R/clustering_sc05Z.R

Defines functions riem.sc05Z

Documented in riem.sc05Z

#' Spectral Clustering by Zelnik-Manor and Perona (2005)
#' 
#' Zelnik-Manor and Perona proposed a method to define a set of data-driven 
#' bandwidth parameters where \eqn{\sigma_i} is the distance from a point \eqn{x_i} to its \code{nnbd}-th 
#' nearest neighbor. Then the affinity matrix is defined as
#' \deqn{A_{ij} = \exp(-d(x_i, d_j)^2 / \sigma_i \sigma_j)} and the standard 
#' spectral clustering of Ng, Jordan, and Weiss (\code{\link{riem.scNJW}}) is applied.
#' 
#' @param riemobj a S3 \code{"riemdata"} class for \eqn{N} manifold-valued data.
#' @param k the number of clusters (default: 2).
#' @param nnbd neighborhood size to define data-driven bandwidth parameter (default: 7).
#' @param geometry (case-insensitive) name of geometry; either geodesic (\code{"intrinsic"}) or embedded (\code{"extrinsic"}) geometry.
#' 
#' @return a named list containing 
#' \describe{
#' \item{cluster}{a length-\eqn{N} vector of class labels (from \eqn{1:k}).} 
#' \item{eigval}{eigenvalues of the graph laplacian's spectral decomposition.}
#' \item{embeds}{an \eqn{(N\times k)} low-dimensional embedding.}
#' }
#' 
#' @examples 
#' #-------------------------------------------------------------------
#' #          Example on Sphere : a dataset with three types
#' #
#' # class 1 : 10 perturbed data points near (1,0,0) on S^2 in R^3
#' # class 2 : 10 perturbed data points near (0,1,0) on S^2 in R^3
#' # class 3 : 10 perturbed data points near (0,0,1) on S^2 in R^3
#' #-------------------------------------------------------------------
#' ## GENERATE DATA
#' mydata = list()
#' for (i in 1:10){
#'   tgt = c(1, stats::rnorm(2, sd=0.1))
#'   mydata[[i]] = tgt/sqrt(sum(tgt^2))
#' }
#' for (i in 11:20){
#'   tgt = c(rnorm(1,sd=0.1),1,rnorm(1,sd=0.1))
#'   mydata[[i]] = tgt/sqrt(sum(tgt^2))
#' }
#' for (i in 21:30){
#'   tgt = c(stats::rnorm(2, sd=0.1), 1)
#'   mydata[[i]] = tgt/sqrt(sum(tgt^2))
#' }
#' myriem = wrap.sphere(mydata)
#' lab    = rep(c(1,2,3), each=10)
#' 
#' ## CLUSTERING WITH DIFFERENT K VALUES
#' cl2 = riem.sc05Z(myriem, k=2)$cluster
#' cl3 = riem.sc05Z(myriem, k=3)$cluster
#' cl4 = riem.sc05Z(myriem, k=4)$cluster
#' 
#' ## MDS FOR VISUALIZATION
#' mds2d = riem.mds(myriem, ndim=2)$embed
#' 
#' ## VISUALIZE
#' opar <- par(no.readonly=TRUE)
#' par(mfrow=c(1,4), pty="s")
#' plot(mds2d, col=lab, pch=19, main="true label")
#' plot(mds2d, col=cl2, pch=19, main="riem.sc05Z: k=2")
#' plot(mds2d, col=cl3, pch=19, main="riem.sc05Z: k=3")
#' plot(mds2d, col=cl4, pch=19, main="riem.sc05Z: k=4")
#' par(opar)
#' 
#' @references 
#' Zelnik-manor L, Perona P (2005). "Self-Tuning Spectral Clustering." In Saul LK, Weiss Y, Bottou L (eds.), \emph{Advances in Neural Information Processing Systems 17}, 1601–1608. MIT Press.
#' 
#' @concept clustering
#' @export
riem.sc05Z <- function(riemobj, k=2, nnbd=7, geometry=c("intrinsic","extrinsic")){
  ## PREPARE
  DNAME = paste0("'",deparse(substitute(riemobj)),"'") 
  if (!inherits(riemobj,"riemdata")){
    stop(paste0("* riem.sc05Z : input ",DNAME," should be an object of 'riemdata' class."))
  }
  mygeom = ifelse(missing(geometry),"intrinsic",
                  match.arg(tolower(geometry),c("intrinsic","extrinsic")))
  myk   = max(1, round(k))
  mynbd = max(5, round(nnbd))
  
  ## COMPUTE DISTANCE
  pdmat   = stats::as.dist(basic_pdist(riemobj$name, riemobj$data, mygeom))
  
  ## RUN SPECTRAL CLUSTERING
  runT4cluster = T4cluster::sc05Z(pdmat, k=myk, nnbd=mynbd)
  
  ## WRAP AND RETURN
  output = list()
  output$cluster = runT4cluster$cluster
  output$eigval  = runT4cluster$eigval
  output$embeds  = runT4cluster$embeds
  return(output)
}

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Riemann documentation built on June 20, 2021, 5:07 p.m.