User:Timothee Flutre/Notebook/Postdoc/2011/12/14
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m (→Learn about mixture models and the EM algorithm: rmv bad examples) 
(→Learn about mixture models and the EM algorithm: clarify E step) 

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''(Caution, this is my own quickanddirty tutorial, see the references at the end for presentations by professional statisticians.)''  ''(Caution, this is my own quickanddirty tutorial, see the references at the end for presentations by professional statisticians.)''  
  * '''Motivation''': a large part of any scientific activity is about measuring things, in other words collecting data, and it is not infrequent to collect ''heterogeneous'' data. It seems therefore natural to say that the samples come from a mixture of clusters. The aim is thus to recover from the data, ie. to infer, (i) how many clusters there are, (ii) what are the features of these clusters, and (  +  * '''Motivation''': a large part of any scientific activity is about measuring things, in other words collecting data, and it is not infrequent to collect ''heterogeneous'' data. It seems therefore natural to say that the samples come from a mixture of clusters. The aim is thus to recover from the data, ie. to infer, (i) how many clusters there are, (ii) what are the features of these clusters, and (iii) from which cluster each sample comes from. In the following, I will focus on points (ii) and (iii). 
* '''Data''': we have N observations, noted <math>X = (x_1, x_2, ..., x_N)</math>. For the moment, we suppose that each observation <math>x_i</math> is univariate, ie. each corresponds to only one number.  * '''Data''': we have N observations, noted <math>X = (x_1, x_2, ..., x_N)</math>. For the moment, we suppose that each observation <math>x_i</math> is univariate, ie. each corresponds to only one number.  
  * '''  +  * '''Assumption''': let's assume that the data are heterogeneous and that they can be partitioned into <math>K</math> clusters (in this document, we suppose that <math>K</math> is known). This means that we expect a subset of the observations to come from cluster <math>k=1</math>, another subset to come from cluster <math>k=2</math>, and so on. 
  
  <math>f(x_i/\theta) = \sum_{k=1}^{K} w_k  +  * '''Model''': technically, we say that the observations were generated according to a [http://en.wikipedia.org/wiki/Probability_density_function density function] <math>f</math>. More precisely, this density is itself a mixture of densities, one per cluster. In our case, we will assume that observations from cluster <math>k</math> are generated from a Normal distribution, which density is here noted <math>\phi</math>, with mean <math>\mu_k</math> and standard deviation <math>\sigma_k</math>. Moreover, as we don't know for sure from which cluster a given observation comes from, we define the mixture weight <math>w_k</math> (also called mixing proportion) to be the probability that any given observation comes from cluster <math>k</math>. As a result, we have the following list of parameters: <math>\theta=(w_1,...,w_K,\mu_1,...\mu_K,\sigma_1,...,\sigma_K)</math>. Finally, for a given observation <math>x_i</math>, we can write the model: 
+  
+  <math>f(x_i\theta) = \sum_{k=1}^{K} w_k \phi(x_i\mu_k,\sigma_k) = \sum_{k=1}^{K} w_k \frac{1}{\sqrt{2\pi} \sigma_k} \exp \left(\frac{1}{2}(\frac{x_i  \mu_k}{\sigma_k})^2 \right)</math>  
The constraints are:  The constraints are:  
