Crate kmedoids

k-Medoids Clustering with the FasterPAM Algorithm

For details on the implemented FasterPAM algorithm, please see:

Erich Schubert, Peter J. Rousseeuw
Fast and Eager k-Medoids Clustering:
O(k) Runtime Improvement of the PAM, CLARA, and CLARANS Algorithms
Information Systems (101), 2021, 101804
https://doi.org/10.1016/j.is.2021.101804 (open access)

Erich Schubert, Peter J. Rousseeuw:
Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms
In: 12th International Conference on Similarity Search and Applications (SISAP 2019), 171-187.
https://doi.org/10.1007/978-3-030-32047-8_16
Preprint: https://arxiv.org/abs/1810.05691

This is a port of the original Java code from ELKI to Rust. But it does not include all functionality in the original benchmarks.

If you use this in scientific work, please consider citing above articles.

Example

Given a dissimilarity matrix of size 4 x 4, use:

let data = ndarray::arr2(&[[0,1,2,3],[1,0,4,5],[2,4,0,6],[3,5,6,0]]);
let mut meds = kmedoids::random_initialization(4, 2, &mut rand::thread_rng());
let (loss, assi, n_iter, n_swap): (f64, _, _, _) = kmedoids::fasterpam(&data, &mut meds, 100);
println!("Loss is: {}", loss);

Re-exports

pub use crate::arrayadapter::ArrayAdapter;

Modules

arrayadapter

Adapter trait for accessing different types of arrays.

Functions

alternating

Run the Alternating algorithm, a k-means-style alternate optimization.

dynmsc

Run the DynMSC algorithm.

fastermsc

Run the FasterMSC algorithm.

fasterpam

Run the FasterPAM algorithm.

fastmsc

Run the FastMSC algorithm, which yields the same results as the original PAMMEDSIL.

fastpam1

Run the FastPAM1 algorithm, which yields the same results as the original PAM.

first_k

Use the first objects as initial medoids.

medoid_silhouette

Compute the Medoid Silhouette of a clustering.

pam

Run the original PAM algorithm (BUILD and SWAP).

pam_build

Run the original PAM BUILD algorithm.

pam_swap

Run the original PAM SWAP algorithm (no BUILD, but given initial medoids).

pammedsil

Run the original PAM BUILD algorithm combined with the PAMMEDSIL SWAP.

pammedsil_swap

Run the original PAMMEDSIL SWAP algorithm (no initialization, but given initial medoids).

pamsil

Run the original PAM BUILD algorithm combined with the PAMSIL SWAP.

pamsil_swap

Run the original PAMSIL SWAP algorithm (no BUILD, but given initial medoids).

par_fasterpam

Run the FasterPAM algorithm (parallel version).

par_silhouette

Compute the Silhouette of a strict partitional clustering (parallel implementation).

rand_fasterpam

Run the FasterPAM algorithm with additional randomization.

random_initialization

Random initialization (requires the rand crate)

silhouette

Compute the Silhouette of a strict partitional clustering.