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PMcrossGBMIIiSBC.R
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PMcrossGBMIIiSBC.R
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##### This file runs Poor Man's cross-validation results on the i-SBC model ######
##### The normal i-SBC code is tested #####
setwd("~/Dropbox/Code/DPmixturemodel/SBC")
rm(list =ls())
source('import.R')
## Set the initial conditions
### The Cross-vaidation repeat number
u =1
### The fold number
v =1
##############################################################################################
#### Load the two data sets ##################################################################
##### Load Pheno Data and Load Verhaak Data Sets ############################################
load('/home/bit/ashar/ExpressionSets/ONE_VIEW/Verhark/phenoVerhaark.RData')
load("/home/bit/ashar/ExpressionSets/TWO_VIEW/TCGA_GBM/IntegratedDataSurv.rda")
load("/home/bit/ashar/ExpressionSets/TWO_VIEW/TCGA_GBM/mRNA.rda")
load("/home/bit/ashar/ExpressionSets/TWO_VIEW/TCGA_GBM/miRNA.rda")
### Selecting the 189 patients which have common type of genomic data ###
patient.tcga <- rownames(mRNA)[(rownames(mRNA) %in% rownames(miRNA)) & (rownames(mRNA) %in% pheno$Patient)]
###############################################################
Y.mrna.tcga <- mRNA[patient.tcga,]
Y.mirna.tcga <- miRNA[patient.tcga,]
######## Getting survival times and status #####################
######## Lets Get the Pheno Data #####################################################################
pheno.ord <- pheno[match(patient.tcga,pheno$Patient),]
pheno.ord$Patient == rownames(Y.mrna.tcga)
pheno.ord$Patient == rownames(Y.mirna.tcga)
time.pre <- as.numeric(pheno.ord[,3])
censoring.pre <- pheno.ord[,2]
c.verhaak <- pheno.ord[,4]
levels(c.verhaak)[1:4] <- c(1:4)
############################# PARAMETERS for GIBB's SAMPLING ####
iter = 200
iter.burnin = 200
iter.thin = 5
Nps = as.integer(iter/ iter.thin)
#############################################################################################
########################## BEGIN THE CROSS-VALIDATION FOLD ###################################
##############################################################################################
set.seed(42*u)
#### Define the folds
folds <- createFolds(c.verhaak, k = 5, list = TRUE, returnTrain = FALSE)
test.index <- folds[[v]]
###############################################################################
####### If we define the splits ourselves #####################################
############### Defining Our data without prefiltering #########################
Y1.pre.train <- Y.mrna.tcga[-test.index, ]
Y2.pre.train <- Y.mirna.tcga[-test.index,]
Y1.pre.test <- Y.mrna.tcga[test.index,]
Y2.pre.test <- Y.mirna.tcga[test.index,]
c.true <- c.verhaak[-test.index]
c.true.new <- c.verhaak[test.index]
time <- time.pre[-test.index]
censoring <- censoring.pre[-test.index]
time.new <- time.pre[test.index]
censoring.new <- censoring.pre[test.index]
#### Use SBC signature ##
source('loadiSBCGBMIIsignature.R')
rel <- loadiSBCGBMIIsignature(Y1.pre.train, Y2.pre.train, time, censoring)
signature1.sbc <- rel$signature1.sbc
signature2.sbc <- rel$signature2.sbc
###### We get the signature and then we can define the folds #####
########## Creating Training and Test Data ##########################
Y1 <- Y1.pre.train[,colnames(Y1.pre.train) %in% signature1.sbc ]
Y2 <- Y2.pre.train[,colnames(Y2.pre.train) %in% signature2.sbc ]
Y1.new <- Y1.pre.test[,colnames(Y1.pre.test) %in% signature1.sbc ]
Y2.new <- Y2.pre.test[,colnames(Y2.pre.test) %in% signature2.sbc]
# ###### If using CCA features on top
# #### Use SBC signature ##
# source('loadiSBCGBMIIsignatureCCA.R')
# rel <- loadiSBCGBMIIsignatureCCA(Y1, Y2, Y1.new, Y2.new)
# Y1 <- rel$Y1
# Y2 <- rel$Y2
# Y1.new <- rel$Y1.new
# Y2.new <- rel$Y2.new
#
###################################################
D1 <- ncol(Y1)
D2 <- ncol(Y2)
#### For other methods ###########################
Y <- as.matrix(cbind(Y1,Y2))
Y.new <- as.matrix(cbind(Y1.new,Y2.new))
D <- D1 + D2
############################# PARAMETERS for GIBB's SAMPLING ####
iter = 100
iter.burnin = 200
iter.thin = 2
k = 2
F =k
N <- nrow(Y1)
K <- as.integer(N/5)
Time <- cbind(time,censoring)
########################### Sourcing key files #################
source('rchinese.R')
source('multiinit.R')
source('multilikelihood.R')
source('priorPARAMETERS.R')
source('multilikelihood.R')
source('multikmeansBlasso.R')
source('posteriorGMM.R')
