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Clustering Metrics in Machine Learning

Last Updated : 21 Mar, 2024
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Clustering is an unsupervised machine-learning approach that is used to group comparable data points based on specific traits or attributes. It is critical to evaluate the quality of the clusters created when using clustering techniques. These metrics are quantitative indicators used to evaluate the performance and quality of clustering algorithms. In this post, we will explore clustering metrics principles, analyze their importance, and implement them using scikit-learn.

Clustering Metrics

Clustering metrics play a pivotal role in evaluating the effectiveness of machine learning algorithms designed to group similar data points. These metrics provide quantitative measures to assess the quality of clusters formed, helping practitioners choose optimal algorithms for diverse datasets. By gauging factors like compactness, separation, and variance, clustering metrics such as silhouette score, Davies–Bouldin index, and Calinski-Harabasz index offer insights into the performance of clustering techniques. Understanding and applying these metrics contribute to the refinement and selection of clustering algorithms, fostering better insights in unsupervised learning scenarios.

Silhouette Score

A metric called the Silhouette Score is employed to assess a dataset’s well-defined clusters. The cohesiveness and separation between clusters are quantified. Better-defined clusters are indicated by higher scores, which range from -1 to 1. An object is said to be well-matched to its own cluster and poorly-matched to nearby clusters if its score is close to 1. A score of about -1, on the other hand, suggests that the object might be in the incorrect cluster. The Silhouette Score is useful for figuring out how appropriate clustering methods are and how many clusters are best for a particular dataset.

Mathematical Formula:

Silhouette Score (S) for a data point i is calculated as:

[Tex]S(i) = \frac{(b(i)- a(i))}{max({a(i),b(i)})}[/Tex]


  • a(i) is the average distance from i to other data points in the same cluster.
  • b(i) is the smallest average distance from i to data points in a different cluster.

Interpretation: It ranges from -1 (poor clustering) to +1 (perfect clustering). A score close to 1 suggests well-separated clusters.

    Davies-Bouldin Index

    A statistic for assessing the effectiveness of clustering algorithms is the Davies-Bouldin Index. It evaluates a dataset’s clusters’ compactness and separation. Better-defined clusters are indicated by a lower Davies-Bouldin Index, which is determined by comparing each cluster’s average similarity-to-dissimilarity ratio to that of its most similar neighbor. Since clusters with the smallest intra-cluster and largest inter-cluster distances provide a lower index, it aids in figuring out the ideal number of clusters. This index helps choose the best clustering solutions for a variety of datasets by offering a numerical assessment of the clustering quality.

    Mathematical Formula:

    Davies-Bouldin Index (DB) is calculated as the average similarity between each cluster and its closest neighbor:

    [Tex]DB = \left ( \frac{1}{n} \right )\sum max(R_{ij})[/Tex]

    • Here,
      • n is the number of clusters.
      • [Tex]R_{ij}[/Tex] is a measure of dissimilarity between cluster i and the cluster most similar to i.

    Interpretation: Lower numbers suggest better clustering solutions.

    Calinski-Harabasz Index (Variance Ratio Criterion)

    A clustering validation metric called the Calinski-Harabasz Index is used to evaluate the quality of clusters within a dataset. Higher values indicate compact and well-separated clusters. It computes the ratio of the within-cluster variance to the between-cluster variance. It helps determine the ideal number of clusters for a given dataset by comparing the index across various clusterings. Improved cluster definition is implied by a higher Calinski-Harabasz Index. This measure is useful for assessing how well clustering algorithms work, which helps choose the best clustering solution for a variety of datasets.

    Mathematical Formula:

    Calinski-Harabasz Index (CH) is calculated as:

    [Tex]CH = \left ( \left ( \frac{B}{W} \right )\ast \left ( \frac{N-K}{K-1} \right ) \right )[/Tex]

    • Here,
      • B is the sum of squares between clusters.
      • W is the sum of squares within clusters.
      • N is the total number of data points.
      • K is the number of clusters.