<math>\forall k, w_k > 0</math> and <math>\sum_{k=1}^K w_k = 1</math>  <math>\forall k, w_k > 0</math> and <math>\sum_{k=1}^K w_k = 1</math>  
  
  +  * '''Maximumlikelihood''': naturally, we can start by maximizing the likelihood in order to estimate the parameters:  
  +  <math>L(\theta) = P(X\theta) = \prod_{i=1}^N f(x_i\theta)</math>  
  <math>  +  
  +  As usual, it's easier to deal with the loglikelihood:  
  <math>  +  <math>l(\theta) = \sum_{i=1}^N ln \left( f(x_i\theta) \right) = \sum_{i=1}^N ln \left( \sum_{k=1}^K w_k \phi(x_i; \theta_k) \right)</math> 
  +  Let's take the derivative with respect to one parameter, eg. <math>\theta_l</math>:  
  +  
  +  <math>\frac{\partial l}{\partial \theta_l} = \sum_{i=1}^N \frac{1}{\sum_{k=1}^K w_k \phi(x_i; \theta_k)} w_l \frac{\partial \phi(x_i; \theta_l)}{\partial \theta_l}</math>  
  <math>\frac{\partial l  +  <math>\frac{\partial l}{\partial \theta_l} = \sum_{i=1}^N \frac{w_l \phi(x_i; \theta_l)}{\sum_{k=1}^K w_k \phi(x_i; \theta_k)} \frac{1}{\phi(x_i; \theta_l)} \frac{\partial \phi(x_i; \theta_l)}{\partial \theta_l}</math> 
  +  <math>\frac{\partial l}{\partial \theta_l} = \sum_{i=1}^N \frac{w_l \phi(x_i; \theta_l)}{\sum_{k=1}^K w_k \phi(x_i; \theta_k)} \frac{\partial ln ( \phi(x_i; \theta_l) )}{\partial \theta_l}</math>  
  +  This shows that maximizing the likelihood of a mixture model is like doing a weighted likelihood maximization. However, these weights depend on the parameters we want to estimate! That's why we now switch to the missingdata formulation of the mixture model.  
  
  <math>  +  * '''Missing data''': we introduce the following N [http://en.wikipedia.org/wiki/Latent_variable latent variables] <math>Z_1,...,Z_i,...,Z_N</math> (also called hidden or allocation variables), one for each observation, such that <math>Z_i=k</math> means that observation <math>x_i</math> belongs to cluster <math>k</math>. In fact, it is much easier to work the equations when defining each <math>Z_i</math> as a vector of length <math>K</math>, with <math>Z_{ik}=1</math> if observation <math>x_i</math> belongs to cluster <math>k</math>, and <math>Z_{ik}=0</math> otherwise ([http://en.wikipedia.org/wiki/Dummy_variable_%28statistics%29 indicator variables]). Thanks to this, we can reinterpret the mixture weights: <math>\forall i, P(Z_i=k\theta)=w_k</math>. Moreover, we can now define the membership probabilities, one for each observation: 
  +  <math>p(ki) = P(Z_{ik}=1x_i,\theta) = \frac{w_k \phi(x_i\mu_k,\sigma_k)}{\sum_{l=1}^K w_l \phi(x_i\mu_l,\sigma_l)}</math>  
  +  The observeddata likelihood (also called sometimes "incomplete" or "marginal", even though these appellations are misnomers) is still written the same way:  
  +  <math>L_{obs}(\theta) = P(X\theta) = \prod_{i=1}^N f(x_i\theta)</math>  
  +  But now we can also write the augmenteddata likelihood, assuming all observations are independent conditionally on their membership:  
  +  <math>L_{aug}(\theta) = P(X,Z\theta) = \prod_{i=1}^N P(x_iZ_i,\theta) P(Z_i\theta) = \prod_{i=1}^N \left( \prod_{k=1}^K \phi(x_i\mu_k,\sigma_k)^{Z_{ik}} w_k^{Z_{ik}} \right)</math>.  
  +  And here is the augmenteddata loglikelihood (useful in the M step of the EM algorithm, see below):  
  +  <math>l_{aug}(\theta) = \sum_{i=1}^N \left( \sum_{k=1}^K Z_{ik} ln(\phi(x_i\mu_k,\sigma_k)) + \sum_{k=1}^K Z_{ik} ln(w_k) \right)</math>  
  +  In terms of [http://en.wikipedia.org/wiki/Graphical_model graphical model], the Gaussian mixture model described here can be represented like [http://en.wikipedia.org/wiki/File:Nonbayesiangaussianmixture.svg this].  
