X, kmeans_labels), index=X.index)
return corr_new, clusters_new, silh_new
print("Algorithm failed")
###
### PLOTTING SILOUHETTE
###
classes_to_test = [2, 3, 4, 5, 6]
for classNumber in classes_to_test:
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
ax1.set_xlim([-0.1, 1])
ax1.set_ylim([0, len(dataset) + (classNumber + 1) * 10])
cluster_labels, centroids = clusterer.predictLabels(dataset, classNumber)
silhouette_avg = silhouette_score(dataset, cluster_labels)
sample_silhouette_values = silhouette_samples(dataset, cluster_labels)
y_lower = 10
for i in range(classNumber):
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.nipy_spectral(float(i) / classNumber)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
__print_pca_info__(pca)
# compute variance per numbers of clusters
cs = range(2, n_clusters + 1)
scores = np.zeros((len(cs), 2))
silhouette = np.zeros((len(cs), 2))
for i, n in enumerate(cs):
# cluster the samples
k = KMeans(n_clusters=n)
k.fit(X)
# compute total variance and average silhouette score
scores[i] = [n, k.inertia_]
silhouette[i] = [n, silhouette_score(X, k.labels_)]
silhouette_sample_values = silhouette_samples(X, k.labels_)
silhouette_sample_values = \
[sorted(silhouette_sample_values[k.labels_ == c], reverse=True) for c in range(n)]
# sample cluster data for plotting
clusters = [X[k.labels_ == c] for c in range(n)]
cluster_samples = [
samples[:, FEATURES][k.labels_ == c] for c in range(n)
]
# create object summaries of the data
cluster_assignments, sample_assignments = summarize(k, samples)
# store a heat map of the distribution of the original samples into the clusters per object
hm = sample_heat_map(sample_assignments, n)
with open(
n_clusters=n_cl,
memory='/home/winz3r/Documents/Data/')
t0 = time.time()
model.fit(X)
tim_spec = time.time() - t0
hier_labels = model.labels_
label_name = dir_name + 'hierarchical_cluster_labels_K' + str(
n_cl) + '_' + str(i) + '.csv'
f_out = open(label_name, 'w')
for w in hier_labels:
f_out.write(str(w) + '\n')
f_out.close()
##Silhouette Calculation
sil_spec = (silhouette_samples(X, hier_labels)).mean(axis=0)
##SSE Calculation
SSE_spec = 0
for k in range(n_cl):
members = hier_labels == k
centre = X[members, :].mean(axis=0)
for x in X[members]:
SSE_spec += np.dot(x - centre, (x - centre).T)
tim.append(n_cl)
SSE.append(n_cl)
sil.append(n_cl)
tim.append(tim_spec)
sil.append(sil_spec)
SSE.append(SSE_spec)
str(i - reduced_data.shape[0]),
color=color,
fontdict={
'weight': 'bold',
'size': size
})
# The silhouette_score gives the average value for all the samples.
# This gives a perspective into the density and separation of the formed
# clusters
silhouette_avg = silhouette_score(reduced_data, assigned_cluster)
print("For n_clusters =", clusters, "The average silhouette_score is :",
silhouette_avg)
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(reduced_data,
assigned_cluster)
#ax1 = plt.subplot(111)
#y_lower = 10
#for i in range(clusters):
# # Aggregate the silhouette scores for samples belonging to
# # cluster i, and sort them
# ith_cluster_silhouette_values = \
# sample_silhouette_values[assigned_cluster == i]
# ith_cluster_silhouette_values.sort()
# size_cluster_i = ith_cluster_silhouette_values.shape[0]
# y_upper = y_lower + size_cluster_i
# color = cm.nipy_spectral(float(i) / clusters)
plt.ylabel("Distortion")
plt.show()
# silhouette analysis
km = KMeans(n_clusters=3,
init="k-means++",
n_init=10,
max_iter=300,
tol=1e-04,
random_state=0)
y_km = km.fit_predict(X)
cluster_labels = np.unique(y_km)
n_clusters = cluster_labels.shape[0]
# 为每个样本计算 silhouette 系数
silhouette_vals = silhouette_samples(X, y_km, metric="euclidean")
y_ax_lower, y_ax_upper = 0, 0 # 用于柱状图在 y 轴上的宽度
yticks = []
for i, c in enumerate(cluster_labels):