source('multiposteriorAFT.R')
source('posteriorhyperGMM.R')
source('posterioralpha.R')
source('multiposteriorCLASS.R')
source('multiupdatetime.R')
########################################################################################################
############################ COMPARISON only with k-means + K-Nearest Neighbours #######################
########################################################################################################
### Comparison with base methods
smod <- Surv(exp(time), censoring)
smod.new <- Surv(exp(time.new), censoring.new)
gr.km <- kmeans(Y, F, nstart =10)
label.train <- as.factor(gr.km$cluster)
### One has to to tune the k-NN classifier for k ###
fitControl <- trainControl(method = "repeatedcv", number = 5,repeats = 5)
### Tune the parameter k
knnFit <- train(x = Y, y = label.train, method = "knn", trControl = fitControl, tuneLength = 5)
knnPredict <- predict(knnFit,newdata = Y.new )
label.test <- knnPredict
recov.logrank.kk <- unlist(survdiff(smod ~ label.train))$chisq
pred.logrank.kk <- unlist(survdiff(smod.new ~ label.test))$chisq
###### penCox on top of the clustering ###################################################################
######## Penalized Cox PH with k-means clustering###########################################
linear.kk.recovery <- c(0)
linear.kk.prediction <- c(0)
for ( q in 1:F){
ind <- which(label.train == q)
ind.new <- which(label.test == q)
reg.cox <- cv.glmnet(x = Y[ind,1:D], y = Surv(time[ind],censoring[ind]), family = "cox", maxit = 10000000)
linear.kk.recovery[ind] <- predict(object =reg.cox, newx = Y[ind,], s= "lambda.min")
linear.kk.prediction[ind.new] <- predict(object =reg.cox, newx = Y.new[ind.new,], s= "lambda.min")
}
recovCIndex.kk.pcox <- as.numeric(survConcordance(smod ~ linear.kk.recovery)[1])
predCIndex.kk.pcox <- as.numeric(survConcordance(smod.new ~ linear.kk.prediction)[1])
############### Use Principal Components without clustering ###############
#### Use PC method of the reviewer #####
Y.pre.train <- as.matrix(cbind(Y1.pre.train, Y2.pre.train))
Y.pre.test <- as.matrix(cbind(Y1.pre.test, Y2.pre.test))
pX <- prcomp(Y.pre.train)
pc.recov <- predict(pX,newdata = Y.pre.train)
pc.pred <- predict(pX,newdata = Y.pre.test)
cox.fit <- coxph(smod ~ ., data=as.data.frame(pc.recov[,1:20]))
linear.PC.recovery <- predict(cox.fit, newdata=as.data.frame(pc.recov[,1:20]))
linear.PC.prediction <- predict(cox.fit, newdata= as.data.frame(pc.pred[,1:20]))
#### Getting the C-Indices ####
recovCIndex.PC <- as.numeric(survConcordance(smod ~ linear.PC.recovery)[1])
predCIndex.PC <- as.numeric(survConcordance(smod.new ~ linear.PC.prediction)[1])
##################################################
####### Initialize ###############################
##################################################
##GIBBS SAMPLING INITIALIZATION ################
#################################################
## HYPER PRIORS
## Hyper parameters of the DP
shape.alpha <- 2
rate.alpha <- 1
alpha = rgamma(1, shape = shape.alpha, rate = rate.alpha )
c <- rchinese(N,alpha)
f <- table(factor(c, levels = 1:max(c)))
#Sparsity controlling hyperparameter of the BAYESIAN LASSO MODEL
r =1
si = 1.78
### LETS MAKE A LIST "gmmx" to store parameters/hyperprameters for X and "regy" to store paameters for Regression Y
## For the First Data Set
gmmx1 <- list(0)
gmmx1$epsilon <- as.vector(apply(Y1,2,mean))
gmmx1$W <- diag(diag(cov(Y1)))
gmmx1$mu <- matrix(data = NA, nrow = K, ncol = D1)
gmmx1$S <- array(data = NA, dim =c(K,D1,D1))
gmmx1$ro <- 0.5
gmmx1$beta <- D1 +1
regy1 <- list(0)
regy1$lambda2 <- numeric(K)
regy1$tau2 = matrix(data = NA, nrow = K, ncol = D1)
regy1$betahat = matrix(data = NA, nrow = K, ncol = D1)
regy1$sigma2 <- rep(NA, K)
regy1$beta0 <- rep(NA, K)
## For the second data set
gmmx2 <- list(0)
gmmx2$epsilon <- as.vector(apply(Y2,2,mean))
gmmx2$W <- diag(diag(cov(Y2)))
gmmx2$mu <- matrix(data = NA, nrow = K, ncol = D2)
gmmx2$S <- array(data = NA, dim =c(K,D2,D2))
gmmx2$ro <- 0.5
gmmx2$beta <- D2 +1
regy2 <- list(0)
regy2$lambda2 <- numeric(K)
regy2$tau2 = matrix(data = NA, nrow = K, ncol = D2)
regy2$betahat = matrix(data = NA, nrow = K, ncol = D2)
regy2$sigma2 <- rep(NA, K)
regy2$beta0 <- rep(NA, K)
###### To initialize the parameters for all the data sets
That <- time
## Fitting a linear model to the whole model
Ysc <- scale(Y[1:N,1:D], center = TRUE, scale =TRUE)
lm.data <- lm(time ~ Ysc)
sig2.dat <- var(lm.data$residuals)