  
  <math>\  +  * '''EM algorithm  definition''': the idea is to iterate two steps, starting from randomlyinitialized parameters. In the Estep, one computes the conditional expectation of the augmenteddata loglikelihood function over the latent variables given the observed data and the parameter estimates from the previous iteration. Second, in the Mstep, one maximizes this expected augmenteddata loglikelihood function to determine the next iterate of the parameter estimates. 
+  ** E step: <math>Q(\thetaX,\theta^{(t)}) = \mathbb{E}_{ZX,\theta^{(t)}} \left[ ln(P(X,Z\theta))X,\theta^{(t)} \right] = \int l_{aug} q(ZX,\theta^{(t)}) dZ</math>  
+  ** Mstep: <math>\theta^{(t+1)} = argmax_{\theta} Q(\thetaX,\theta^{(t)})</math> so that <math>\forall \theta \in \Theta, Q(\theta^{(t+1)}X,\theta^{(t)}) \ge Q(\thetaX,\theta^{(t)})</math>  
  The  +  
+  * '''EM algorithm  theory''': stated like this above doesn't necessarily allow oneself to understand it immediately, at least in my case. Hopefully, Matthew Beal presents it in a great and simple way in his PhD thesis (see references at the bottom of the page).  
+  
+  Here is the observeddata loglikelihood:  
+  
+  <math>l_{obs}(\theta) = \sum_{i=1}^N ln \left( f(x_i\theta) \right)</math>  
+  
+  First we introduce the hidden variables by integrating them out:  
+  
+  <math>l_{obs}(\theta) = \sum_{i=1}^N ln \left( \int p(x_i,z_i\theta) dz_i \right)</math>  
+  
+  Then, we use any probability distribution <math>q</math> on these hidden variables (in fact, we use a distinct distribution <math>q_{z_i}</math> for each observation):  
+  
+  <math>l_{obs}(\theta) = \sum_{i=1}^N ln \left( \int q_{z_i}(z_i) \frac{p(x_i,z_i\theta)}{q_{z_i}(z_i)} dz_i \right)</math>  
+  
+  And here is the great trick, as explained by Beal: "any probability distribution over the hidden variables gives rise to a lower bound on <math>l_{obs}</math>". This is due to to the [http://en.wikipedia.org/wiki/Jensen%27s_inequality Jensen inequality] (the logarithm is concave):  
+  
+  <math>l_{obs}(\theta) \ge \sum_{i=1}^N \int q_{z_i}(z_i) ln \left( \frac{p(x_i,z_i\theta)}{q_{z_i}(z_i)} \right) dz_i = \mathcal{F}(q_{z_1}(z_1), ..., q_{z_N}(z_N), \theta)</math>  
+  
+  At each iteration, the E step maximizes the lower bound (<math>\mathcal{F}</math>) with respect to the <math>q_{z_i}(z_i)</math>:  
+  * E step: <math>q^{(t+1)}_{z_i} \leftarrow argmax_{q_{z_i}} \mathcal{F}(q_z(z), \theta^{(t)}) \forall i</math>  
+  * M step: <math>\theta^{(t+1)} \leftarrow argmax_\theta \mathcal{F}(q^{(t+1)}_z(z), \theta)</math>  
+  
+  The Estep amounts to inferring the posterior distribution of the hidden variables <math>q^{(t+1)}_{z_i}</math> given the current parameter <math>\theta^{(t)}</math>:  
+  
+  <math>q^{(t+1)}_{z_i}(z_i) = p(z_i  x_i, \theta^{(t)})</math>  
+  
