scikit-clarans 0.2.0

A scikit-learn compatible implementation of CLARANS clustering algorithm

scikit-clarans

A scikit-learn compatible implementation of the CLARANS (Clustering Large Applications based on RANdomized Search) algorithm.

CLARANS acts as a bridge between the high quality of PAM (Partition Around Medoids) and the speed required for large datasets. By using randomized search instead of exhaustive search, it finds high-quality medoids efficiently without exploring the entire graph of solutions.

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Features

• Scikit-Learn Native: Use it just like KMeans or DBSCAN. Drop-in compatibility for pipelines and cross-validation.
• Scalable: Designed to handle datasets where standard PAM/k-medoids is too slow.
• Flexible: Choose from multiple initialization strategies (k-medoids++, build, etc.) and distance metrics (euclidean, manhattan, cosine, etc.).

Installation

Install simply via pip:

pip install scikit-clarans

Or install from source:

pip install .

For development

pip install -e ".[dev]"

Quick Start

CLARANS

from clarans import CLARANS
from sklearn.datasets import make_blobs

# 1. Create dummy data
X, _ = make_blobs(n_samples=1000, centers=5, random_state=42)

# 2. Initialize CLARANS
#    - n_clusters: 5 clusters
#    - numlocal: 3 restarts for better quality
#    - init: 'k-medoids++' for smart starting points
clarans = CLARANS(n_clusters=5, numlocal=3, init='k-medoids++', random_state=42)

# 3. Fit
clarans.fit(X)

# 4. Results
print("Medoid Indices:", clarans.medoid_indices_)
print("Labels:", clarans.labels_)

FastCLARANS

FastCLARANS implements the faster variant from Schubert & Rousseeuw (2021). It evaluates swaps with all k medoids simultaneously using FastPAM1 delta formulas, exploring k edges of the search graph in the time CLARANS explores one:

from clarans import FastCLARANS

# FastCLARANS computes distances on-the-fly (memory efficient)
# and samples 2.5% of non-medoid points per iteration
fast_model = FastCLARANS(n_clusters=5, numlocal=3, random_state=42)
fast_model.fit(X)

Key differences from CLARANS:

• Samples only non-medoid candidates (not medoid-candidate pairs)
• Evaluates swap with all k medoids at once (O(k) speedup per evaluation)
• Memory efficient: O(n) instead of O(n²)

Examples

This repository includes a number of runnable examples in the examples/ folder showing common usage patterns, integrations and a Jupyter notebook (examples/clarans_examples.ipynb) with many interactive recipes. Run any example with::

python examples/01_quick_start.py

Documentation

For full API reference and usage guides, please see the Documentation.

Contributing

Contributions are welcome! Please check out CONTRIBUTING.md for guidelines.

Citation

If you use scikit-clarans in your research, please cite:

@software{scikit_clarans,
  author       = {Nguyen, Ngoc Thien},
  title        = {scikit-clarans: A Python Library for CLARANS Clustering},
  year         = {2026},
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.18366801},
  url          = {https://github.com/ThienNguyen3001/scikit-clarans}
}

License

This project is licensed under the MIT License - see the LICENSE file for details.