5/6/24, 12:16 AM 2020-06-06-02-Hierarchical-Clustering.

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keyboard_arrow_down Hierarchical Clustering

A Summary of lecture "Cluster Analysis in Python", via datacamp

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author: Chanseok Kang
categories: [Python, Datacamp, Machine Learning]
image: images/fifa_cluster.png

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns

keyboard_arrow_down Basics of hierarchical clustering

Creating a distance matrix using linkage

method : how to calculate the proximity of clusters

metric : distance metric
optimal_ordering : order data points

Type of Methods

single: based on two closest objects

complete: based on two farthest objects
average: based on the arithmetic mean of all objects
centroids: based on the geometric mean of all objects
median: based on the median of all objects
ward: based on the sum of squares

keyboard_arrow_down Hierarchical clustering: ward method

It is time for Comic-Con! Comic-Con is an annual comic-based convention held in major cities in the world. You have the data of last year's
footfall, the number of people at the convention ground at a given time. You would like to decide the location of your stall to maximize sales.
Using the ward method, apply hierarchical clustering to find the two points of attraction in the area.

Preprocess

comic_con = pd.read_csv('./dataset/comic_con.csv', index_col=0)

comic_con.head()

x_coordinate y_coordinate

0 17 4

1 20 6

2 35 0

3 14 0

4 37 4

from scipy.cluster.vq import whiten

comic_con['x_scaled'] = whiten(comic_con['x_coordinate'])
comic_con['y_scaled'] = whiten(comic_con['y_coordinate'])

from scipy.cluster.hierarchy import linkage, fcluster

# Use the linkage()

distance_matrix = linkage(comic_con[['x_scaled', 'y_scaled']], method='ward', metric='euclidean')

# Assign cluster labels

comic_con['cluster_labels'] = fcluster(distance_matrix, 2, criterion='maxclust')

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# Plot clusters
sns.scatterplot(x='x_scaled', y='y_scaled', hue='cluster_labels', data=comic_con);

keyboard_arrow_down Hierarchical clustering: single method

Let us use the same footfall dataset and check if any changes are seen if we use a different method for clustering.

# Use the linkage()

distance_matrix = linkage(comic_con[['x_scaled', 'y_scaled']], method='single', metric='euclidean')

# Assign cluster labels

comic_con['cluster_labels'] = fcluster(distance_matrix, 2, criterion='maxclust')

# Plot clusters
sns.scatterplot(x='x_scaled', y='y_scaled', hue='cluster_labels', data=comic_con);

keyboard_arrow_down Hierarchical clustering: complete method

For the third and final time, let us use the same footfall dataset and check if any changes are seen if we use a different method for clustering.

# Use the linkage()

distance_matrix = linkage(comic_con[['x_scaled', 'y_scaled']], method='complete', metric='euclidean')

# Assign cluster labels

comic_con['cluster_labels'] = fcluster(distance_matrix, 2, criterion='maxclust')

# Plot clusters
sns.scatterplot(x='x_scaled', y='y_scaled', hue='cluster_labels', data=comic_con);

keyboard_arrow_down Visualize clusters

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Why visualize clusters?

Try to make sense of the clusters formed

An additional step in validation of clusters
Spot trends in data

keyboard_arrow_down Visualize clusters with matplotlib

We have discussed that visualizations are necessary to assess the clusters that are formed and spot trends in your data. Let us now focus on
visualizing the footfall dataset from Comic-Con using the matplotlib module.

# Define a colors dictionary for clusters

colors = {1:'red', 2:'blue'}

# Plot the scatter plot

comic_con.plot.scatter(x='x_scaled', y='y_scaled', c=comic_con['cluster_labels'].apply(lambda x: colors[x]));

keyboard_arrow_down Visualize clusters with seaborn

Let us now visualize the footfall dataset from Comic Con using the seaborn module. Visualizing clusters using seaborn is easier with the inbuild
hue function for cluster labels.

# Plot a scatter plot using seaborn

sns.scatterplot(x='x_scaled', y='y_scaled', hue='cluster_labels', data=comic_con)

<matplotlib.axes._subplots.AxesSubplot at 0x27d3a82d1c8>

keyboard_arrow_down How many clusters?

Introduction to dendrograms

Strategy till now - decide clusters on visual inspection

Dendrograms help in showing progressions as clusters are merged
A dendrogram is a branching diagram that demonstrates how each cluster is composed by branching out into its child nodes

keyboard_arrow_down Create a dendrogram

Dendrograms are branching diagrams that show the merging of clusters as we move through the distance matrix. Let us use the Comic Con
footfall data to create a dendrogram.

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from scipy.cluster.hierarchy import dendrogram

# Create a dendrogram
dn = dendrogram(distance_matrix)

Limitations of hierarchical clustering

Comparison of runtime of linkage method

Increasing runtime with data points

Quadratic increase of runtime
Not feasible for large datasets

keyboard_arrow_down Timing run of hierarchical clustering

In earlier exercises of this chapter, you have used the data of Comic-Con footfall to create clusters. In this exercise you will time how long it
takes to run the algorithm on DataCamp's system.

Remember that you can time the execution of small code snippets with:

%timeit sum([1, 3, 2])

%timeit linkage(comic_con[['x_scaled', 'y_scaled']], method='ward', metric='euclidean')

459 µs ± 377 ns per loop (mean ± std. dev. of 7 runs, 1000 loops each)

keyboard_arrow_down FIFA 18: exploring defenders

In the FIFA 18 dataset, various attributes of players are present. Two such attributes are:

sliding tackle: a number between 0-99 which signifies how accurate a player is able to perform sliding tackles
aggression: a number between 0-99 which signifies the commitment and will of a player These are typically high in defense-minded
players. In this exercise, you will perform clustering based on these attributes in the data.

This data consists of 5000 rows, and is considerably larger than earlier datasets. Running hierarchical clustering on this data can take up to 10
seconds.

Preprocess

fifa = pd.read_csv('./dataset/fifa_18_dataset.csv')
fifa.head()

sliding_tackle aggression

0 23 63

1 26 48

2 33 56

3 38 78

4 11 29

fifa['scaled_sliding_tackle'] = whiten(fifa['sliding_tackle'])
fifa['scaled_aggression'] = whiten(fifa['aggression'])

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# Fit the data into a hierarchical cluster
distance_matrix = linkage(fifa[['scaled_sliding_tackle', 'scaled_aggression']], method='ward')

# Assign cluster labels to each row of data

fifa['cluster_labels'] = fcluster(distance_matrix, 3, criterion='maxclust')

# Display cluster centers of each cluster

print(fifa[['scaled_sliding_tackle', 'scaled_aggression', 'cluster_labels']].groupby('cluster_labels').mean())

# Create a scatter plot through seaborn

sns.scatterplot(x='scaled_sliding_tackle', y='scaled_aggression', hue='cluster_labels', data=fifa)
plt.savefig('../images/fifa_cluster.png')

scaled_sliding_tackle scaled_aggression
cluster_labels
1 0.987373 1.849142
2 3.013487 4.063492
3 1.934455 3.210802

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