DPMGibbsN_SeqPrior: Slice Sampling of Dirichlet Process Mixture of Gaussian...

In borishejblum/NPflow: Bayesian Nonparametrics for Automatic Gating of Flow-Cytometry Data

Slice Sampling of Dirichlet Process Mixture of Gaussian distributions

Description

Slice Sampling of Dirichlet Process Mixture of Gaussian distributions

Usage

DPMGibbsN_SeqPrior(
  z,
  prior_inform,
  hyperG0,
  N,
  nbclust_init,
  add.vagueprior = TRUE,
  weightnoninfo = NULL,
  doPlot = TRUE,
  plotevery = N/10,
  diagVar = TRUE,
  verbose = TRUE,
  ...
)

Arguments

z	data matrix d x n with d dimensions in rows and n observations in columns.
prior_inform	an informative prior such as the approximation computed by summary.DPMMclust.
hyperG0	a non informative prior component for the mixing distribution. Only used if add.vagueprior is TRUE.
N	number of MCMC iterations.
nbclust_init	number of clusters at initialization. Default to 30 (or less if there are less than 30 observations).
add.vagueprior	logical flag indicating whether a non informative component should be added to the informative prior. Default is TRUE.
weightnoninfo	a real between 0 and 1 giving the weights of the non informative component in the prior.
doPlot	logical flag indicating whether to plot MCMC iteration or not. Default to TRUE.
plotevery	an integer indicating the interval between plotted iterations when doPlot is TRUE.
diagVar	logical flag indicating whether the variance of each cluster is estimated as a diagonal matrix, or as a full matrix. Default is TRUE (diagonal variance).
verbose	logical flag indicating whether partition info is written in the console at each MCMC iteration.
...	additional arguments to be passed to plot_DPM. Only used if doPlot is TRUE.

Value

a object of class DPMclust with the following attributes:

mcmc_partitions:	a list of length N. Each element mcmc_partitions[n] is a vector of length n giving the partition of the n observations.
alpha:	a vector of length N. cost[j] is the cost associated to partition c[[j]]
listU_mu:	a list of length N containing the matrices of mean vectors for all the mixture components at each MCMC iteration
listU_Sigma:	a list of length N containing the arrays of covariances matrices for all the mixture components at each MCMC iteration
U_SS_list:	a list of length N containing the lists of sufficient statistics for all the mixture components at each MCMC iteration
weights_list:
logposterior_list:	a list of length N containing the logposterior values at each MCMC iterations
data:	the data matrix d x n with d dimensions in rows and n observations in columns.
nb_mcmcit:	the number of MCMC iterations
clust_distrib:	the parametric distribution of the mixture component - "gaussian"
hyperG0:	the prior on the cluster location

Author(s)

Boris Hejblum, Chariff Alkhassim

References

Hejblum BP, Alkhassim C, Gottardo R, Caron F and Thiebaut R (2019) Sequential Dirichlet Process Mixtures of Multivariate Skew t-distributions for Model-based Clustering of Flow Cytometry Data. The Annals of Applied Statistics, 13(1): 638-660. <doi: 10.1214/18-AOAS1209> <arXiv: 1702.04407> https://arxiv.org/abs/1702.04407 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1214/18-AOAS1209")}

See Also

postProcess.DPMMclust DPMGibbsN

Examples

rm(list=ls())
library(NPflow)
#Number of data
n <- 1500
# Sample data
#m <- matrix(nrow=2, ncol=4, c(-1, 1, 1.5, 2, 2, -2, 0.5, -2))
m <- matrix(nrow=2, ncol=4, c(-.8, .7, .5, .7, .5, -.7, -.5, -.7))
p <- c(0.2, 0.1, 0.4, 0.3) # frequence des clusters

sdev <- array(dim=c(2,2,4))
sdev[, ,1] <- matrix(nrow=2, ncol=2, c(0.3, 0, 0, 0.3))
sdev[, ,2] <- matrix(nrow=2, ncol=2, c(0.1, 0, 0, 0.3))
sdev[, ,3] <- matrix(nrow=2, ncol=2, c(0.3, 0.15, 0.15, 0.3))
sdev[, ,4] <- .3*diag(2)
c <- rep(0,n)
z <- matrix(0, nrow=2, ncol=n)
for(k in 1:n){
 c[k] = which(rmultinom(n=1, size=1, prob=p)!=0)
 z[,k] <- m[, c[k]] + sdev[, , c[k]]%*%matrix(rnorm(2, mean = 0, sd = 1), nrow=2, ncol=1)
 #cat(k, "/", n, " observations simulated\n", sep="")
}

d<-2
# Set parameters of G0
hyperG0 <- list()
hyperG0[["mu"]] <- rep(0,d)
hyperG0[["kappa"]] <- 0.001
hyperG0[["nu"]] <- d+2
hyperG0[["lambda"]] <- diag(d)/10

# hyperprior on the Scale parameter of DPM
a <- 0.0001
b <- 0.0001

# Number of iterations
N <- 30

# do some plots
doPlot <- TRUE
nbclust_init <- 20



## Data
########
library(ggplot2)
p <- (ggplot(data.frame("X"=z[1,], "Y"=z[2,]), aes(x=X, y=Y))
      + geom_point()
      + ggtitle("Toy example Data"))
p


if(interactive()){
# Gibbs sampler for Dirichlet Process Mixtures
##############################################

MCMCsample <- DPMGibbsN(z, hyperG0, a, b, N=1500, doPlot, nbclust_init, plotevery=200,
                        gg.add=list(theme_bw(),
                                 guides(shape=guide_legend(override.aes = list(fill="grey45")))),
                        diagVar=FALSE)

s <- summary(MCMCsample, posterior_approx=TRUE, burnin = 1000, thin=5)
F1 <- FmeasureC(pred=s$point_estim$c_est, ref=c)
F1


MCMCsample2 <- DPMGibbsN_SeqPrior(z, prior_inform=s$param_posterior,
                                  hyperG0, N=1500,
                                  add.vagueprior = TRUE,
                                  doPlot=TRUE, plotevery=100,
                                  nbclust_init=nbclust_init,
                                  gg.add=list(theme_bw(),
                                 guides(shape=guide_legend(override.aes = list(fill="grey45")))),
                                  diagVar=FALSE)


s2 <- summary(MCMCsample2, burnin = 500, thin=5)
F2 <- FmeasureC(pred=s2$point_estim$c_est, ref=c)
F2
}

borishejblum/NPflow documentation built on Feb. 2, 2024, 1:51 a.m.