When we want to do some cluster analysis to identify groups in our data, we often use algorithms like K-Means, which require the specification of a number of clusters. But the issue is that we usually don’t know how many clusters there are.
There are many methods on how to determine the correct number, like silhouettes or elbow plot, to name a few. But they usually don’t give much insight into what is happening between different options, so the numbers are a bit abstract.
Matthias Schonlau proposed another approach – a clustergram. Clustergram is a two-dimensional plot capturing the flows of observations between classes as you add more clusters. It tells you how your data reshuffles and how good your splits are. Tal Galili later implemented clustergram for K-Means in R. And I have used Tal’s implementation, ported it to Python and created
clustergram – a Python package to make clustergrams.
clustergram currently supports K-Means and using
scikit-learn (inlcuding Mini-Batch implementation) and RAPIDS.AI
cuML (if you have a CUDA-enabled GPU), Gaussian Mixture Model (
scikit-learn only) and hierarchical clustering based on
scipy.hierarchy. Alternatively, we can create clustergram based on labels and data derived from alternative custom clustering algorithms. It provides a sklearn-like API and plots clustergram using matplotlib, which gives it a wide range of styling options to match your publication style.
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