Validation of Poisson kernel-based clustering results

Method for objects of class pkbc which computes evaluation measures for clustering results. The following evaluation measures are computed: In-Group Proportion (Kapp and Tibshirani (2007)). If true label are provided, ARI, Average Silhouette Width (Rousseeuw (1987)), Macro-Precision and Macro-Recall are computed.

Usage

pkbc_validation(object, true_label = NULL)

Arguments

object: Object of class pkbc
true_label: factor or vector of true membership to clusters (if available). It must have the same length of final memberships.

Value

List with the following components:

metrics Table of computed evaluation measures for each value of number of clusters in the pkbc object. The number of cluster is indicated as column name.
IGP List of in-group proportions for each value of number of clusters specified.

Details

The IGP is a statistical measure that quantifies the proportion of observations within a group that belong to the same predefined category or class. It is often used to assess the homogeneity of a group by evaluating how many of its members share the same label. A higher IGP indicates that the group is more cohesive, while a lower proportion suggests greater diversity or misclassification within the group (Kapp and Tibshirani 2007).

The Adjusted Rand Index (ARI) is a statistical measure used in data clustering analysis. It quantifies the similarity between two partitions of a dataset by comparing the assignments of data points to clusters. The ARI value ranges from 0 to 1, where a value of 1 indicates a perfect match between the partitions and a value close to 0 indicates a random assignment of data points to clusters.

Each cluster can represented by a so-called silhouette which is based on the comparison of its tightness and separation. The average silhouette width provides an evaluation of clustering validity, and might be used to select an appropriate number of clusters (Rousseeuw 1987).

Macro Precision is a metric used in multi-class classification that calculates the precision for each class independently and then takes the average of these values. Precision for a class is defined as the proportion of true positive predictions out of all predictions made for that class.

Macro Recall is similar to Macro Precision but focuses on recall. Recall for a class is the proportion of true positive predictions out of all actual instances of that class. Macro Recall is the average of the recall values computed for each class.

Note

Note that Macro Precision and Macro Recall depend on the assigned labels, while the ARI measures the similarity between partition up to label switching.

If the required packages (mclust for ARI, clusterRepro for IGP, and cluster for ASW) are not installed, the function will display a message asking the user to install the missing package(s).

References

Kapp, A.V. and Tibshirani, R. (2007) "Are clusters found in one dataset present in another dataset?", Biostatistics, 8(1), 9–31, https://doi.org/10.1093/biostatistics/kxj029

Rousseeuw, P.J. (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics, 20, 53–65.

Examples

#We generate three samples of 100 observations from 3-dimensional
#Poisson kernel-based densities with rho=0.8 and different mean directions

size<-20
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,method='rejvmf')
data2<-rpkb(size, c(0,1,0),rho,method='rejvmf')
data3<-rpkb(size, c(1,0,0),rho,method='rejvmf')
data<-rbind(data1$x,data2$x, data3$x)

#Perform the clustering algorithm
pkbc_res<- pkbc(data, 3)
pkbc_validation(pkbc_res)
#> $metrics
#>              3
#> ASW 0.03602451
#> 
#> $IGP
#> $IGP[[1]]
#> NULL
#> 
#> $IGP[[2]]
#> NULL
#> 
#> $IGP[[3]]
#> [1] 0.952381 1.000000 1.000000
#> 
#>