Hierarchical clustering: structured vs unstructured ward

Example builds a swiss roll dataset and runs hierarchical clustering on their position.

For more information, see Hierarchical clustering.

In a first step, the hierarchical clustering is performed without connectivity constraints on the structure and is solely based on distance, whereas in a second step the clustering is restricted to the k-Nearest Neighbors graph: it’s a hierarchical clustering with structure prior.

Some of the clusters learned without connectivity constraints do not respect the structure of the swiss roll and extend across different folds of the manifolds. On the opposite, when opposing connectivity constraints, the clusters form a nice parcellation of the swiss roll.

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Out:

Compute unstructured hierarchical clustering...
Elapsed time: 0.04s
Number of points: 1500
/home/circleci/project/examples/cluster/plot_ward_structured_vs_unstructured.py:56: MatplotlibDeprecationWarning: Axes3D(fig) adding itself to the figure is deprecated since 3.4. Pass the keyword argument auto_add_to_figure=False and use fig.add_axes(ax) to suppress this warning. The default value of auto_add_to_figure will change to False in mpl3.5 and True values will no longer work in 3.6.  This is consistent with other Axes classes.
  ax = p3.Axes3D(fig)
Compute structured hierarchical clustering...
Elapsed time: 0.06s
Number of points: 1500
/home/circleci/project/examples/cluster/plot_ward_structured_vs_unstructured.py:91: MatplotlibDeprecationWarning: Axes3D(fig) adding itself to the figure is deprecated since 3.4. Pass the keyword argument auto_add_to_figure=False and use fig.add_axes(ax) to suppress this warning. The default value of auto_add_to_figure will change to False in mpl3.5 and True values will no longer work in 3.6.  This is consistent with other Axes classes.
  ax = p3.Axes3D(fig)

# Authors : Vincent Michel, 2010
#           Alexandre Gramfort, 2010
#           Gael Varoquaux, 2010
# License: BSD 3 clause

import time as time
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d.axes3d as p3
from sklearn.cluster import AgglomerativeClustering
from sklearn.datasets import make_swiss_roll

# #############################################################################
# Generate data (swiss roll dataset)
n_samples = 1500
noise = 0.05
X, _ = make_swiss_roll(n_samples, noise=noise)
# Make it thinner
X[:, 1] *= 0.5

# #############################################################################
# Compute clustering
print("Compute unstructured hierarchical clustering...")
st = time.time()
ward = AgglomerativeClustering(n_clusters=6, linkage="ward").fit(X)
elapsed_time = time.time() - st
label = ward.labels_
print("Elapsed time: %.2fs" % elapsed_time)
print("Number of points: %i" % label.size)

# #############################################################################
# Plot result
fig = plt.figure()
ax = p3.Axes3D(fig)
ax.view_init(7, -80)
for l in np.unique(label):
    ax.scatter(
        X[label == l, 0],
        X[label == l, 1],
        X[label == l, 2],
        color=plt.cm.jet(float(l) / np.max(label + 1)),
        s=20,
        edgecolor="k",
    )
plt.title("Without connectivity constraints (time %.2fs)" % elapsed_time)


# #############################################################################
# Define the structure A of the data. Here a 10 nearest neighbors
from sklearn.neighbors import kneighbors_graph

connectivity = kneighbors_graph(X, n_neighbors=10, include_self=False)

# #############################################################################
# Compute clustering
print("Compute structured hierarchical clustering...")
st = time.time()
ward = AgglomerativeClustering(
    n_clusters=6, connectivity=connectivity, linkage="ward"
).fit(X)
elapsed_time = time.time() - st
label = ward.labels_
print("Elapsed time: %.2fs" % elapsed_time)
print("Number of points: %i" % label.size)

# #############################################################################
# Plot result
fig = plt.figure()
ax = p3.Axes3D(fig)
ax.view_init(7, -80)
for l in np.unique(label):
    ax.scatter(
        X[label == l, 0],
        X[label == l, 1],
        X[label == l, 2],
        color=plt.cm.jet(float(l) / np.max(label + 1)),
        s=20,
        edgecolor="k",
    )
plt.title("With connectivity constraints (time %.2fs)" % elapsed_time)

plt.show()