## Set Some Initial Values for the Cluster Parameters
## For the first data set
cont1 <- multiinit(Y1,c, gmmx1$beta, gmmx1$W, gmmx1$epsilon, gmmx1$ro, r, si,N,D1, sig2.dat)
gmmx1$mu <- cont1$mu
gmmx1$S <- cont1$S
regy1$lambda2 <- cont1$lambda2
regy1$tau2 <- cont1$tau2
regy1$betahat <- cont1$betahat
regy1$sigma2 <- cont1$sigma2
regy1$beta0 <- cont1$beta0
## For the second data set
cont2 <- multiinit(Y2,c, gmmx1$beta, gmmx2$W, gmmx2$epsilon, gmmx2$ro, r, si,N,D2, sig2.dat)
gmmx2$mu <- cont2$mu
gmmx2$S <- cont2$S
regy2$lambda2 <- cont2$lambda2
regy2$tau2 <- cont2$tau2
regy2$betahat <- cont2$betahat
regy2$sigma2 <- cont2$sigma2
regy2$beta0 <- cont2$beta0
## Initialization part for the parmaters of AFT Model with k-means and Bayesian Lasso and Normal Bayesian Regression
km <- multikmeansBlasso(c,Y1,Y2,D1,D2,That,K, r, si,sig2.dat,gmmx1, gmmx2, regy1, regy2,surv.obj )
c <- km$c
c.kmeans <- c
gmmx1 <- km$gmmx1
gmmx2 <- km$gmmx2
regy1 <- km$regy1
regy2 <- km$regy2
## Initial Likelihood
likli.int <- multiloglikelihood( c,Y1,Y2,D1,D2,That,K, beta, ro, r, si,sig2.dat,gmmx1, gmmx2, regy1, regy2)
###############################################################################################################
######################## Train the Model ######################################################################
param <- NA
paramtime1 <- NA
paramtime2 <- NA
cognate <- NA
hypercognate1 <- NA
hypercognate2 <- NA
loglike<- rep(0, iter)
burnin.likli <- c(0)
gmm.likli <- c(0)
aft.likli <- c(0)
randy <- c(0)
#################### BURNIN PHASE ###################################################
print("BURNIN...PHASE")
for (o in 1:iter.burnin) {
################## PARAMETERS OF THE DP Mixture Model ######################################################
## Updating the parameters based on the observations
param <- posteriorGMMparametrs(c,Y1,gmmx1$mu,gmmx1$S, alpha, K, gmmx1$epsilon, gmmx1$W, gmmx1$beta, gmmx1$ro,N,D1 )
gmmx1$mu <- param$mean
gmmx1$S <- param$precision
param2 <- posteriorGMMparametrs(c,Y2,gmmx2$mu,gmmx2$S, alpha,K, gmmx2$epsilon, gmmx2$W, gmmx2$beta, gmmx2$ro,N,D2 )
gmmx2$mu <- param2$mean
gmmx2$S <- param2$precision
paramtime2 <- posteriortimeparameterspenalized(c,Y2, That, regy2$lambda2, regy2$tau2, regy2$sigma2, regy2$beta0, regy2$betahat, K, gmmx2$epsilon, gmmx2$W, gmmx2$beta, gmmx2$ro, r, si, sig2.data,N, D2)
regy2$beta0 <- paramtime2$beta0
regy2$betahat <- paramtime2$betahat
regy2$sigma2 <- paramtime2$sigma2
regy2$lambda2 <- paramtime2$lambda2
regy2$tau2 <- paramtime2$tau2
paramtime1 <- posteriortimeparameterspenalized(c,Y1, That, regy1$lambda2, regy1$tau2, regy1$sigma2, regy1$beta0, regy1$betahat, K, gmmx1$epsilon, gmmx1$W, gmmx1$beta, gmmx1$ro, r, si, sig2.data,N, D1)
regy1$beta0 <- paramtime1$beta0
regy1$betahat <- paramtime1$betahat
regy1$sigma2 <- paramtime1$sigma2
regy1$lambda2 <- paramtime1$lambda2
regy1$tau2 <- paramtime1$tau2
########################## THE HYPERPARAMETERS OF THE GMM #################################
# Updating the hyper paramters for the first data set
hypercognate <- posteriorhyperPLUS(c, Y1, gmmx1$mu, gmmx1$S, gmmx1$epsilon, gmmx1$W, gmmx1$beta, gmmx1$ro )
gmmx1$epsilon <- hypercognate$epsilon
tmpW <- hypercognate$W
gmmx1$W <- matrix(as.matrix(tmpW),nrow = D1, ncol =D1)
gmmx1$ro <- hypercognate$ro
##Updating the hyper parameter for the second data set
hypercognate2 <- posteriorhyperPLUS(c, Y2, gmmx2$mu, gmmx2$S, gmmx2$epsilon, gmmx2$W, gmmx2$beta, gmmx2$ro)
gmmx2$epsilon <- hypercognate2$epsilon
tmpW2 <- hypercognate2$W
gmmx2$W <- matrix(as.matrix(tmpW2),nrow = D2, ncol =D2)
gmmx2$ro <- hypercognate2$ro
################# INDICATOR VARIABLE ##################################################################
## Updating the indicator variables and the parameters
cognate <- multiposteriorchineseAFT(c,Y1,Y2,D1,D2,That, K, r, si,sig2.dat,gmmx1, gmmx2, regy1, regy2)
c <- cognate$c
gmmx1 <- cognate$gmmx1
gmmx2 <- cognate$gmmx2
regy1 <- cognate$regy1
regy2 <- cognate$regy2
########################### The Concentration Parameter #################################################################
# Updating the concentration parameter
alpha <- posterioralpha(c, N, alpha, shape.alpha, rate.alpha)
####################### The Censored Times ###########################################################
# Updating the Time Variable
ti <- NA
ti <- multiupdatetime(c, Y1, Y2, Time,That, regy1, regy2)
That <- ti$time
##################### Print SOME Statistics #####################################################
randy[o] <- adjustedRandIndex(c.kmeans,as.factor(c))
print(randy[o])
