pkbc: Poisson kernel-based clustering on the sphere

In QuadratiK: Collection of Methods Constructed using Kernel-Based Quadratic Distances

Poisson kernel-based clustering on the sphere

Description

The function pkbc() performs the Poisson kernel-based clustering algorithm on the sphere proposed by Golzy and Markatou (2020). The proposed algorithm is based on a mixture, with M components, of Poisson kernel-based densities on the hypersphere \mathcal{S}^{d-1} given by

f(x|\Theta) = \sum_{j=1}^M \alpha_j f_j(x|\rho_j, \mu_j)

where \alpha_j's are the mixing proportions and f_j(x|\rho_j, \mu_j)'s denote the probability density function of a d-variate Poisson kernel-based density given as

f(\mathbf{x}|\rho, \mathbf{\mu}) = \frac{1-\rho^2}{\omega_d ||\mathbf{x} - \rho \mathbf{\mu}||^d}.

The parameters \alpha_j, \mu_j, \rho_j are estimated through a iterative reweighted EM algorithm.
The proposed clustering algorithm exhibits excellent results when (1) the clusters are not well separated; (2) the data points are fairly well concentrated around the vectors \mu_j of each cluster; (3) the percentage of noise in the data increases.

Usage

pkbc(
  dat,
  nClust = NULL,
  maxIter = 300,
  stoppingRule = "loglik",
  initMethod = "sampleData",
  numInit = 10
)

## S4 method for signature 'ANY'
pkbc(
  dat,
  nClust = NULL,
  maxIter = 300,
  stoppingRule = "loglik",
  initMethod = "sampleData",
  numInit = 10
)

## S4 method for signature 'pkbc'
show(object)

Arguments

dat	Data matrix or data.frame of data points on the sphere to be clustered. The observations in dat are normalized by dividing with the length of the vector to ensure that they lie on the d-dimensional sphere. Note that d > 1.
nClust	Number of clusters. It can be a single value or a numeric vector.
maxIter	The maximum number of iterations before a run is terminated.
stoppingRule	String describing the stopping rule to be used within each run. Currently must be either 'max', 'membership', or 'loglik'.
initMethod	String describing the initialization method to be used. Currently must be 'sampleData'.
numInit	Number of initialization.
object	Object of class pkbc

Details

We set all concentration parameters equal to 0.5 and all mixing proportions to be equal.
The initialization method 'sampleData' indicates that observation points are randomly chosen as initializers of the centroids \mu_j. This random starts strategy has a chance of not obtaining initial representatives from the underlying clusters, then the clustering is performed numInit times and the random start with the highest likelihood is chosen as the final estimate of the parameters.

The possible stoppingRule for each iteration are:

• 'loglik' run the algorithm until the change in log-likelihood from one iteration to the next is less than a given threshold (1e-7)
  

• 'membership' run the algorithm until the membership is unchanged for all points from one iteration to the next
  

• 'max' reach a maximum number of iterations maxIter

The obtained estimates are used for assigning final memberships, identifying the nClust clusters, according to the following rule

P(x_i, \Theta) = \arg\max_{j \in \{1, \ldots, k\}} \{ \frac{\alpha_j f_j(x_i|\mu_j, \rho_j)}{f(x_i, \Theta)}\}.

The number of clusters nClust must be provided as input to the clustering algorithm.

Value

An S4 object of class pkbc containing the results of the clustering procedure based on Poisson kernel-based distributions. The object contains the following slots:

res_k: List of results of the Poisson kernel-based clustering algorithm for each value of number of clusters specified in nClust. Each object in the list contains:

• postProbs Posterior probabilities of each observation for the indicated clusters.

• LogLik Maximum value of log-likelihood function

• wcss Values of within-cluster sum of squares computed with Euclidean distance and cosine similarity, respectively.

• params List of estimated parameters of the mixture model

  • mu estimated centroids

  • rho estimated concentration parameters rho

  • alpha estimated mixing proportions

• finalMemb Vector of final memberships

• runInfo List of information of the EM algorithm iterations

  • lokLikVec vector of log-likelihood values

  • numIterPerRun number of E-M iterations per run

input: List of input information.

Note

The clustering algorithm is tailored for data points on the sphere \mathcal{S}^{d-1}, but it can also be performed on spherically transformed observations, i.e. data points on the Euclidean space \mathbb{R}^d that are normalized such that they lie on the corresponding d-dimensional sphere \mathcal{S}^{d-1}.

References

Golzy, M. and Markatou, M. (2020) Poisson Kernel-Based Clustering on the Sphere: Convergence Properties, Identifiability, and a Method of Sampling, Journal of Computational and Graphical Statistics, 29:4, 758-770, DOI: 10.1080/10618600.2020.1740713.

See Also

dpkb() and rpkb() for more information on the Poisson kernel-based distribution.
pkbc for the class definition.

Examples

#We generate three samples of 100 observations from 3-dimensional
#Poisson kernel-based densities with rho=0.8 and different mean directions
size<-100
groups<-c(rep(1, size), rep(2, size),rep(3,size))
rho<-0.8
set.seed(081423)
data1<-rpkb(size, c(1,0,0),rho)
data2<-rpkb(size, c(0,1,0),rho)
data3<-rpkb(size, c(0,0,1),rho)
dat<-rbind(data1$x,data2$x, data3$x)

#Perform the clustering algorithm with number of clusters k=3.
pkbd<- pkbc(dat=dat, nClust=3)
show(pkbd)

QuadratiK documentation built on Oct. 29, 2024, 5:08 p.m.