    The B and W are calculated as:

    • Calculating between group sum of squares (B)

    [Tex]B= \sum_{k=1}^{K} n_k \times ||C_k – C||^2[/Tex]

    • Here,
      • [Tex]n_k [/Tex] is the number of observation in cluster ‘k’
      • [Tex]C_k [/Tex] is the centroid of cluster ‘k’
      • C is the centroid of the dataset
      • K is number of clusters
    • Calculating within the group sum of squares (W)

    [Tex]W = \sum_{i=1}^{n_k} ||X_{ik} – C_{k}||^2[/Tex]

    • Here,
      • [Tex]n_k [/Tex] is the number of observation in cluster ‘k’
      • [Tex]X_{ik} [/Tex] is the i-th observation of cluster ‘k’
      • [Tex]C_k [/Tex] is the centroid of cluster ‘k’

    Interpretation: Higher numbers suggest better-defined clusters.

    Adjusted Rand Index (ARI)

    The Adjusted Rand Index (ARI) is a metric that compares findings from segmentation or clustering to a ground truth in order to assess how accurate the results are. It evaluates whether data point pairs are clustered together or apart in both the true and anticipated clusterings. Higher values of the index imply better agreement; it corrects for chance agreement and produces a score between -1 and 1. ARI is reliable and appropriate in situations when the cluster sizes in the ground truth may differ. It offers a thorough assessment of clustering performance in situations where class labels are known.

    Mathematical Formula:

    Adjusted Rand Index (ARI) is calculated as:

    [Tex]ARI = \frac{(RI - Expected_{RI})}{(max(RI) - Expected_{RI})}[/Tex]

    • Here,
      • RI is the Rand Index.
      • Expected_RI is the expected value of the Rand Index.

    Interpretation: It ranges from -1 to 1, where 1 indicates perfect clustering, 0 indicates random clustering, and negative values suggest poor clustering.

    Mutual Information (MI)

    A metric called mutual information is used to quantify how dependent two variables are on one another. It evaluates the degree of agreement between the actual and expected cluster designations in the context of clustering evaluation. Mutual Information measures the degree to which the knowledge of one variable reduces uncertainty about the other, hence capturing the quality of clustering outcomes. Better agreement is indicated by higher values; zero denotes no agreement and higher scores signify more mutual information. It provides a reliable indicator of how well clustering algorithms are working and sheds light on how closely anticipated and actual clusters match up.

    Mathematical Formula (MI):

    MI between true labels Y and predicted labels Z is calculated as:

    [Tex]MI(y, z) = \sum \sum p(y_i, z_j)\ast \log \left ( \frac{p(y_i, z_j) }{p(y_i) * p'(z_j)} \right )[/Tex]

    • Here,
      • [Tex]y_i[/Tex] is a true label.
      • [Tex]z_i[/Tex] is a predicted label.
      • [Tex]p(y_i, z_i)[/Tex] is the joint probability of yi and zj.
      • [Tex]p(y_i)[/Tex] and [Tex]p'(z_i)[/Tex] are the marginal probabilities.

    Interpretation: High MI values indicate better alignment between clusters and true labels, signifying good clustering results.

    These clustering metrics help in evaluating the quality and performance of clustering algorithms, allowing for informed decisions when selecting the most suitable clustering solution for a given dataset.

    Steps to Evaluate Clustering Using Sklearn

    Let’s consider an example using the Iris dataset and the K-Means clustering algorithm. We will calculate the Silhouette Score, Davies-Bouldin Index, Calinski-Harabasz Index, and Adjusted Rand Index to evaluate the clustering.

    Import Libraries

    Import the necessary libraries, including scikit-learn (sklearn).


    from sklearn.cluster import KMeans from sklearn.metrics import silhouette_score, davies_bouldin_score, calinski_harabasz_score from sklearn.metrics import mutual_info_score, adjusted_rand_score

    Load Your Data

    Load or generate your dataset for clustering. Iris dataset consists of 150 samples of iris flowers. There are three species of iris flower: setosa, versicolor, and virginica with four features: sepal length, sepal width, petal length, and petal width.