cg <- multiloglikelihood(c,Y1,Y2,D1,D2,That,K, beta, ro, r, si,sig2.dat,gmmx1, gmmx2, regy1, regy2)
burnin.likli[o] <- cg$loglikelihood
gmm.likli[o] <- cg$GMMlikelihood
aft.likli[o] <- cg$AFTlikelihood
print(burnin.likli[o])
print(gmm.likli[o])
print(aft.likli[o])
print(o/iter.burnin)
}
param <- NA
paramtime1 <- NA
paramtime2 <- NA
cognate <- NA
hypercognate1 <- NA
hypercognate2 <- NA
loglike<- rep(0, iter)
est.regy1 <- list(0)
est.regy2 <- list(0)
est.gmmx1 <- list(0)
est.gmmx2 <- list(0)
c.list <- list(0)
That.list <- list(0)
alpha.list <- list(0)
randy <- c(0)
likli <- c(0)
print("GIBB'S SAMPLING")
pb <- txtProgressBar(min = 1, max = iter , style = 3)
count = 1
#################### GIBBS ITERATION ###################################################
for (o in 1:iter) {
################## PARAMETERS OF THE DP Mixture Model ######################################################
## Updating the parameters based on the observations
param <- posteriorGMMparametrs(c,Y1,gmmx1$mu,gmmx1$S, alpha, K, gmmx1$epsilon, gmmx1$W, gmmx1$beta, gmmx1$ro,N,D1 )
gmmx1$mu <- param$mean
gmmx1$S <- param$precision
param2 <- posteriorGMMparametrs(c,Y2,gmmx2$mu,gmmx2$S, alpha,K, gmmx2$epsilon, gmmx2$W, gmmx2$beta, gmmx2$ro,N,D2 )
gmmx2$mu <- param2$mean
gmmx2$S <- param2$precision
paramtime2 <- posteriortimeparameterspenalized(c,Y2, That, regy2$lambda2, regy2$tau2, regy2$sigma2, regy2$beta0, regy2$betahat, K, gmmx2$epsilon, gmmx2$W, beta, ro, r, si, sig2.data,N, D2)
regy2$beta0 <- paramtime2$beta0
regy2$betahat <- paramtime2$betahat
regy2$sigma2 <- paramtime2$sigma2
regy2$lambda2 <- paramtime2$lambda2
regy2$tau2 <- paramtime2$tau2
paramtime1 <- posteriortimeparameterspenalized(c,Y1, That, regy1$lambda2, regy1$tau2, regy1$sigma2, regy1$beta0, regy1$betahat, K, gmmx1$epsilon, gmmx1$W, beta, ro, r, si, sig2.data,N, D1)
regy1$beta0 <- paramtime1$beta0
regy1$betahat <- paramtime1$betahat
regy1$sigma2 <- paramtime1$sigma2
regy1$lambda2 <- paramtime1$lambda2
regy1$tau2 <- paramtime1$tau2
########################## THE HYPERPARAMETERS OF THE GMM #################################
# Updating the hyper paramters for the first data set
hypercognate <- posteriorhyperPLUS(c, Y1, gmmx1$mu, gmmx1$S, gmmx1$epsilon, gmmx1$W, gmmx1$beta, gmmx1$ro )
gmmx1$epsilon <- hypercognate$epsilon
tmpW <- hypercognate$W
gmmx1$W <- matrix(as.matrix(tmpW),nrow = D1, ncol =D1)
gmmx1$ro <- hypercognate$ro
##Updating the hyper parameter for the second data set
hypercognate2 <- posteriorhyperPLUS(c, Y2, gmmx2$mu, gmmx2$S, gmmx2$epsilon, gmmx2$W, gmmx2$beta, gmmx2$ro )
gmmx2$epsilon <- hypercognate2$epsilon
tmpW2 <- hypercognate2$W
gmmx2$W <- matrix(as.matrix(tmpW2),nrow = D2, ncol =D2)
gmmx2$ro <- hypercognate2$ro
### Updating Beta parameter for the first view #################
# source('posteriorbeta.R')
# if( o%%10 == 0){
# res <- try(posteriorbeta(c, gmmx1$beta, D1, gmmx1$S, gmmx1$W))
# if (class(res) == "try-error"){
# gmmx1$beta = gmmx1$beta
# } else{
# gmmx1$beta <- posteriorbeta(gmmx1$beta, D1, gmmx1$S, gmmx1$W)
#
# }
# }
# ### Updating Beta parameter for the second view #################
# source('posteriorbeta.R')
# if( o%%10 == 0){
# res <- try(posteriorbeta(c, gmmx2$beta, D2, gmmx2$S, gmmx2$W))
# if (class(res) == "try-error"){
# gmmx2$beta = gmmx2$beta
# } else{
# gmmx2$beta <- posteriorbeta(gmmx2$beta, D2, gmmx2$S, gmmx2$W)
#
# }
# }
#
################# INDICATOR VARIABLE ##################################################################
## Updating the indicator variables and the parameters
cognate <- multiposteriorchineseAFT(c,Y1,Y2,D1,D2,That, K, r, si,sig2.dat,gmmx1, gmmx2, regy1, regy2)
c <- cognate$c
gmmx1 <- cognate$gmmx1
gmmx2 <- cognate$gmmx2
regy1 <- cognate$regy1
regy2 <- cognate$regy2
########################### The Concentration Parameter #################################################################
# Updating the concentration parameter
alpha <- posterioralpha(c, N, alpha, shape.alpha, rate.alpha)
######################## The Censored Times ###########################################################
source('multiupdatetime.R')
# Updating the Time Variable
ti <- NA
ti <- multiupdatetime(c, Y1, Y2, Time,That, regy1, regy2)
That <- ti$time
if(o%% iter.thin == 0 ){
est.regy1[[count]] <- regy1
est.regy2[[count]] <- regy2
est.gmmx1[[count]] <- gmmx1
est.gmmx2[[count]] <- gmmx2
c.list[[count]] <- c
That.list[[count]] <- That
alpha.list[[count]] <- alpha
count <- count +1
}
Sys.sleep(0.1)
setTxtProgressBar(pb, o)
}
#######################################################################################################