+  Indeed, the <math>q^{(t+1)}_{z_i}(z_i)</math> make the bound tight (the inequality becomes an equality):  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = \sum_{i=1}^N \int q^{(t+1)}_{z_i}(z_i) ln \left( \frac{p(x_i,z_i\theta^{(t)})}{q^{(t+1)}_{z_i}(z_i)} \right) dz_i</math>  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = \sum_{i=1}^N \int p(z_i  x_i, \theta^{(t)}) ln \left( \frac{p(x_i,z_i\theta^{(t)})}{p(z_i  x_i, \theta^{(t)})} \right) dz_i</math>  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = \sum_{i=1}^N \int p(z_i  x_i, \theta^{(t)}) ln \left( \frac{p(x_i\theta^{(t)}) p(z_ix_i,\theta^{(t)})}{p(z_i  x_i, \theta^{(t)})} \right) dz_i</math>  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = \sum_{i=1}^N \int p(z_i  x_i, \theta^{(t)}) ln \left( p(x_i\theta^{(t)}) \right) dz_i</math>  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = \sum_{i=1}^N ln \left( p(x_i\theta^{(t)}) \right)</math>  
+  
+  <math>\mathcal{F}(q^{(t+1)}_z(z), \theta^{(t)}) = l_{obs}(\theta^{(t)})</math>  
+  
+  Then, at the M step, we use these statistics to maximize the new lower bound <math>\mathcal{F}</math> with respect to <math>\theta</math>, and therefore find <math>\theta^{(t+1)}</math>.  
+  
+  
+  * '''EM algorithm  variational''': if the posterior distributions <math>p(z_ix_i,\theta)</math> are intractable, we can use a variational approach to constrain them to be of a particular, tractable form. In the E step, maximizing <math>\mathcal{F}</math> with respect to <math>q_{z_i}</math> is equivalent to minimizing the [http://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence KullbackLeibler divergence] between the variational distribution <math>q(z_i)</math> and the exact hidden variable posterior <math>p(z_ix_i,\theta)</math>:  
+  
+  <math>KL[q_{z_i}(z_i)  p(z_ix_i,\theta)] = \int q_{z_i}(z_i) ln \left( \frac{q_{z_i}(z_i)}{p(z_ix_i,\theta)} \right)</math>  
+  
+  As a result, the E step may not always lead to a tight bound.  
+  
+  
+  * '''Formulas of both steps''': in both steps we need to use <math>Q</math>, whether to evaluate it or maximize it.  
+  
+  <math>Q(\thetaX,\theta^{(t)}) = \mathbb{E}_{ZX,\theta^{(t)}} \left[ ln(P(X,Z\theta))X,\theta^{(t)} \right]</math>  
+  
+  <math>Q(\thetaX,\theta^{(t)}) = \mathbb{E}_{ZX,\theta^{(t)}} \left[ l_{aug}(\theta)X,\theta^{(t)} \right]</math>  
+  
+  <math>Q(\thetaX,\theta^{(t)}) = \sum_{i=1}^N \left( \sum_{k=1}^K \mathbb{E}_{ZX,\theta^{(t)}}[Z_{ik}x_i,\theta_k^{(t)}] ln(\phi(x_i\mu_k,\sigma_k)) + \sum_{k=1}^K \mathbb{E}_{ZX,\theta^{(t)}}[Z_{ik}x_i,\theta_k^{(t)}] ln(w_k) \right)</math>  
+  
+  
+  * '''Formulas of the E step''': as indicated above, the E step consists in evaluating <math>Q</math>, i.e. simply evaluating the conditional expectation over the latent variables of the augmenteddata loglikelihood given the observed data and the current estimates of the parameters.  