c_silhouette_vals = silhouette_vals[y_km == c] # 某一集群的 silhouette 系数
c_silhouette_vals.sort()
y_ax_upper += len(c_silhouette_vals)
color = cm.jet(i / n_clusters)
plt.barh(
range(y_ax_lower, y_ax_upper), # 就是 len(c_silouette_vals 的长度
c_silhouette_vals,
height=1.0,
edgecolor="none",
color=color)
yticks.append((y_ax_lower + y_ax_upper) / 2) # y 轴提示的位置
cluster = KMeans(n_clusters=n_clusters, random_state=0).fit(X)
y_pred = cluster.labels_
pre = cluster.fit_predict(X)
cluster_smallsub = KMeans(n_clusters=n_clusters, random_state=0).fit(X[:200])
y_pred_ = cluster_smallsub.predict(X)
centroid = cluster.cluster_centers_
inertia = cluster.inertia_
print("总距离", inertia)
color = ["red", "pink", "orange", "gray"]
fig, ax1 = plt.subplots(1)
for i in range(n_clusters):
ax1.scatter(X[y_pred == i, 0], X[y_pred == i, 1], marker='o', s=8, c=color[i]
)
ax1.scatter(centroid[:, 0], centroid[:, 1], marker="x", s=15, c="black")
plt.show()
# 轮廓系数，评估模型的分类结果，越接近1越好,可以看到4是最好的聚类分组
n_clusters = 4
cluster_4 = KMeans(n_clusters=n_clusters, random_state=0).fit(X)
n_clusters = 5
cluster_5 = KMeans(n_clusters=n_clusters, random_state=0).fit(X)
score3 = silhouette_score(X, y_pred)
score4 = silhouette_score(X, cluster_4.labels_)
score5 = silhouette_score(X, cluster_5.labels_)
silhouette_samples(X, y_pred)
score_cal = calinski_harabasz_score(X, y_pred) # 这个运行速度更快很多
time = datetime.datetime.fromtimestamp(time()).strftime("%Y-%m-%d %H:%M:%S")
def plot_silhouettes(instance_matrix, origin_path, plot_title):
"""
"translated" from https://towardsdatascience.com/k-means-clustering-algorithm-applications-evaluation-methods-and-drawbacks-aa03e644b48a
:param X_std:
:param max_range:
:return:
"""
files = os.listdir(f"{origin_path}")
if ".DS_Store" in files:
files.remove(".DS_Store")
if plot_title + ".png" in files:
files.remove(plot_title + ".png")
sorted_files = sorted(files,
key=lambda s: int(s.split("_")[0].split("=")[1]))
#sorted_files = sorted(os.listdir("resources/small/clustering/m_1.5"), key=str.lower)
not_odd_files = sorted_files[0::2] # return just every 2nd item
print(not_odd_files)
list_k = sorted(
[int(file.split("_")[0].split("=")[1]) for file in not_odd_files])
for k, filename in zip(list_k, not_odd_files):
file = origin_path + "/" + filename
fig, (ax1, ax2) = plt.subplots(1, 2)
fig.set_size_inches(18, 7)
# Kmeans object
k_means = pickle.load(open(file, "rb"))
labels = k_means.cluster_mapping
centroids = np.vstack(k_means.centroids)
#X = np.vstack(k_means.instances)
instance_matrix_less = instance_matrix[:len(labels)]
# Get silhouette samples
silhouette_vals = silhouette_samples(instance_matrix_less, labels)
# Silhouette plot
y_ticks = []
y_lower, y_upper = 0, 0
for i, cluster in enumerate(np.unique(labels)):
cluster_silhouette_vals = silhouette_vals[labels == cluster]
cluster_silhouette_vals.sort()
y_upper += len(cluster_silhouette_vals)
ax1.barh(range(y_lower, y_upper),
cluster_silhouette_vals,
edgecolor='none',
height=1)
ax1.text(-0.03, (y_lower + y_upper) / 2, str(i + 1))
y_lower += len(cluster_silhouette_vals)
# Get the average silhouette score and plot it
avg_score = np.mean(silhouette_vals)
ax1.axvline(avg_score, linestyle='--', linewidth=2, color='green')
ax1.set_yticks([])
ax1.set_xlim([-0.1, 1])
ax1.set_xlabel('Silhouette coefficient values')
ax1.set_ylabel('Cluster labels')
ax1.set_title('Silhouette plot for the various clusters', y=1.02)
# Scatter plot of data colored with labels
ax2.scatter(instance_matrix[:, 0], instance_matrix[:, 1], c=labels)
ax2.scatter(centroids[:, 0], centroids[:, 1], marker='*', c='r', s=250)
ax2.set_xlim([-2, 2])
ax2.set_xlim([-2, 2])
ax2.set_xlabel('Eruption time in mins')
ax2.set_ylabel('Waiting time to next eruption')
ax2.set_title('Visualization of clustered data', y=1.02)
ax2.set_aspect('equal')