############################ Analyzing the MCMC output #################################################
#######################################################################################################
Y <- as.matrix(cbind(Y1,Y2))
Y.new <- as.matrix(cbind(Y1.new, Y2.new))
Y.test <- Y.new
#######################################################################
############# TRAININIG DATA ###########################################
#######################################################################
########################################################################
#### This function calculates some important metrices for the TRAINING DATA Data
#### C-Index
#### Point Estimate of Clsuter Assignments based on m-pear
########## ANLAYSING THE MCMC samples AND CALCULATING METRICES #######################################################
Nps = as.integer(iter/ iter.thin)
count <- Nps
############ The Matrices that will store the results #################################################
cindex.final1 <- c(0)
cindex.final2 <- c(0)
recovCIndex.isbc <- c(0)
recovCIndex.isbc.paft <- c(0)
################ Begin Analysig the MCMC samples #######################################################
for (h in 1:Nps){
### Adjusted Rand Indices
surv.aft <- Surv(exp(time),censoring)
### Predict Time from the model
source('linearprediction.R')
tem.tim1 <- as.vector(unlist(predicttime(c.list[[h]], Y1, That, Time, est.regy1[[h]]$beta0, est.regy1[[h]]$betahat, est.regy1[[h]]$sigma2)))
tem.tim2 <- as.vector(unlist(predicttime(c.list[[h]], Y2, That, Time, est.regy2[[h]]$beta0, est.regy2[[h]]$betahat, est.regy2[[h]]$sigma2)))
cindex.final1[h] <- survConcordance(surv.aft ~ exp(-tem.tim1))[[1]]
cindex.final2[h] <- survConcordance(surv.aft ~ exp(-tem.tim2))[[1]]
source('multilinearprediction.R')
tem.tim <- as.vector(unlist(multipredictlinear(c.list[[h]], est.regy1[[h]], est.regy2[[h]] )))
recovCIndex.isbc[h] <- survConcordance(surv.aft ~ exp(-tem.tim))[[1]]
###### penAFT ###################################################################
######## Penalized AFT with k-means clustering ######################################################
isbc.aft <- c(0)
for ( q in 1:F){
ind <- which((c.list[[h]]) == q)
L= length(ind)
time.tmp <- time[ind]
censoring.tmp <- censoring[ind]
Y.tmp <- Y[ind,]
reg <- cv.glmnet(x = Y.tmp, y = time.tmp, family = "gaussian")
coeff.pred <- coef(object =reg, newx = Y.tmp, s= "lambda.min")
isbc.aft[ind] <- predict(object = reg, newx = Y.tmp, s = "lambda.min")
}
recovCIndex.isbc.paft[h] <- as.numeric(survConcordance(smod ~ exp(-isbc.aft))[1])
}
###############################################
###### Calculating POINT ESTIMATES ############
###############################################
##### Class Assignments ########################
c.matrix <- matrix(NA, nrow = N, ncol = count)
for ( i in 1:count){
c.matrix[,i] <- c.list[[i]]
}
###############################################
###### Calculating POINT ESTIMATES ############
###############################################
psm <- comp.psm(t(c.matrix))
mpear <- maxpear(psm)
### If we build a cluster specific sbc approach
c.final <- mpear$cl
c.sbc <- mpear$cl
active <- as.numeric(rownames(table(c.final)))
############ Time Covariate Slopes FOR Relevant Clusters and Heatmap Plots ############
list.betahat1 <- list(0)
for ( i in 1:count){
list.betahat1[[i]] <- (est.regy1[[i]]$betahat[active,] != 0) +0
}
Q <- length(active)
matrix.betahat1 <- array(data = NA, dim =c(Q,count,D1))
for ( z in 1:Q){
for ( x in 1:count){
matrix.betahat1[z,x,] <- list.betahat1[[x]][z,]
}
}
final.betahat1 <- apply(matrix.betahat1,c(1,3),mean)
### Probability of betahat of genes FOR ONE SIMULATION
##colnames(final.betahat) = c(rep("relevant",rel.D),rep("irrelevant",irrel.D))
heatmapdata1 <- as.data.frame(final.betahat1)
#heatmap.2(t(as.matrix(heatmapdata1)),dendrogram="none", col =cm.colors(180), margins=c(6,10), main = "Posterior prob. \n for Selection for Data set 1 ", cexCol = 0.85, cexRow = 0.7, Rowv = FALSE)
########################## For the second data set ####################################################
list.betahat2 <- list(0)
for ( i in 1:count){
list.betahat2[[i]] <- (est.regy2[[i]]$betahat[active,] != 0) +0
}
Q <- length(active)
matrix.betahat2 <- array(data = NA, dim =c(Q,count,D2))
for ( z in 1:Q){
for ( x in 1:count){
matrix.betahat2[z,x,] <- list.betahat2[[x]][z,]
}
}
final.betahat2 <- apply(matrix.betahat2,c(1,3),mean)
heatmapdata2 <- as.data.frame(final.betahat2)