    # Example using a built-in dataset (e.g., Iris dataset) from sklearn.datasets import load_iris iris = load_iris() X =

    Perform Clustering

    Choose a clustering algorithm, such as K-Means, and fit it to your data.

    K means is an unsupervised technique used for creating cluster based on similarity. It iteratively assigns data points to the nearest cluster center and updates the centroids until convergence.


    kmeans = KMeans(n_clusters=3)

    Calculate Clustering Metrics

    Use the appropriate clustering metrics to evaluate the clustering results.


    # Calculate clustering metrics silhouette = silhouette_score(X, kmeans.labels_) db_index = davies_bouldin_score(X, kmeans.labels_) ch_index = calinski_harabasz_score(X, kmeans.labels_) ari = adjusted_rand_score(, kmeans.labels_) mi = mutual_info_score(, kmeans.labels_) # Print the metric scores print(f"Silhouette Score: {silhouette:.2f}") print(f"Davies-Bouldin Index: {db_index:.2f}") print(f"Calinski-Harabasz Index: {ch_index:.2f}") print(f"Adjusted Rand Index: {ari:.2f}") print(f"Mutual Information (MI): {mi:.2f}")


    Silhouette Score: 0.55
    Davies-Bouldin Index: 0.67
    Calinski-Harabasz Index: 561.59
    Adjusted Rand Index: 0.72
    Mutual Information (MI): 0.81

    Interpret the Metrics

    Analyze the metric scores to assess the quality of your clustering results. Higher scores are generally better.

    Here’s an interpretation of the metric scores obtained:

    • Silhouette Score (0.55): This score reveals how similar data points are inside their clusters when compared to data points from other clusters. A result of 0.55 indicates that there is some separation between the clusters, but there is still space for improvement. Closer to 1 values suggest better-defined clusters.
    • Davies-Bouldin Index (0.66): This index calculates the average similarity between each cluster and its closest neighbors. A lower score is preferable, and 0.66 suggests a pretty strong separation across clusters.
    • The score Index (561.63) calculates the ratio of between-cluster variation to within-cluster variance. Higher values suggest more distinct groups. Your clusters are distinct and independent with a score of 561.63.
    • The Adjusted Rand Index (0.73) compares the resemblance of genuine class labels to predicted cluster labels. A rating of 0.73 shows that the clustering findings and the actual class labels correspond rather well.
    • Mutual Information (MI) (0.75): This metric measures the agreement between the true class labels and the predicted cluster labels. A score of 0.75 indicates a substantial amount of shared information between the true labels and the clusters assigned by the algorithm. It signifies that the clustering solution captures a significant portion of the underlying structure in the data, aligning well with the actual class labels.

    In this article, we have demonstrated how to apply clustering metrics using scikit-learn in machine learning using Iris dataset and K means clustering. These metrics provide quantifiable estimates of how well data points are clustered and how closely these clusters fit with the data’s underlying structure. These metrics allow data scientists to measure the quality of clustering findings quantitatively, resulting in more informed judgments and improvements to clustering algorithms and applications.

    Frequently Asked Questions (FAQs) on Clustering Metrics

    Q. What are clustering metrics?

    Clustering metrics are measures used to evaluate the performance and quality of clustering algorithms by assessing the similarity of data points within the same cluster and dissimilarity across different clusters.

    Q. Why are clustering metrics important?

    Clustering metrics help quantify the effectiveness of clustering algorithms, allowing practitioners to choose or optimize algorithms based on specific objectives and characteristics of the data.

    Q. How is the silhouette score calculated?

    The silhouette score measures how similar an object is to its cluster compared to other clusters. It is calculated as the difference between the average intra-cluster distance and the nearest-cluster distance, normalized by the maximum of the two.

    Q. Can clustering metrics handle different shapes of clusters?

    Yes, clustering metrics can handle various cluster shapes. However, the choice of metric may depend on the expected shapes and characteristics of the clusters.

    Q. Is it possible to use clustering metrics for hierarchical clustering?

    Yes, clustering metrics can be applied to hierarchical clustering by assessing the quality of the resulting dendrogram or clusters at different levels.

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