+  
+  <math>\mathbb{E}_{ZX,\theta^{(t)}}[Z_{ik}x_i,\theta_k^{(t)}] = P(Z_{ik}=1x_i,\theta_k^{(t)}) = \frac{w_k^{(t)} \phi(x_i\mu_k^{(t)},\sigma_k^{(t)})}{\sum_{l=1}^K w_l^{(t)} \phi(x_i\mu_l^{(t)},\sigma_l^{(t)})} = p(ki)</math>  
+  
+  
+  * '''Formulas of the M step''': in this step, we need to maximize <math>Q</math> (also written <math>\mathcal{F}</math> above), w.r.t. each <math>\theta_k</math>. A few important rules are required to write down the analytical formulas of the MLEs, but only from a highschool level (see [http://en.wikipedia.org/wiki/Differentiation_%28mathematics%29#Rules_for_finding_the_derivative here]).  
+  
+  
+  * '''M step  weights''': let's start by finding the maximumlikelihood estimates of the weights <math>w_k</math>. But remember the constraint <math>\sum_{k=1}^K w_k = 1</math>. To enforce it, we can use a [http://en.wikipedia.org/wiki/Lagrange_multiplier Lagrange multiplier], <math>\lambda</math>. This means that we now need to maximize the following equation where <math>\Lambda</math> is a Lagrange function (only the part of Q being a function of the weights is kept):  
+  
+  <math>\Lambda(w_k,\lambda) = \sum_{i=1}^N \left( \sum_{k=1}^K p(ki) ln(w_k) \right) + \lambda (1  \sum_{k=1}^K w_k)</math>  
+  
+  As usual, to find the maximum, we derive and equal to zero:  
+  
+  <math>\frac{\Lambda}{\partial w_k} = \sum_{i=1}^N \left( p(ki) \frac{1}{\hat{w}_k^{(t+1)}} \right)  \lambda = 0</math>  
+  
+  <math>\hat{w}_k^{(t+1)} = \frac{1}{\lambda} \sum_{i=1}^N p(ki)</math>  
+  
+  Now, to find the multiplier, we go back to the constraint:  
+  
+  <math>\sum_{k=1}^K \hat{w}_k^{(t+1)} = 1 \rightarrow \lambda = \sum_{i=1}^N \sum_{k=1}^K p(ki) = N</math>  
+  
+  Finally:  
+  
+  <math>\hat{w}_k^{(t+1)} = \frac{1}{N} \sum_{i=1}^N p(ki)</math>  
+  
+  
+  * '''M step  means''':  
+  
+  <math>\frac{\partial Q}{\partial \mu_k} = \sum_{i=1}^N p(ki) \frac{\partial ln(\phi(x_i\mu_k,\sigma_k))}{\partial \mu_k}</math>  
+  
+  <math>\frac{\partial Q}{\partial \mu_k} = \sum_{i=1}^N p(ki) \frac{1}{\phi(x_i\mu_k,\sigma_k)} \frac{\partial \phi(x_i\mu_k,\sigma_k)}{\partial \mu_k}</math>  
+  
+  <math>\frac{\partial Q}{\partial \mu_k} = 0 = \sum_{i=1}^N p(ki) (x_i  \hat{\mu}_k^{(t+1)})</math>  
+  
+  Finally:  
+  
+  <math>\hat{\mu}_k^{(t+1)} = \frac{\sum_{i=1}^N p(k/i) x_i}{\sum_{i=1}^N p(k/i)}</math>  
+  
+  
+  * '''M step  variances''': same kind of algebra  
+  
+  <math>\frac{\partial Q}{\partial \sigma_k} = \sum_{i=1}^N p(k/i) (\frac{1}{\sigma_k} + \frac{(x_i  \mu_k)^2}{\sigma_k^3})</math>  
+  
+  <math>\hat{\sigma}_k^{(t+1)} = \sqrt{\frac{\sum_{i=1}^N p(k/i) (x_i  \hat{\mu}_k^{(t+1)})^2}{\sum_{i=1}^N p(k/i)}}</math>  
+  
+  
+  * '''M step  weights (2)''': we can write them in terms of unconstrained variables <math>\gamma_k</math> ([http://en.wikipedia.org/wiki/Softmax_activation_function softmax function]):  
+  
+  <math>w_k = \frac{e^{\gamma_k}}{\sum_{k=1}^K e^{\gamma_k}}</math>  
+  
+  <math>\frac{\partial w_k}{\partial \gamma_j} =  
+  \begin{cases}  
+  w_k  w_k^2 & \mbox{if }j = k \\  
+  w_kw_j & \mbox{otherwise}  
+  \end{cases}</math>  
<math>\frac{\partial l(\theta)}{\partial w_k} = \sum_{i=1}^N (p(k/i)  w_k)</math>  <math>\frac{\partial l(\theta)}{\partial w_k} = \sum_{i=1}^N (p(k/i)  w_k)</math>  
  Finally  +  Finally: 
<math>\hat{w}_k = \frac{1}{N} \sum_{i=1}^N p(k/i)</math>  <math>\hat{w}_k = \frac{1}{N} \sum_{i=1}^N p(k/i)</math>  
  
  * '''R code to simulate data''':  +  * '''R code to simulate data''': if you read up to there, nothing is better than implementing the EM algorithm yourself! 
