forked from scikit-learn/scikit-learn
-
Notifications
You must be signed in to change notification settings - Fork 6
/
plot_mini_batch_kmeans.py
142 lines (116 loc) · 3.93 KB
/
plot_mini_batch_kmeans.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
"""
====================================================================
Comparison of the K-Means and MiniBatchKMeans clustering algorithms
====================================================================
We want to compare the performance of the MiniBatchKMeans and KMeans:
the MiniBatchKMeans is faster, but gives slightly different results (see
:ref:`mini_batch_kmeans`).
We will cluster a set of data, first with KMeans and then with
MiniBatchKMeans, and plot the results.
We will also plot the points that are labelled differently between the two
algorithms.
"""
# %%
# Generate the data
# -----------------
#
# We start by generating the blobs of data to be clustered.
import numpy as np
from sklearn.datasets import make_blobs
np.random.seed(0)
batch_size = 45
centers = [[1, 1], [-1, -1], [1, -1]]
n_clusters = len(centers)
X, labels_true = make_blobs(n_samples=3000, centers=centers, cluster_std=0.7)
# %%
# Compute clustering with KMeans
# ------------------------------
import time
from sklearn.cluster import KMeans
k_means = KMeans(init="k-means++", n_clusters=3, n_init=10)
t0 = time.time()
k_means.fit(X)
t_batch = time.time() - t0
# %%
# Compute clustering with MiniBatchKMeans
# ---------------------------------------
from sklearn.cluster import MiniBatchKMeans
mbk = MiniBatchKMeans(
init="k-means++",
n_clusters=3,
batch_size=batch_size,
n_init=10,
max_no_improvement=10,
verbose=0,
)
t0 = time.time()
mbk.fit(X)
t_mini_batch = time.time() - t0
# %%
# Establishing parity between clusters
# ------------------------------------
#
# We want to have the same color for the same cluster from both the
# MiniBatchKMeans and the KMeans algorithm. Let's pair the cluster centers per
# closest one.
from sklearn.metrics.pairwise import pairwise_distances_argmin
k_means_cluster_centers = k_means.cluster_centers_
order = pairwise_distances_argmin(k_means.cluster_centers_, mbk.cluster_centers_)
mbk_means_cluster_centers = mbk.cluster_centers_[order]
k_means_labels = pairwise_distances_argmin(X, k_means_cluster_centers)
mbk_means_labels = pairwise_distances_argmin(X, mbk_means_cluster_centers)
# %%
# Plotting the results
# --------------------
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(8, 3))
fig.subplots_adjust(left=0.02, right=0.98, bottom=0.05, top=0.9)
colors = ["#4EACC5", "#FF9C34", "#4E9A06"]
# KMeans
ax = fig.add_subplot(1, 3, 1)
for k, col in zip(range(n_clusters), colors):
my_members = k_means_labels == k
cluster_center = k_means_cluster_centers[k]
ax.plot(X[my_members, 0], X[my_members, 1], "w", markerfacecolor=col, marker=".")
ax.plot(
cluster_center[0],
cluster_center[1],
"o",
markerfacecolor=col,
markeredgecolor="k",
markersize=6,
)
ax.set_title("KMeans")
ax.set_xticks(())
ax.set_yticks(())
plt.text(-3.5, 1.8, "train time: %.2fs\ninertia: %f" % (t_batch, k_means.inertia_))
# MiniBatchKMeans
ax = fig.add_subplot(1, 3, 2)
for k, col in zip(range(n_clusters), colors):
my_members = mbk_means_labels == k
cluster_center = mbk_means_cluster_centers[k]
ax.plot(X[my_members, 0], X[my_members, 1], "w", markerfacecolor=col, marker=".")
ax.plot(
cluster_center[0],
cluster_center[1],
"o",
markerfacecolor=col,
markeredgecolor="k",
markersize=6,
)
ax.set_title("MiniBatchKMeans")
ax.set_xticks(())
ax.set_yticks(())
plt.text(-3.5, 1.8, "train time: %.2fs\ninertia: %f" % (t_mini_batch, mbk.inertia_))
# Initialize the different array to all False
different = mbk_means_labels == 4
ax = fig.add_subplot(1, 3, 3)
for k in range(n_clusters):
different += (k_means_labels == k) != (mbk_means_labels == k)
identical = np.logical_not(different)
ax.plot(X[identical, 0], X[identical, 1], "w", markerfacecolor="#bbbbbb", marker=".")
ax.plot(X[different, 0], X[different, 1], "w", markerfacecolor="m", marker=".")
ax.set_title("Difference")
ax.set_xticks(())
ax.set_yticks(())
plt.show()