ppclust: pfcm – R documentation

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pfcm

Possibilistic Fuzzy C-Means Clustering Algorithm

Description

Partitions a numeric data set by using the Possibilistic Fuzzy C-Means (PFCM) clustering algorithm proposed by Pal et al (2005).

Usage

pfcm(x, centers, memberships, m=2, eta=2, K=1, omega, a, b,
    dmetric="sqeuclidean", pw=2, alginitv="kmpp", alginitu="imembrand", 
    nstart=1, iter.max=1000, con.val=1e-09, 
    fixcent=FALSE, fixmemb=FALSE, stand=FALSE, numseed)

Arguments

`x`	a numeric vector, data frame or matrix.
`centers`	an integer specifying the number of clusters or a numeric matrix containing the initial cluster centers.
`memberships`	a numeric matrix containing the initial membership degrees. If missing, it is internally generated.
`m`	a number greater than 1 to be used as the fuzziness exponent. The default is 2.
`eta`	a number greater than 1 to be used as the typicality exponent. The default is 2.
`a`	a number for the relative importance of the fuzzy part of the objective function. The default is 1.
`b`	a number for the relative importance of the possibilistic part of the objective function. The default is 1.
`K`	a number greater than 0 to be used as the weight of penalty term. The default is 1.
`omega`	a numeric vector of reference distances. If missing, it is internally generated.
`dmetric`	a string for the distance metric. The default is sqeuclidean for the squared Euclidean distances. See `get.dmetrics` for the alternative options.
`pw`	a number for the power of Minkowski distance calculation. The default is 2 if the `dmetric` is minkowski.
`alginitv`	a string for the initialization of cluster prototypes matrix. The default is kmpp for K-means++ initialization method (Arthur & Vassilvitskii, 2007). For the list of alternative options see `get.algorithms`.
`alginitu`	a string for the initialization of memberships degrees matrix. The default is imembrand for random sampling of initial membership degrees.
`nstart`	an integer for the number of starts for clustering. The default is 1.
`iter.max`	an integer for the maximum number of iterations allowed. The default is 1000.
`con.val`	a number for the convergence value between the iterations. The default is 1e-09.
`fixcent`	a logical flag to fix the initial cluster centers. The default is `FALSE`. If it is `TRUE`, the initial centers are not changed in the successive starts of the algorithm when the `nstart` is greater than 1.
`fixmemb`	a logical flag to fix the initial membership degrees. The default is `FALSE`. If it is `TRUE`, the initial memberships are not changed in the successive starts of the algorithm when the `nstart` is greater than 1.
`stand`	a logical flag to standardize data. Its default value is `FALSE`. If its value is `TRUE`, the data matrix `x` is standardized.
`numseed`	a seeding number to set the seed of R's random number generator.

Details

In FPCM, the constraint corresponding to the sum of all the typicality values of all data objects to a cluster must be equal to one causes problems; particularly for a big data set. In order to avoid this problem Pal et al (2005) proposed Possibilistic Fuzzy C-Means (PFCM) clustering algorithm with following objective function:

J_{PFCM}(\mathbf{X}; \mathbf{V}, \mathbf{U}, \mathbf{T})=∑\limits_{j=1}^k ∑\limits_{i=1}^n (a \; u_{ij}^m + b \; t_{ij}^η) \; d^2(\vec{x}_i, \vec{v}_j) + ∑\limits_{j=1}^k Ω_j ∑\limits_{i=1}^n (1-t_{ij})^η

The fuzzy membership degrees in the probabilistic part of the objective function J_{PFCM} is calculated in the same way as in FCM, as follows:

u_{ij} = \Bigg[∑\limits_{j=1}^k \Big(\frac{d^2(\vec{x}_i, \vec{v}_j)}{d^2(\vec{x}_i, \vec{v}_l)}\Big)^{1/(m-1)} \Bigg]^{-1} \;;\; 1 ≤q i ≤q n, \; 1 ≤q l ≤q k

The typicality degrees in the possibilistic part of the objective function J_{PFCM} is calculated as follows:

t_{ij} = \Bigg[1 + \Big(\frac{b \; d^2(\vec{x}_i, \vec{v}_j)}{Ω_j}\Big)^{1/(η -1)}\Bigg]^{-1} \;;\; 1 ≤q i ≤q n, \; 1 ≤q j ≤q k