  #' Generate univariate observations from a mixture of Normals  +  <nowiki> 
  +  #' Generate univariate observations from a mixture of Normals  
  +  #'  
  +  #' @param K number of components  
  +  #' @param N number of observations  
  +  #' @param gap difference between all component means  
  +  GetUnivariateSimulatedData < function(K=2, N=100, gap=6){  
  +  mus < seq(0, gap*(K1), gap)  
  +  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))  
+  }  
+  </nowiki>  
* '''R code for the E step''':  * '''R code for the E step''':  
  #' Return probas of latent variables given data and parameters from previous iteration  +  <nowiki> 
  +  #' 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$mix.weights)  
+  }  
  +  #' Return the membership probabilities P(zi=k/xi,theta)  
  +  #'  
  +  #' @param data Nx1 vector of observations  
  +  #' @param mus Kx1 vector of means  
  +  #' @param sigmas Kx1 vector of std deviations  
  +  #' @param mix.weights Kx1 vector of mixture weights w_k=P(zi=k/theta)  
  +  #' @return NxK matrix of membership probas  
  +  GetMembershipProbas < function(data, mus, sigmas, mix.weights){  
  +  N < length(data)  
  +  K < length(mus)  
  +  tmp < matrix(unlist(lapply(1:N, function(i){  
  +  x < data[i]  
  +  norm.const < sum(unlist(Map(function(mu, sigma, mix.weight){  
  +  mix.weight * GetUnivariateNormalDensity(x, mu, sigma)}, mus, sigmas, mix.weights)))  
  +  unlist(Map(function(mu, sigma, mix.weight){  
  +  mix.weight * GetUnivariateNormalDensity(x, mu, sigma) / norm.const  
  +  }, mus[K], sigmas[K], mix.weights[K]))  
  +  })), ncol=K1, byrow=TRUE)  
  +  membership.probas < cbind(tmp, apply(tmp, 1, function(x){1  sum(x)}))  
  +  names(membership.probas) < NULL  
  +  return(membership.probas)  
  +  }  
  +  #' Univariate Normal density  
  +  GetUnivariateNormalDensity < function(x, mu, sigma){  
  +  return( 1/(sigma * sqrt(2*pi)) * exp(1/(2*sigma^2)*(xmu)^2) )  
  +  }  
+  </nowiki>  
* '''R code for the M step''':  * '''R code for the M step''':  
  #' Return ML estimates of parameters  +  <nowiki> 
  +  #' Return ML estimates of parameters  
  +  #'  
  +  #' @param data Nx1 vector of observations  
  +  #' @param params list which components are mus, sigmas and mix.weights  
  +  #' @param membership.probas NxK matrix with entry i,k being P(zi=k/xi,theta)  
  +  Mstep < function(data, params, membership.probas){  
  +  params.new < list()  
  +  sum.membership.probas < apply(membership.probas, 2, sum)  
  +  params.new$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]  
  +  })  
  +  }  
+  </nowiki>  
  +  * '''R code for the loglikelihood''':  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  
  +  <nowiki>  
  +  GetLogLikelihood < function(data, mus, sigmas, mix.weights){  
  +  loglik < sum(sapply(data, function(x){  
  +  log(sum(unlist(Map(function(mu, sigma, mix.weight){  
  +  mix.weight * GetUnivariateNormalDensity(x, mu, sigma)  
  +  }, mus, sigmas, mix.weights))))  
  +  }))  
  +  return(loglik)  
  +  }  
  +  </nowiki>  