#heatmap.2(t(as.matrix(heatmapdata2)),dendrogram="none", col =cm.colors(180), margins=c(6,10), main = "Posterior prob. \n for Selection for Data set 2 ", cexCol = 0.85, cexRow = 0.7, Rowv = FALSE)
############# Calculating the recovery logrank statistic
recov.logrank.sbc <- unlist(survdiff(smod ~ c.sbc))$chisq
##### Predicting the Class of the new data points ##################
Y1.test <- Y1.new
Y2.test <- Y2.new
N.new <- nrow(Y1.test)
c.new.list <- list(0)
## The number of posterior samples
Nps <- as.integer(iter/ iter.thin)
That.new <- time.new
print("GOING THROUGH MCMC Samples")
pb <- txtProgressBar(min = 1, max = Nps , style = 3)
gmmx1.tmp <- list(0)
gmmx2.tmp <- list(0)
regy1.tmp <- list(0)
regy2.tmp <- list(0)
Ytemp1 <- Y1.test
Ytemp2 <- Y2.test
Ytemp1.scaled <- matrix(NA, nrow = N, ncol = D1)
Ytemp2.scaled <- matrix(NA, nrow = N, ncol = D2)
modelweights <- c(0)
for (count in 1:Nps){
## Assign the parameters to the posterior sample
ctemp <- c.list[[count]]
gmmx1.tmp <- est.gmmx1[[count]]
gmmx2.tmp <- est.gmmx2[[count]]
regy1.tmp <- est.regy1[[count]]
regy2.tmp <- est.regy2[[count]]
g <- table(factor(ctemp, levels = 1:K))
activeclass <- which(g!=0)
## The table function helps converting the data point specific indicator variables to class specific indicator variables
kminus <- length(activeclass)
## Two Auxilary Variables
## The name of the auxilary variables are taken to be one and two more than the maximum value in the already active cluster set
activeclass <- append(activeclass, max(activeclass)+1)
activeclass <- append(activeclass, max(activeclass)+1)
active <- activeclass
### Assigning values to parameters
priorone1 <- NA
priorone2 <- NA
### Draw the values of two auxilary parameters from Prior Distribution
source('priorPARAMETERS.R')
#priorone1 <- priordraw(beta, gmmx1$W, gmmx1$epsilon, ro, r, si,N,D1, sig2.dat)
repeat {
priorone1 <- priordraw(gmmx1.tmp$beta, gmmx1.tmp$W, gmmx1.tmp$epsilon, gmmx1.tmp$ro, r, si,N,D1, sig2.dat)
res <- try(chol(priorone1$Sigma), silent = TRUE)
if (class(res) != "try-error"){
break
}
}
gmmx1.tmp$mu[active[kminus+1],1:D1] <- priorone1$mu
gmmx1.tmp$S[active[kminus+1],1:D1,1:D1] <- priorone1$Sigma
regy1.tmp$beta0[active[kminus+1]] <- priorone1$beta0
regy1.tmp$sigma2[active[kminus+1]] <- priorone1$sigma2
regy1.tmp$betahat[active[kminus+1],1:D1] <- priorone1$betahat
regy1.tmp$lambda2[active[kminus+1]] <- priorone1$lambda2
regy1.tmp$tau2[active[kminus+1], 1:D1] <- priorone1$tau2
repeat {
priorone2 <- priordraw(gmmx2.tmp$beta, gmmx2.tmp$W, gmmx2.tmp$epsilon, gmmx2.tmp$ro, r, si,N, D2, sig2.dat)
res <- try(chol(priorone2$Sigma), silent = TRUE)
if (class(res) != "try-error"){
break
}
}
gmmx2.tmp$mu[active[kminus+1],1:D2] <- priorone2$mu
gmmx2.tmp$S[active[kminus+1],1:D2,1:D2] <- priorone2$Sigma
regy2.tmp$beta0[active[kminus+1]] <- priorone2$beta0
regy2.tmp$sigma2[active[kminus+1]] <- priorone2$sigma2
regy2.tmp$betahat[active[kminus+1],1:D2] <- priorone2$betahat
regy2.tmp$lambda2[active[kminus+1]] <- priorone2$lambda2
regy2.tmp$tau2[active[kminus+1], 1:D2] <- priorone2$tau2
source('priorPARAMETERS.R')
#priorone1 <- priordraw(beta, gmmx1$W, gmmx1$epsilon, ro, r, si,N,D1, sig2.dat)
repeat {
priorone1 <- priordraw(beta, gmmx1$W, gmmx1$epsilon, gmmx1$ro, r, si,N,D1, sig2.dat)
res <- try(chol(priorone1$Sigma),silent = TRUE)
if (class(res) != "try-error"){
break
}
}
gmmx1.tmp$mu[active[kminus+2],1:D1] <- priorone1$mu
gmmx1.tmp$S[active[kminus+2],1:D1,1:D1] <- priorone1$Sigma
regy1.tmp$beta0[active[kminus+2]] <- priorone1$beta0
regy1.tmp$sigma2[active[kminus+2]] <- priorone1$sigma2
regy1.tmp$betahat[active[kminus+2],1:D1] <- priorone1$betahat
regy1.tmp$lambda2[active[kminus+2]] <- priorone1$lambda2
regy1.tmp$tau2[active[kminus+2], 1:D1] <- priorone1$tau2
##priorone2 <- priordraw(beta, gmmx2$W, gmmx2$epsilon, ro, r, si,N,D2, sig2.dat)
repeat {
priorone2 <- priordraw(beta, gmmx2$W, gmmx2$epsilon, gmmx2$ro, r, si,N,D2, sig2.dat)
res <- try(chol(priorone2$Sigma), silent = TRUE)
if (class(res) != "try-error"){
break
}
}
gmmx2.tmp$mu[active[kminus+2],1:D2] <- priorone2$mu
gmmx2.tmp$S[active[kminus+2],1:D2,1:D2] <- priorone2$Sigma
regy2.tmp$beta0[active[kminus+2]] <- priorone2$beta0
regy2.tmp$sigma2[active[kminus+2]] <- priorone2$sigma2
regy2.tmp$betahat[active[kminus+2],1:D2] <- priorone2$betahat
regy2.tmp$lambda2[active[kminus+2]] <- priorone2$lambda2
regy2.tmp$tau2[active[kminus+2], 1:D2] <- priorone2$tau2
#######################################################
ctemp.new = c(0)
weights.final <- c(0)
