Limitations of hierarchical clustering

Cluster Analysis in Python

Shaumik Daityari

Business Analyst

Measuring speed in hierarchical clustering

timeit module
Measure the speed of .linkage() method
Use randomly generated points
Run various iterations to extrapolate

Use of timeit module

from scipy.cluster.hierarchy import linkage
import pandas as pd
import random, timeit

points = 100
df = pd.DataFrame({'x': random.sample(range(0, points), points),
                   'y': random.sample(range(0, points), points)})

%timeit linkage(df[['x', 'y']], method = 'ward', metric = 'euclidean')

1.02 ms ± 133 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

Comparison of runtime of linkage method

Increasing runtime with data points
Quadratic increase of runtime
Not feasible for large datasets

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Cluster Analysis in Python