  +  
  +  
  +  
* '''R code for the EM loop''':  * '''R code for the EM loop''':  
  ... <  +  <nowiki> 
+  EMalgo < function(data, params, threshold.convergence=10^(2), nb.iter=10,  
+  verbose=1){  
+  logliks < vector()  
+  i < 1  
+  if(verbose > 0) cat(paste("iter ", i, "\n", sep=""))  
+  membership.probas < Estep(data, params)  
+  params < Mstep(data, params, membership.probas)  
+  loglik < GetLogLikelihood(data, params$mus, params$sigmas,  
+  params$mix.weights)  
+  logliks < append(logliks, loglik)  
+  while(i < nb.iter){  
+  i < i + 1  
+  if(verbose > 0) cat(paste("iter ", i, "\n", sep=""))  
+  membership.probas < Estep(data, params)  
+  params < Mstep(data, params, membership.probas)  
+  loglik < GetLogLikelihood(data, params$mus, params$sigmas, params$mix.weights)  
+  if(loglik < logliks[length(logliks)]){  
+  msg < paste("the loglikelihood is decreasing:", loglik, "<", logliks[length(logliks)])  
+  stop(msg, call.=FALSE)  
+  }  
+  logliks < append(logliks, loglik)  
+  if(abs(logliks[i]  logliks[i1]) <= threshold.convergence)  
+  break  
+  }  
+  return(list(params=params, membership.probas=membership.probas, logliks=logliks, nb.iters=i))  
+  }  
+  </nowiki>  
* '''Example''': and now, let's try it!  * '''Example''': and now, let's try it!  
  ## simulate data  +  <nowiki> 
  +  ## simulate data  
  +  K < 3  
  +  N < 300  
  +  simul < GetUnivariateSimulatedData(K, N)  
+  data < simul$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$mix.weights[3] * ds[[3]][i]  
  +  })  
  +  lines(rx, f, col="red", lwd=2)  
  +  dev.off()  
+  </nowiki>  
It seems to work well, which was expected as the clusters are well separated from each other...  It seems to work well, which was expected as the clusters are well separated from each other...  
Line 247:  Line 407:  
The classification of each observation can be obtained via the following command:  The classification of each observation can be obtained via the following command:  
  ## get the classification of the observations  +  <nowiki> 
  +  ## get the classification of the observations  
  +  memberships < apply(res$membership.probas, 1, function(x){which(x > 0.5)})  
+  table(memberships)  
+  </nowiki>  
* '''References''':  * '''References''':  
  **  +  ** chapter 1 from the PhD thesis of Matthew Stephens (Oxford, 2000) freely available [http://www.stat.washington.edu/stephens/papers/tabstract.html online] 
  **  +  ** chapter 2 from the PhD thesis of Matthew Beal (UCL, 2003) freely available [http://www.cse.buffalo.edu/faculty/mbeal/thesis/ online] 
+  ** lecture "Mixture Models, Latent Variables and the EM Algorithm" from Cosma Shalizi freely available [http://www.stat.cmu.edu/~cshalizi/uADA/12/ online]  
** book "Introducing Monte Carlo Methods with R" from Robert and and Casella (2009)  ** book "Introducing Monte Carlo Methods with R" from Robert and and Casella (2009)  
Revision as of 18:33, 8 May 2013
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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.)
