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I am using KMeans clustering in Python (Scikit-learn) with around 70 input features per sample and a little over 1,000 samples. It is performing rather well, which is good. However, I would quite like to visualize the results on a single graph, to better inspect the clusters and see the distance between each cluster.

I have seen examples such as below for visualising clusters with 2 input features per sample, but I can't find any way of doing something similar for 3+ input features. Is there a way to adapt the below in a way that solves my issue?

enter image description here

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The most intuitive way of visualizing your cluster results would be by using a linear projection like PCA.

In this way you can visualize for example the first 3 components and assign a color to each point according to cluster_id

Also important, you should in this case check the explained_variance as measure of how reliable the projection is, since you are projecting your original space into a 3D dimension space.

from sklearn.cluster import KMeans
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler, FunctionTransformer
from sklearn.decomposition import PCA

import plotly.express as px

kmeans = Pipeline([("scaling",StandardScaler()),("clustering",KMeans(n_clusters=3, init='k-means++', max_iter=300, n_init=10, random_state=0))]).fit(X)

pca = Pipeline([("standarize", StandardScaler()), ("pca",PCA(n_components = 3)), ("dataframe", FunctionTransformer(lambda x: pd.DataFrame(x, columns = ["first_comp", "second_comp", "third_comp"])))]).fit(X)

X3D = pca.transform(X)

exaplained_variance = pca["pca"].explained_variance_.cumsum()

px.scatter_3d(x = "first_comp", y = "second_comp",z = "third_comp", data_frame= X3D, color= kmeans["clustering"].labels_, title= f"Explained variance: {round(exaplained_variance,3)}")

You should obtain a plot similar to this one:

enter image description here

Hope it helps!

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  • $\begingroup$ Thank you! I'll project my data like this and see how it looks $\endgroup$
    – Robin
    Jul 21, 2021 at 10:22

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