The constraints with PFCM are:

0 ≤q u_{ij}, t_{ij} ≤q 1

0 ≤q ∑\limits_{i=1}^n u_{ij} ≤q n \;\;;\; 1 ≤q j ≤q k

0 ≤q ∑\limits_{j=1}^k t_{ij} ≤q k \;\;;\; 1 ≤q i ≤q n

∑\limits_{j=1}^k u_{ij} = 1 \;\;;\; 1 ≤q i≤q n

a and b are the coefficients to define the relative importance of fuzzy membership and typicality degrees for weighting the probabilistic and possibilistic terms of the objective function, a > 0; \; b > 0.

m is the fuzzifier to specify the amount of fuzziness for the clustering; 1≤q m≤q ∞. It is usually chosen as 2.

η is the typicality exponent to specify the amount of typicality for the clustering; 1≤q η≤q ∞. It is usually chosen as 2.

Ω is the possibilistic penalty terms for controlling the variance of the clusters.

The update equation for cluster prototypes:

\vec{v}_j =\frac{∑\limits_{i=1}^n (a \; u_{ij}^m + b \; t_{ij}^η) \; \vec{x}_i}{∑\limits_{i=1}^n (a \; u_{ij}^m + b \; t_{ij}^η)} \;;\; 1 ≤q j ≤q k

Value

an object of class ‘ppclust’, which is a list consists of the following items:

`v`	a numeric matrix containing the final cluster prototypes.
`t`	a numeric matrix containing the typicality degrees of the data objects.
`d`	a numeric matrix containing the distances of objects to the final cluster prototypes.
`x`	a numeric matrix containing the processed data set.
`cluster`	a numeric vector containing the cluster labels found by defuzzifying the typicality degrees of the objects.
`csize`	a numeric vector for the number of objects in the clusters.
`k`	an integer for the number of clusters.
`m`	a number for the used fuzziness exponent.
`eta`	a number for the used typicality exponent.
`a`	a number for the fuzzy part of the objective function.
`b`	a number for the possibilistic part of the objective function.
`omega`	a numeric vector of reference distances.
`iter`	an integer vector for the number of iterations in each start of the algorithm.
`best.start`	an integer for the index of start that produced the minimum objective functional.
`func.val`	a numeric vector for the objective function values in each start of the algorithm.
`comp.time`	a numeric vector for the execution time in each start of the algorithm.
`stand`	a logical value, `TRUE` shows that `x` data set contains the standardized values of raw data.
`wss`	a number for the within-cluster sum of squares for each cluster.
`bwss`	a number for the between-cluster sum of squares.
`tss`	a number for the total within-cluster sum of squares.
`twss`	a number for the total sum of squares.
`algorithm`	a string for the name of partitioning algorithm. It is ‘PCM’ with this function.
`call`	a string for the matched function call generating this ‘ppclust’ object.

Author(s)

Zeynel Cebeci, Alper Tuna Kavlak & Figen Yildiz

References

Arthur, D. & Vassilvitskii, S. (2007). K-means++: The advantages of careful seeding, in Proc. of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms, p. 1027-1035. <http://ilpubs.stanford.edu:8090/778/1/2006-13.pdf>

Pal, N. R., Pal, K. & Bezdek, J. C. (2005). A possibilistic fuzzy c-means clustering algorithm. IEEE Trans. Fuzzy Systems, 13 (4): 517-530. <doi:10.1109/TFUZZ.2004.840099>

Examples

# Load the dataset X12
data(x12)

# Set the initial centers of clusters
v0 <- matrix(nrow=2, ncol=2, c(-3.34, 1.67, 1.67, 0.00), byrow=FALSE)

# Run FCM with the initial centers in v0
res.fcm <- fcm(x12, centers=v0, m=2)

# Run PFCM with the final centers and memberhips from FCM
res.pfcm <- pfcm(x12, centers=res.fcm$v, memberships=res.fcm$u, m=2, eta=2)

# Show the typicality and fuzzy membership degrees from PFCM
res.pfcm$t
res.pfcm$u

ppclust

Probabilistic and Possibilistic Cluster Analysis

v1.1.0

GPL (>= 2)

Authors

Zeynel Cebeci [aut, cre], Figen Yildiz [aut], Alper Tuna Kavlak [aut], Cagatay Cebeci [aut], Hasan Onder [aut]

Initial release

2020-02-08