plt.tight_layout()
plt.suptitle(f'Silhouette analysis using k = {k}',
fontsize=16,
fontweight='semibold',
y=1.05)
plt.show()
# elbow method to reduce distortion
distortions = []
for i in range(1, 11):
km = KMeans(n_clusters=i, n_init=10, max_iter=300, random_state=0)
km.fit(x)
distortions.append(km.inertia_)
plt.plot(range(1, 11), distortions, marker='o')
plt.xlabel('Number of cluster')
plt.ylabel('Distortion')
plt.show()
# quantifying qual by silhouette plots
cluster_labels = np.unique(y_km)
n_clusters = cluster_labels.shape[0]
silhouette_vals = silhouette_samples(x, y_km, metric='euclidean')
y_ax_lower, y_ax_upper = 0, 0
yticks = []
for i, c in enumerate(cluster_labels):
c_silhouette_vals = silhouette_vals[y_km == c]
c_silhouette_vals.sort()
y_ax_upper += len(c_silhouette_vals)
color = cm.jet(i / n_clusters)
plt.barh(range(y_ax_lower, y_ax_upper),
c_silhouette_vals,
height=1.0,
edgecolor='none',
color=color)
yticks.append((y_ax_lower + y_ax_upper) / 2)
y_ax_lower += len(c_silhouette_vals)
def get_silhouette_graph(self, document_list, df_result, num_clusters):
X = self.__get_tfidf_matrix(document_list)
figures = []
color_list = [
'#1f77b4', # muted blue
'#ff7f0e', # safety orange
'#2ca02c', # cooked asparagus green
'#d62728', # brick red
'#9467bd', # muted purple
'#8c564b', # chestnut brown
'#e377c2', # raspberry yogurt pink
'#7f7f7f', # middle gray
'#bcbd22', # curry yellow-green
'#17becf' # blue-teal
]
cmap = cm.get_cmap("Spectral")
fig = tools.make_subplots(rows=1,
cols=2,
print_grid=False,
subplot_titles=('Silhouette Graph',
'Clutering Graph'))
# Initialize Silhouette Graph
fig['layout']['xaxis1'].update(title='Silhouette Coefficient',
range=[-0.1, 1])
fig['layout']['yaxis1'].update(
title='Cluster Label',
showticklabels=False,
range=[0, len(X) + (num_clusters + 1) * 10])
# Compute K-Means Cluster
clusterer = KMeans(n_clusters=num_clusters, random_state=10)
#KMeans(n_clusters = num_clutsers, init='k-means++', n_init=num_init, max_iter=max_iterations, random_state=0)
cluster_labels = clusterer.fit_predict(X)
# Compute Average Silhouette Score
silhouette_avg = silhouette_score(X, cluster_labels)
print("For n_clusters =", num_clusters,
"The average silhouette_score is :", silhouette_avg)
# Compute the Silhouette Scores for Each Sample
sample_silhouette_values = silhouette_samples(X, cluster_labels)
y_lower = 10
for i in range(num_clusters):
ith_cluster_silhouette_values = sample_silhouette_values[
cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
colors = cmap(cluster_labels.astype(float) / num_clusters)
filled_area = go.Scatter(y=np.arange(y_lower, y_upper),
x=ith_cluster_silhouette_values,
mode='lines',
showlegend=False,
line=dict(width=0.5, color=colors),
fill='tozerox')
fig.append_trace(filled_area, 1, 1)
y_lower = y_upper + 10 # 10 for the 0 samples
# Vertical Line for Average Silhouette Score
axis_line = go.Scatter(x=[silhouette_avg],
y=[0, len(X) + (num_clusters + 1) * 10],
showlegend=False,
mode='lines',
line=dict(color="red", dash='dash',
width=1))
fig.append_trace(axis_line, 1, 1)
# Cluster Graph
colors = matplotlib.colors.colorConverter.to_rgb(
cmap(float(i) / num_clusters))
colors = 'rgb' + str(colors)
clusters = go.Scatter(x=df_result['x'],
y=df_result['y'],
showlegend=False,
mode='markers',
text=cluster_labels,
marker=dict(color=[
color_list[cluster_label]
for cluster_label in cluster_labels
],
size=10))
fig.append_trace(clusters, 1, 2)
fig['layout']['xaxis2'].update(
title='Feature space for the 1st feature', zeroline=False)
fig['layout']['yaxis2'].update(
title='Feature space for the 2nd feature', zeroline=False)
fig['layout'].update(
title="Silhouette Analysis for KMeans Clustering - " +
str(num_clusters) + " Cluster")
return iplot(fig, filename='basic-line')
