scikit-clarans

Scikit-learn compatible implementation of CLARANS and FastCLARANS for $k$-medoids clustering.

scikit-clarans implements $k$-medoids clustering in Python using the scikit-learn estimator interface. While $k$-means calculates artificial cluster centroids, $k$-medoids picks actual data points from the dataset as cluster centers.

Why use k-medoids?

Outlier resistance: Medoids minimize absolute distances ($\sum d$) rather than squared Euclidean distances ($\sum d^2$), keeping centers stable when the dataset contains extreme values.
Custom distance metrics: Supports metrics such as Manhattan, cosine, or precomputed distances, whereas standard $k$-means requires Euclidean space.
Direct interpretability: Every cluster center corresponds to a real record in the input data.

Choosing between CLARANS and FastCLARANS

FastCLARANS: Evaluates swaps across all $k$ medoids in a single pass using FastPAM1 delta calculations (Schubert & Rousseeuw, 2021). It uses $O(n)$ memory and is faster for most workloads.
CLARANS: The classic randomized search algorithm from Ng & Han (2002). It supports delta cost evaluations with cached distances as well as brute-force recalculation.

Features

Scikit-learn compatibility: Extends BaseEstimator and ClusterMixin for use in Pipeline, GridSearchCV, and model evaluation workflows.
C acceleration: Core delta computations run in Cython with a pure Python and NumPy fallback.
Distance routing: Automatically routes distance calculations to SciPy cdist for dense arrays, scikit-learn DistanceMetric for sparse matrices, or pairwise_distances.
Low memory overhead: Computes distances as needed with $O(n)$ working memory instead of storing a full $O(n^2)$ matrix.
Initialization options: Supports k-medoids++, build, heuristic, uniform random sampling, or user-supplied medoid indices.

Installation

Install from PyPI:

pip install scikit-clarans

Install from source:

git clone https://github.com/ThienNguyen3001/scikit-clarans.git
cd scikit-clarans
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
clarans = CLARANS(n_clusters=5, num_local=3, init='k-medoids++', cost_evaluation='delta', random_state=42)

# 3. Fit
clarans.fit(X)

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

FastCLARANS

FastCLARANS evaluates swaps across all $k$ medoids simultaneously using the FastPAM1 formulation from Schubert & Rousseeuw (2021):

from clarans import FastCLARANS

fast_model = FastCLARANS(n_clusters=5, num_local=3, random_state=42)
fast_model.fit(X)

Differences from CLARANS:

Samples non-medoid candidates instead of medoid-candidate pairs.
Evaluates swaps against all $k$ medoids in a single pass ($O(k)$ fewer distance queries).
Operates in $O(n)$ memory instead of $O(n^2)$.

Examples

Runnable scripts are located in the examples/ directory:

python examples/plot_quick_start.py

Documentation

Full API documentation and guides are available at https://scikit-clarans.readthedocs.io.

Contributing

Contributions and bug reports are welcome. See CONTRIBUTING.md for development setup and testing instructions.

Citation

If you use scikit-clarans in your research or software, 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}
}

Academic References

The core algorithms implemented in this package originate from:

CLARANS:

Ng, R. T., & Han, J. (2002). CLARANS: A method for clustering objects for spatial data mining. IEEE Transactions on Knowledge and Data Engineering, 14(5), 1003-1016. doi:10.1109/TKDE.2002.1033770
FastCLARANS & FastPAM1:

Schubert, E., & Rousseeuw, P. J. (2021). Fast and eager k-medoids clustering: O(k) runtime improvement of the PAM, CLARA, and CLARANS algorithms. Information Systems, 101, 101804. doi:10.1016/j.is.2021.101804
Seeding & Initialization:

Initialization strategies (k-medoids++, heuristic, build) are adapted from the scikit-learn-extra KMedoids implementation.

License

This project is licensed under the MIT License. See LICENSE for details.

