BisectingKMeans: Performs clustering according to the bisecting k-means...

In rgudhi: An Interface to the GUDHI Library for Topological Data Analysis

Performs clustering according to the bisecting k-means algorithm

Description

This is a wrapper around the Python class sklearn.cluster.BisectingKMeans.

Super classes

rgudhi::PythonClass -> rgudhi::SKLearnClass -> rgudhi::BaseClustering -> BisectingKMeans

Methods

Public methods

• BisectingKMeans$new()

• BisectingKMeans$clone()

Inherited methods

• rgudhi::PythonClass$get_python_class()
• rgudhi::PythonClass$set_python_class()
• rgudhi::SKLearnClass$apply()
• rgudhi::SKLearnClass$fit()
• rgudhi::SKLearnClass$fit_transform()
• rgudhi::SKLearnClass$get_params()
• rgudhi::SKLearnClass$set_params()
• rgudhi::SKLearnClass$transform()

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Method new()

The BisectingKMeans class constructor.

Usage

BisectingKMeans$new(
  n_clusters = 2L,
  init = c("k-means++", "random"),
  n_init = 10L,
  max_iter = 300L,
  tol = 1e-04,
  verbose = 0L,
  random_state = NULL,
  copy_x = TRUE,
  algorithm = c("lloyd", "elkan"),
  bisecting_strategy = c("biggest_inertia", "largest_cluster")
)

Arguments

n_clusters

An integer value specifying the number of clusters to form as well as the number of centroids to generate. Defaults to 2L.

init

Either a string or a numeric matrix of shape \mathrm{n_clusters} \times \mathrm{n_features} specifying the method for initialization. If a string, choices are:

• "k-means++": selects initial cluster centroids using sampling based on an empirical probability distribution of the points’ contribution to the overall inertia. This technique speeds up convergence, and is theoretically proven to be \mathcal{O}(\log(k))-optimal. See the description of n_init for more details;

• "random": chooses n_clusters observations (rows) at random from data for the initial centroids. Defaults to "k-means++".

n_init

An integer value specifying the number of times the k-means algorithm will be run with different centroid seeds. The final results will be the best output of n_init consecutive runs in terms of inertia. Defaults to 10L.

max_iter

An integer value specifying the maximum number of iterations of the k-means algorithm for a single run. Defaults to 300L.

tol

A numeric value specifying the relative tolerance with regards to Frobenius norm of the difference in the cluster centers of two consecutive iterations to declare convergence. Defaults to 1e-4.

verbose

An integer value specifying the level of verbosity. Defaults to 0L which is equivalent to no verbose.

random_state

An integer value specifying the initial seed of the random number generator. Defaults to NULL which uses the current timestamp.

copy_x

A boolean value specifying whether the original data is to be modified. When pre-computing distances it is more numerically accurate to center the data first. If copy_x is TRUE, then the original data is not modified. If copy_x is FALSE, the original data is modified, and put back before the function returns, but small numerical differences may be introduced by subtracting and then adding the data mean. Note that if the original data is not C-contiguous, a copy will be made even if copy_x is FALSE. If the original data is sparse, but not in CSR format, a copy will be made even if copy_x is FALSE. Defaults to TRUE.

algorithm

A string specifying the k-means algorithm to use. The classical EM-style algorithm is "lloyd". The "elkan" variation can be more efficient on some datasets with well-defined clusters, by using the triangle inequality. However it’s more memory-intensive due to the allocation of an extra array of shape \mathrm{n_samples} \times \mathrm{n_clusters}. Defaults to "lloyd".

bisecting_strategy

A string specifying how bisection should be performed. Choices are:

• "biggest_inertia": means that it will always check all calculated cluster for cluster with biggest SSE (Sum of squared errors) and bisect it. This approach concentrates on precision, but may be costly in terms of execution time (especially for larger amount of data points).

• "largest_cluster": means that it will always split cluster with largest amount of points assigned to it from all clusters previously calculated. That should work faster than picking by SSE and may produce similar results in most cases. Defaults to "biggest_inertia".

Returns

An object of class BisectingKMeans.

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Method clone()

The objects of this class are cloneable with this method.

Usage

BisectingKMeans$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cl <- BisectingKMeans$new()

rgudhi documentation built on March 31, 2023, 11:38 p.m.