CS250: Python for Data Science

Unsupervised learning is a class of machine learning methods where we are just trying to identify patterns in the data without any labels. This is in contrast to supervised learning, which are the modeling methods we have discussed above.

Most unsupervised learning methods fall broadly into a set of algorithms called cluster analysis. scikit-learn provides several clustering algorithms.

We will demonstrate the two more popular choices – K-Means and Agglomerative clustering (also known as hierarchical clustering). We will use the classic Fisher's Iris data for this demonstration.

import statsmodels.api as sm
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns

from sklearn.cluster import KMeans, AgglomerativeClustering

iris = sm.datasets.get_rdataset('iris').data
sns.relplot(data=iris, x = 'Sepal.Length',y = 'Sepal.Width', hue = 'Species');

/Users/abhijit/opt/miniconda3/envs/ds/lib/python3.8/site-packages/seaborn/axisgrid.py:324:
RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface
(`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory.
(To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(nrow, ncol, **kwargs)

The K-Means algorithm takes a pre-specified number of clusters as input and then tries to find contiguous regions of the data to parse into clusters.

km = KMeans(n_clusters = 3)
km.fit(iris[['Sepal.Length','Sepal.Width']]);

km.labels_

array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 1, 1, 1, 2, 1, 2, 1, 2, 1, 2, 2, 2, 2, 2, 2, 1,
       2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2,
       2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1,
       1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1,
       1, 2, 2, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 2], dtype=int32)

iris['km_labels'] = km.labels_
iris['km_labels'] = iris.km_labels.astype('category')

sns.relplot(data=iris, x = 'Sepal.Length', y = 'Sepal.Width', 
           hue = 'km_labels');

/Users/abhijit/opt/miniconda3/envs/ds/lib/python3.8/site-packages/seaborn/axisgrid.py:324:
RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot
interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume
too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(nrow, ncol, **kwargs)

Agglomerative clustering takes a different approach. It starts by coalescing individual points successively, based on a distance metric and a principle for how to coalesce groups of points (called linkage). The number of clusters can then be determined either visually or via different cutoffs.

hc = AgglomerativeClustering(distance_threshold=0, n_clusters=None, 
                             linkage='complete')

hc.fit(iris[['Sepal.Length','Sepal.Width']])

AgglomerativeClustering(distance_threshold=0, linkage='complete',
                        n_clusters=None)

hc.linkage

'complete'

from scipy.cluster.hierarchy import dendrogram

## The following is from https://scikit-learn.org/stable/auto_examples/cluster/plot_agglomerative_dendrogram.html
def plot_dendrogram(model, **kwargs):
    # Create linkage matrix and then plot the dendrogram

    # create the counts of samples under each node
    counts = np.zeros(model.children_.shape[0])
    n_samples = len(model.labels_)
    for i, merge in enumerate(model.children_):
        current_count = 0
        for child_idx in merge:
            if child_idx < n_samples:
                current_count += 1  # leaf node
            else:
                current_count += counts[child_idx - n_samples]
        counts[i] = current_count

    linkage_matrix = np.column_stack([model.children_, model.distances_,
                                      counts]).astype(float)

    # Plot the corresponding dendrogram
    dendrogram(linkage_matrix, **kwargs)

plot_dendrogram(hc, truncate_mode='level', p=3)
plt.xlabel("Number of points in node (or index of point if no parenthesis).")
plt.show()

findfont: Font family ['Future Medium'] not found. Falling back to DejaVu Sans.

hc = AgglomerativeClustering( n_clusters=3,
                             linkage='average')

hc.fit(iris[['Sepal.Length','Sepal.Width']]);

hc.labels_

array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 2, 2, 2, 2, 2, 2, 2, 0, 2, 0, 0, 2, 2, 2, 2, 2,
       2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
       2, 2, 2, 2, 2, 0, 2, 2, 2, 2, 0, 2, 2, 2, 1, 2, 2, 1, 0, 1, 2, 1,
       2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1,
       2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2])

iris['hc_labels'] = pd.Series(hc.labels_).astype('category')

sns.relplot(data=iris, x = 'Sepal.Length', y= 'Sepal.Width', 
           hue = 'hc_labels');

/Users/abhijit/opt/miniconda3/envs/ds/lib/python3.8/site-packages/seaborn/axisgrid.py:324:
RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface
(`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory.
(To control this warning, see the rcParam `figure.max_open_warning`).
  fig, axes = plt.subplots(nrow, ncol, **kwargs)

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Source: Abhijit Dasgupta, https://www.araastat.com/BIOF085/machine-learning-using-python.html#unsupervised-learning
This work is licensed under a Creative Commons Attribution 4.0 License.