Metadata

Release files for scikit-clarans 0.3.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for scikit-clarans 0.3.2
File	Size	Uploaded
scikit_clarans-0.3.2.tar.gz	91.2 kB	Sep 30, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for scikit-clarans 0.3.2
File	Interpreter	ABI	Platform	Reset
scikit_clarans-0.3.2-cp313-cp313-win_amd64.whl 177.4 kB Sep 30, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
scikit_clarans-0.3.2-cp313-cp313-musllinux_1_2_x86_64.whl 205.3 kB Sep 30, 2026	CPython 3.13	CPython 3.13	Linux musl 1.2+ x86-64	Details
scikit_clarans-0.3.2-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl 202.5 kB Sep 30, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ x86-64, Linux glibc 2.28+ x86-64	Details
scikit_clarans-0.3.2-cp313-cp313-macosx_11_0_arm64.whl 180.5 kB Sep 30, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
scikit_clarans-0.3.2-cp313-cp313-macosx_10_13_x86_64.whl 186.4 kB Sep 30, 2026	CPython 3.13	CPython 3.13	macOS 10.13+ x86-64	Details
scikit_clarans-0.3.2-cp312-cp312-win_amd64.whl 177.6 kB Sep 30, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
scikit_clarans-0.3.2-cp312-cp312-musllinux_1_2_x86_64.whl 204.3 kB Sep 30, 2026	CPython 3.12	CPython 3.12	Linux musl 1.2+ x86-64	Details
scikit_clarans-0.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl 202.8 kB Sep 30, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.17+ x86-64, Linux glibc 2.28+ x86-64	Details
scikit_clarans-0.3.2-cp312-cp312-macosx_11_0_arm64.whl 180.8 kB Sep 30, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
scikit_clarans-0.3.2-cp312-cp312-macosx_10_13_x86_64.whl 186.6 kB Sep 30, 2026	CPython 3.12	CPython 3.12	macOS 10.13+ x86-64	Details
scikit_clarans-0.3.2-cp311-cp311-win_amd64.whl 179.9 kB Sep 30, 2026	CPython 3.11	CPython 3.11	Windows x86-64	Details
scikit_clarans-0.3.2-cp311-cp311-musllinux_1_2_x86_64.whl 214.5 kB Sep 30, 2026	CPython 3.11	CPython 3.11	Linux musl 1.2+ x86-64	Details
scikit_clarans-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl 211.3 kB Sep 30, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.17+ x86-64, Linux glibc 2.28+ x86-64	Details
scikit_clarans-0.3.2-cp311-cp311-macosx_11_0_arm64.whl 178.0 kB Sep 30, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details
scikit_clarans-0.3.2-cp311-cp311-macosx_10_9_x86_64.whl 183.5 kB Sep 30, 2026	CPython 3.11	CPython 3.11	macOS 10.9+ x86-64	Details
scikit_clarans-0.3.2-cp310-cp310-win_amd64.whl 179.2 kB Sep 30, 2026	CPython 3.10	CPython 3.10	Windows x86-64	Details
scikit_clarans-0.3.2-cp310-cp310-musllinux_1_2_x86_64.whl 215.5 kB Sep 30, 2026	CPython 3.10	CPython 3.10	Linux musl 1.2+ x86-64	Details
scikit_clarans-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl 214.1 kB Sep 30, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.17+ x86-64, Linux glibc 2.28+ x86-64	Details
scikit_clarans-0.3.2-cp310-cp310-macosx_11_0_arm64.whl 179.4 kB Sep 30, 2026	CPython 3.10	CPython 3.10	macOS 11.0+ ARM64	Details
scikit_clarans-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl 185.0 kB Sep 30, 2026	CPython 3.10	CPython 3.10	macOS 10.9+ x86-64	Details
scikit_clarans-0.3.2-cp39-cp39-win_amd64.whl 179.5 kB Sep 30, 2026	CPython 3.9	CPython 3.9	Windows x86-64	Details
scikit_clarans-0.3.2-cp39-cp39-musllinux_1_2_x86_64.whl 216.5 kB Sep 30, 2026	CPython 3.9	CPython 3.9	Linux musl 1.2+ x86-64	Details
scikit_clarans-0.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl 214.3 kB Sep 30, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ x86-64, Linux glibc 2.28+ x86-64	Details
scikit_clarans-0.3.2-cp39-cp39-macosx_11_0_arm64.whl 179.9 kB Sep 30, 2026	CPython 3.9	CPython 3.9	macOS 11.0+ ARM64	Details
scikit_clarans-0.3.2-cp39-cp39-macosx_10_9_x86_64.whl 185.3 kB Sep 30, 2026	CPython 3.9	CPython 3.9	macOS 10.9+ x86-64	Details

Total release size: 4.9 MB

Release files / scikit_clarans-0.3.2.tar.gz

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp312-cp312-macosx_11_0_arm64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp312-cp312-macosx_10_13_x86_64.whl

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Identity

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Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp311-cp311-win_amd64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
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Release files / scikit_clarans-0.3.2-cp311-cp311-musllinux_1_2_x86_64.whl

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Provenance

Identity

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Publishing repository: github.com/ThienNguyen3001/scikit-clarans
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Release files / scikit_clarans-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp311-cp311-macosx_11_0_arm64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp311-cp311-macosx_10_9_x86_64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp310-cp310-win_amd64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
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Release files / scikit_clarans-0.3.2-cp310-cp310-musllinux_1_2_x86_64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp310-cp310-macosx_11_0_arm64.whl

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Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Artifact

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Release files / scikit_clarans-0.3.2-cp39-cp39-win_amd64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Artifact

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Release files / scikit_clarans-0.3.2-cp39-cp39-musllinux_1_2_x86_64.whl

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Upload date	Sep 30, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

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Publishing platform: GitHub Actions
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Release files / scikit_clarans-0.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Release files / scikit_clarans-0.3.2-cp39-cp39-macosx_11_0_arm64.whl

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Release files / scikit_clarans-0.3.2-cp39-cp39-macosx_10_9_x86_64.whl

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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing repository: github.com/ThienNguyen3001/scikit-clarans
Publishing commit: github.com/ThienNguyen3001/scikit-clarans/tree/801e78dfdd418f0e9d91133c30b0c740f4a69100

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Publishing logs: github.com/ThienNguyen3001/scikit-clarans/actions/runs/36677418743/attempts/1

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Release history Release notifications | RSS feed

0.3.4

Oct 11, 2026 26 release files

0.3.3

Oct 5, 2026 26 release files

This release

0.3.2 This release

Sep 30, 2026 26 release files

0.3.1

Sep 23, 2026 26 release files

0.3.0

Sep 16, 2026 26 release files

0.2.2

Sep 9, 2026 2 release files

0.2.1

Feb 7, 2026 2 release files

0.2.0

Feb 3, 2026 2 release files

0.1.3

Jan 28, 2026 2 release files

0.1.2

Jan 26, 2026 2 release files

0.1.1

Jan 26, 2026 2 release files

scikit-clarans 0.3.2

scikit-clarans

Why use k-medoids?

Choosing between CLARANS and FastCLARANS

Features

Installation

Quick Start

CLARANS

FastCLARANS

Examples

Documentation

Contributing

Citation

Academic References

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1 maintainer

Credits

GitHub Statistics

License

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Metadata

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Key dates

1 maintainer

Credits

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Release files for scikit-clarans 0.3.2

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Release files / scikit_clarans-0.3.2.tar.gz

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