The constraints are: and
As usual, it's easier to deal with the loglikelihood:
Let's take the derivative with respect to one parameter, eg. θ_{l}:
This shows that maximizing the likelihood of a mixture model is like doing a weighted likelihood maximization. However, these weights depend on the parameters we want to estimate! That's why we now switch to the missingdata formulation of the mixture model.
The observeddata likelihood (also called sometimes "incomplete" or "marginal", even though these appellations are misnomers) is still written the same way:
But now we can also write the augmenteddata likelihood, assuming all observations are independent conditionally on their membership: . And here is the augmenteddata loglikelihood (useful in the M step of the EM algorithm, see below):
In terms of graphical model, the Gaussian mixture model described here can be represented like this.
Here is the observeddata loglikelihood:
First we introduce the hidden variables by integrating them out:
Then, we use any probability distribution q on these hidden variables (in fact, we use a distinct distribution for each observation):
And here is the great trick, as explained by Beal: "any probability distribution over the hidden variables gives rise to a lower bound on l_{obs}". This is due to to the Jensen inequality (the logarithm is concave):
At each iteration, the E step maximizes the lower bound () with respect to the :
The Estep amounts to inferring the posterior distribution of the hidden variables given the current parameter θ^{(t)}:
Indeed, the make the bound tight (the inequality becomes an equality):
Then, at the M step, we use these statistics to maximize the new lower bound with respect to θ, and therefore find θ^{(t + 1)}.
As a result, the E step may not always lead to a tight bound.
As usual, to find the maximum, we derive and equal to zero:
Now, to find the multiplier, we go back to the constraint:
Finally:
Finally:
Finally:
#' Generate univariate observations from a mixture of Normals #' #' @param K number of components #' @param N number of observations #' @param gap difference between all component means GetUnivariateSimulatedData < function(K=2, N=100, gap=6){ mus < seq(0, gap*(K1), gap) 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] }) }
GetLogLikelihood < function(data, mus, sigmas, mix.weights){ loglik < sum(sapply(data, function(x){ log(sum(unlist(Map(function(mu, sigma, mix.weight){ mix.weight * GetUnivariateNormalDensity(x, mu, sigma) }, mus, sigmas, mix.weights)))) })) return(loglik) }
EMalgo < function(data, params, threshold.convergence=10^(2), nb.iter=10, verbose=1){ logliks < vector() i < 1 if(verbose > 0) cat(paste("iter ", i, "\n", sep="")) membership.probas < Estep(data, params) params < Mstep(data, params, membership.probas) loglik < GetLogLikelihood(data, params$mus, params$sigmas, params$mix.weights) logliks < append(logliks, loglik) while(i < nb.iter){ i < i + 1 if(verbose > 0) cat(paste("iter ", i, "\n", sep="")) membership.probas < Estep(data, params) params < Mstep(data, params, membership.probas) loglik < GetLogLikelihood(data, params$mus, params$sigmas, params$mix.weights) if(loglik < logliks[length(logliks)]){ msg < paste("the loglikelihood is decreasing:", loglik, "<", logliks[length(logliks)]) stop(msg, call.=FALSE) } logliks < append(logliks, loglik) if(abs(logliks[i]  logliks[i1]) <= threshold.convergence) break } return(list(params=params, membership.probas=membership.probas, logliks=logliks, nb.iters=i)) }
## simulate data K < 3 N < 300 simul < GetUnivariateSimulatedData(K, N) data < simul$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$mix.weights[3] * ds[[3]][i] }) lines(rx, f, col="red", lwd=2) dev.off() It seems to work well, which was expected as the clusters are well separated from each other... The classification of each observation can be obtained via the following command: ## get the classification of the observations memberships < apply(res$membership.probas, 1, function(x){which(x > 0.5)}) table(memberships)
