User:Timothee Flutre/Notebook/Postdoc/2011/12/14
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** introduction (ch.1) of the PhD thesis from Matthew Stephens (Oxford, 2000)  ** introduction (ch.1) of the PhD thesis from Matthew Stephens (Oxford, 2000)  
** tutorial from Carlo Tomasi (Duke University)  ** tutorial from Carlo Tomasi (Duke University)  
+  ** book "Introducing Monte Carlo Methods with R" from Robert and and Casella (2009)  
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Revision as of 19:45, 3 January 2012
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Learn about mixture models and the EM algorithm(Caution, this is my own quickanddirty tutorial, see the references at the end for presentations by professional statisticians.)
We can now write the complete likelihood, ie. the likelihood of the augmented model (even if we don't need it in the following), where I_{k} = {i / Z_{i} = k}: . And, more useful, the incomplete (or marginal) likelihood, assuming all observations are independent:
As we derive with respect to μ_{k}, all the others means μ_{l} with are constant, and thus disappear:
And finally:
Once we put all together, we end up with:
By convention, we note the maximumlikelihood estimate of μ_{k}:
Therefore, we finally obtain:
By doing the same kind of algebra, we derive the loglikelihood w.r.t. σ_{k}:
And then we obtain the ML estimates for the standard deviation of each cluster:
The partial derivative of l(θ) w.r.t. w_{k} is tricky. ... <TO DO> ...
Finally, here are the ML estimates for the mixture weights:
#' Generate univariate observations from a mixture of Normals #' #' @param K number of components #' @param N number of observations GetUnivariateSimulatedData < function(K=2, N=100){ mus < seq(0, 6*(K1), 6) sigmas < runif(n=K, min=0.5, max=1.5) tmp < floor(rnorm(n=K1, mean=floor(N/K), sd=5)) ns < c(tmp, N  sum(tmp)) clusters < as.factor(matrix(unlist(lapply(1:K, function(k){rep(k, ns[k])})), ncol=1)) obs < matrix(unlist(lapply(1:K, function(k){ rnorm(n=ns[k], mean=mus[k], sd=sigmas[k]) }))) new.order < sample(1:N, N) obs < obs[new.order] rownames(obs) < NULL clusters < clusters[new.order] return(list(obs=obs, clusters=clusters, mus=mus, sigmas=sigmas, mix.weights=ns/N)) }
#' Return probas of latent variables given data and parameters from previous iteration #' #' @param data Nx1 vector of observations #' @param params list which components are mus, sigmas and mix.weights Estep < function(data, params){ GetMembershipProbas(data, params$mus, params$sigmas, params$mix.weights) } #' Return the membership probabilities P(zi=k/xi,theta) #' #' @param data Nx1 vector of observations #' @param mus Kx1 vector of means #' @param sigmas Kx1 vector of std deviations #' @param mix.weights Kx1 vector of mixture weights w_k=P(zi=k/theta) #' @return NxK matrix of membership probas GetMembershipProbas < function(data, mus, sigmas, mix.weights){ N < length(data) K < length(mus) tmp < matrix(unlist(lapply(1:N, function(i){ x < data[i] norm.const < sum(unlist(Map(function(mu, sigma, mix.weight){ mix.weight * GetUnivariateNormalDensity(x, mu, sigma)}, mus, sigmas, mix.weights))) unlist(Map(function(mu, sigma, mix.weight){ mix.weight * GetUnivariateNormalDensity(x, mu, sigma) / norm.const }, mus[K], sigmas[K], mix.weights[K])) })), ncol=K1, byrow=TRUE) membership.probas < cbind(tmp, apply(tmp, 1, function(x){1  sum(x)})) names(membership.probas) < NULL return(membership.probas) } #' Univariate Normal density GetUnivariateNormalDensity < function(x, mu, sigma){ return( 1/(sigma * sqrt(2*pi)) * exp(1/(2*sigma^2)*(xmu)^2) ) }
#' Return ML estimates of parameters #' #' @param data Nx1 vector of observations #' @param params list which components are mus, sigmas and mix.weights #' @param membership.probas NxK matrix with entry i,k being P(zi=k/xi,theta) Mstep < function(data, params, membership.probas){ params.new < list() sum.membership.probas < apply(membership.probas, 2, sum) params.new$mus < GetMlEstimMeans(data, membership.probas, sum.membership.probas) params.new$sigmas < GetMlEstimStdDevs(data, params.new$mus, membership.probas, sum.membership.probas) params.new$mix.weights < GetMlEstimMixWeights(data, membership.probas, sum.membership.probas) return(params.new) } #' Return ML estimates of the means (1 per cluster) #' #' @param data Nx1 vector of observations #' @param membership.probas NxK matrix with entry i,k being P(zi=k/xi,theta) #' @param sum.membership.probas Kx1 vector of sum per column of matrix above #' @return Kx1 vector of means GetMlEstimMeans < function(data, membership.probas, sum.membership.probas){ K < ncol(membership.probas) sapply(1:K, function(k){ sum(unlist(Map("*", membership.probas[,k], data))) / sum.membership.probas[k] }) } #' Return ML estimates of the std deviations (1 per cluster) #' #' @param data Nx1 vector of observations #' @param membership.probas NxK matrix with entry i,k being P(zi=k/xi,theta) #' @param sum.membership.probas Kx1 vector of sum per column of matrix above #' @return Kx1 vector of std deviations GetMlEstimStdDevs < function(data, means, membership.probas, sum.membership.probas){ K < ncol(membership.probas) sapply(1:K, function(k){ sqrt(sum(unlist(Map(function(p_ki, x_i){ p_ki * (x_i  means[k])^2 }, membership.probas[,k], data))) / sum.membership.probas[k]) }) } #' Return ML estimates of the mixture weights #' #' @param data Nx1 vector of observations #' @param membership.probas NxK matrix with entry i,k being P(zi=k/xi,theta) #' @param sum.membership.probas Kx1 vector of sum per column of matrix above #' @return Kx1 vector of mixture weights GetMlEstimMixWeights < function(data, membership.probas, sum.membership.probas){ K < ncol(membership.probas) sapply(1:K, function(k){ 1/length(data) * sum.membership.probas[k] }) }
... <TO DO> ...
## simulate data K < 3 N < 300 simul < GetUnivariateSimulatedData(K, N) data < simul$obs ## run the EM algorithm params0 < list(mus=runif(n=K, min=min(data), max=max(data)), sigmas=rep(1, K), mix.weights=rep(1/K, K)) res < EMalgo(data, params0, 10^(3), 1000, 1) ## check its convergence plot(res$logliks, xlab="iterations", ylab="loglikelihood", main="Convergence of the EM algorithm", type="b") ## plot the data along with the inferred densities png("mixture_univar_em.png") hist(data, breaks=30, freq=FALSE, col="grey", border="white", ylim=c(0,0.15), main="Histogram of data overlaid with densities inferred by EM") rx < seq(from=min(data), to=max(data), by=0.1) ds < lapply(1:K, function(k){dnorm(x=rx, mean=res$params$mus[k], sd=res$params$sigmas[k])}) f < sapply(1:length(rx), function(i){ res$params$mix.weights[1] * ds[[1]][i] + res$params$mix.weights[2] * ds[[2]][i] + res$params$mix.weights[3] * ds[[3]][i] }) lines(rx, f, col="red", lwd=2) dev.off() It seems to work well, which was expected as the clusters are well separated from each other...