## This can't be parallelized !!!!!
for(l in 1:N.new) {
posterior <- matrix(NA, nrow = length(active), ncol = 1)
Y.new.sc1 <- matrix(0, nrow = N.new, ncol =D1)
Y.new.sc2 <- matrix(0, nrow = N.new, ncol =D2)
## Calculating the probabalities for drawing the value of c_i from the active classes
for (j in 1:kminus) {
clust <- which(ctemp == active[j])
posterior[j] <- log(g[active[j]] /(N-1+alpha)) + dMVN(x = as.vector(t(Ytemp1[l,])), mean = gmmx1.tmp$mu[active[j],1:D1], Q = gmmx1.tmp$S[active[j],1:D1,1:D1], log = TRUE) + dMVN(x = as.vector(t(Ytemp2[l,])), mean = gmmx2.tmp$mu[active[j],1:D2], Q = gmmx2.tmp$S[active[j],1:D2,1:D2], log =TRUE)
}
posterior[kminus+1] <- log((0.5 * alpha) /(N-1+alpha)) + dMVN(x = as.vector(t(Ytemp1[l,])), mean = gmmx1.tmp$mu[active[kminus+1],1:D1], Q = gmmx1.tmp$S[active[kminus+1],1:D1,1:D1], log = TRUE) + dMVN(x = as.vector(t(Ytemp2[l,])), mean = gmmx2.tmp$mu[active[kminus+1],1:D2], Q = gmmx2.tmp$S[active[kminus+1],1:D2,1:D2], log = TRUE)
posterior[kminus+2] <- log((0.5 * alpha) /(N-1+alpha)) + dMVN(x = as.vector(t(Ytemp1[l,])), mean = gmmx1.tmp$mu[active[kminus+2],1:D1], Q = gmmx1.tmp$S[active[kminus+2],1:D1,1:D1], log = TRUE) + dMVN(x = as.vector(t(Ytemp2[l,])), mean = gmmx2.tmp$mu[active[kminus+2],1:D2], Q = gmmx2.tmp$S[active[kminus+2],1:D2,1:D2], log = TRUE)
## Calculating the normalization constant for probabilities
post <- exp(posterior)
if (sum(post) > 0){
ctemp.new[l] <- sample(active, 1, prob= post, replace = TRUE)
} else {
ctemp.new[l] <- sample(active, 1)
}
weights.final[l] <- dMVN(x = as.vector(t(Ytemp1[l,1:D1])), mean = gmmx1.tmp$mu[ctemp.new[l] ,1:D1], Q = gmmx1.tmp$S[ctemp.new[l] ,1:D1,1:D1], log = TRUE) + dMVN(x = as.vector(t(Ytemp2[l,1:D2])), mean = gmmx2.tmp$mu[ctemp.new[l],1:D2], Q = gmmx2.tmp$S[ctemp.new[l],1:D2,1:D2], log =TRUE)
}
modelweights[count] <- sum(weights.final)
c.new.list[[count]] <- ctemp.new
Sys.sleep(0.1)
setTxtProgressBar(pb, count)
}
c.matrix.new <- matrix(NA, nrow = N.new, ncol = Nps)
for( h in 1:Nps){
c.matrix.new[,h] <- c.new.list[[h]]
}
####### Use Ad-hoc methods to calculate the actual separability and C-Index ##################
### This function takes the posterior parameters AND predicts CLUSTER MEMEBERSHIP for the new points
### The posterior parameters being the RECOVERED CLUSTER MEMBERSHIP
#### THEN IT FITS A LOGISTIC/MULTINOMIAL regression FOR LINEAR SEPARABILITY
#### WE CAN ALSO EXPLORE NON-LINEAR Classifiers as k-SVM (RBF kernel)
### Check to see if this gives differences to state of the art
### POSSIBLE APPROACHES TO GET POINT ESTIMATES #####
### POSSIBILITY 1
### Use MPEAR APPROACH to get POINT ESTIMATES #############################################################################
psm2 <- comp.psm(t(c.matrix.new))
mpear2 <- maxpear(psm2)
### Generally the MPEAR output needs post-processing
c.sbc.new.mpear <- mpear2$cl
### POSSIBILITY 2
### Use Logistic regression to get the labels
reg <- cv.glmnet(x = Y, y = as.factor(c.sbc), family = "binomial")
reg.new <- predict(object = reg, newx = Y.new, s = "lambda.min", type="class")
c.sbc.new.log <- as.numeric(reg.new)
### POSSIBILITY 3
### Use k-Nearest neighbour
label.train <- as.factor(c.sbc)
### One has to to tune the k-NN classifier for k ###
fitControl <- trainControl(method = "repeatedcv", number = 5,repeats = 5)
### Tune the parameter k
knnFit <- train(x = Y, y = label.train, method = "knn", trControl = fitControl, tuneLength = 5)
c.sbc.new.knn <- predict(knnFit,newdata = Y.new )
