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Preprocessing for Clustering

Reference for clustering-algorithm-selector · 64 lines

AI & Machine Learning / Classical Machine Learningv1.0.0Updated OCT 25 20264 references2 scripts

Clusters are defined by distances, so preprocessing is the model.

Feature choice

  • Use features that describe the behaviour the segments should differ on (for customer segments: recency, frequency, monetary, product mix, channel), not IDs, dates or outcome labels.
  • Drop near-duplicates: two copies of the same signal double its weight.
  • Fewer, meaningful features beat many weak ones (distances concentrate in high dimensions).

Scaling

SituationTransform
Mixed unitsStandardScaler (or RobustScaler with outliers)
Skewed amounts / countslog1p, then standardise
Proportionskeep in [0, 1] or logit
Features of different importancemultiply scaled columns by weights deliberately

Unscaled, the widest column decides the clusters (feature-scaling-advisor's scale_impact.py shows the dominance).

Categorical features

OptionNotes
k-prototypes / k-modesnative mixed / categorical objective
Gower distanceproper mixed dissimilarity; O(n²)
One-hot + scalinga binary column's variance depends on its frequency; down-weight one-hot blocks (e.g. divide by sqrt(levels)) or the categorical features dominate
Target-free embeddingse.g. from an autoencoder or entity embeddings

Dimensionality

  • PCA to retain ~80-90% variance removes noise and speeds k-means/GMM.
  • UMAP (n_components 5-20, min_dist=0.0) before HDBSCAN works well for complex manifolds; do not cluster on a 2-D t-SNE plot (it distorts densities and distances).
  • Check that clusters found in the reduced space are visible in the original feature profiles.

Distance metrics

DataMetric
Continuous, scaledEuclidean
High-dimensional embeddings / textcosine (or L2-normalise then Euclidean)
Counts / profilescosine, Bray-Curtis
Lat/lonhaversine (radians)
MixedGower
BinaryJaccard, Hamming

Outliers

Extreme rows pull centroids (k-means) and steal mixture components (GMM). Either cap features (winsorise), remove obvious errors, or use a density method that labels noise.

Checklist

  • IDs, dates, labels removed
  • Skewed features transformed
  • Features scaled; weights deliberate
  • Categoricals handled with a suitable dissimilarity
  • Redundant features removed
  • Dimensionality reduced if > ~20-50 features
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