#### Choose that configuration which has the highest difference in survival curves ####################
### POSSIBILITY 4
### Use k-svm
library(e1071)
library(kernlab)
df <- data.frame(cbind(c.sbc,Y))
sig <- sigest(c.sbc ~.,data = df)
range.sig <- seq(from = sig[1],to = sig[3], length.out = 25)
obj.base <- tune(svm, train.x = Y, train.y = factor(c.sbc), ranges = list(gamma = 2^(-10:14), cost = 2^(-10:14)), tunecontrol = tune.control(sampling = "cross"))
sigma.final <- obj.base$best.parameters$gamma
cost.final <- obj.base$best.parameters$cost
# Training the Classifier
ksvm.verk = ksvm(Y, factor(c.sbc), kernel = "rbfdot",kpar = list(sigma =sigma.final),C= cost.final, prob.model =TRUE)
## Predicting
labels.ksvm <- predict(ksvm.verk ,Y.new, type = "response")
pred.logrank.rbf <- survdiff(smod.new ~ labels.ksvm)
c.sbc.new.rbf <- labels.ksvm
### POSSIBILITY 5
### Use one of the actual cluster assignments
c.matrix.new.sbc <- matrix(0, nrow = N.new, ncol = Nps + 4)
c.matrix.new.sbc[,1:Nps] <- c.matrix.new[,1:Nps]
c.matrix.new.sbc[,(Nps+1)] <- c.sbc.new.mpear
c.matrix.new.sbc[,(Nps+2)] <- c.sbc.new.log
c.matrix.new.sbc[,(Nps+3)] <- c.sbc.new.knn
c.matrix.new.sbc[,(Nps+4)] <- c.sbc.new.rbf
Nps.mod <- Nps +4
lr <- c(0)
for (j in 1:Nps.mod){
lr[j] <- 1 - pchisq(unlist(survdiff(smod.new ~ c.matrix.new.sbc[,j]))$chisq,df = nlevels(as.factor(c.matrix.new.sbc[,i])) -1 )
}
c.sbc.new <- c.matrix.new.sbc[,which.min(lr)]
c.new.list <- list(0)
## The number of posterior samples
post.time = matrix(NA,nrow = nrow(Y1.test), ncol = Nps)
cind <- c(0)
N.new <- nrow(Y1.test)
gmmx1.tmp <- list(0)
gmmx2.tmp <- list(0)
regy1.tmp <- list(0)
regy2.tmp <- list(0)
Ytemp1 <- Y1.test
Ytemp2 <- Y2.test
predCIndex.sbc <- c(0)
print("GOING THROUGH MCMC Samples")
pb <- txtProgressBar(min = 1, max = Nps , style = 3)
for (count in 1:Nps){
ctemp <- c.list[[count]]
gmmx1.tmp <- est.gmmx1[[count]]
gmmx2.tmp <- est.gmmx2[[count]]
regy1.tmp <- est.regy1[[count]]
regy2.tmp <- est.regy2[[count]]
g <- table(factor(ctemp, levels = 1:K))
activeclass <- which(g!=0)
## The table function helps converting the data point specific indicator variables to class specific indicator variables
kminus <- length(activeclass)
## Two Auxilary Variables
## The name of the auxilary variables are taken to be one and two more than the maximum value in the already active cluster set
activeclass <- append(activeclass, max(activeclass)+1)
activeclass <- append(activeclass, max(activeclass)+1)
active <- activeclass
### Assigning values to parameters
priorone1 <- NA
priorone2 <- NA
### Draw the values of two auxilary parameters from Prior Distribution
source('priorPARAMETERS.R')
#priorone1 <- priordraw(beta, gmmx1$W, gmmx1$epsilon, ro, r, si,N,D1, sig2.dat)
repeat {
priorone1 <- priordraw(gmmx1.tmp$beta, gmmx1.tmp$W, gmmx1.tmp$epsilon, gmmx1.tmp$ro, r, si,N,D1, sig2.dat)
res <- try(chol(priorone1$Sigma), silent = TRUE)
if (class(res) != "try-error"){
break
}
}
gmmx1.tmp$mu[active[kminus+1],1:D1] <- priorone1$mu
gmmx1.tmp$S[active[kminus+1],1:D1,1:D1] <- priorone1$Sigma
regy1.tmp$beta0[active[kminus+1]] <- priorone1$beta0
regy1.tmp$sigma2[active[kminus+1]] <- priorone1$sigma2
regy1.tmp$betahat[active[kminus+1],1:D1] <- priorone1$betahat
regy1.tmp$lambda2[active[kminus+1]] <- priorone1$lambda2
regy1.tmp$tau2[active[kminus+1], 1:D1] <- priorone1$tau2
repeat {
priorone2 <- priordraw(gmmx2.tmp$beta, gmmx2.tmp$W, gmmx2.tmp$epsilon, gmmx2.tmp$ro, r, si,N, D2, sig2.dat)
res <- try(chol(priorone2$Sigma), silent = TRUE)
if (class(res) != "try-error"){
break
}
}