diff toolboxes/FullBNT-1.0.7/HMM/mhmm_em.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/FullBNT-1.0.7/HMM/mhmm_em.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,173 @@
+function [LL, prior, transmat, mu, Sigma, mixmat] = ...
+     mhmm_em(data, prior, transmat, mu, Sigma, mixmat, varargin);
+% LEARN_MHMM Compute the ML parameters of an HMM with (mixtures of) Gaussians output using EM.
+% [ll_trace, prior, transmat, mu, sigma, mixmat] = learn_mhmm(data, ...
+%   prior0, transmat0, mu0, sigma0, mixmat0, ...) 
+%
+% Notation: Q(t) = hidden state, Y(t) = observation, M(t) = mixture variable
+%
+% INPUTS:
+% data{ex}(:,t) or data(:,t,ex) if all sequences have the same length
+% prior(i) = Pr(Q(1) = i), 
+% transmat(i,j) = Pr(Q(t+1)=j | Q(t)=i)
+% mu(:,j,k) = E[Y(t) | Q(t)=j, M(t)=k ]
+% Sigma(:,:,j,k) = Cov[Y(t) | Q(t)=j, M(t)=k]
+% mixmat(j,k) = Pr(M(t)=k | Q(t)=j) : set to [] or ones(Q,1) if only one mixture component
+%
+% Optional parameters may be passed as 'param_name', param_value pairs.
+% Parameter names are shown below; default values in [] - if none, argument is mandatory.
+%
+% 'max_iter' - max number of EM iterations [10]
+% 'thresh' - convergence threshold [1e-4]
+% 'verbose' - if 1, print out loglik at every iteration [1]
+% 'cov_type' - 'full', 'diag' or 'spherical' ['full']
+%
+% To clamp some of the parameters, so learning does not change them:
+% 'adj_prior' - if 0, do not change prior [1]
+% 'adj_trans' - if 0, do not change transmat [1]
+% 'adj_mix' - if 0, do not change mixmat [1]
+% 'adj_mu' - if 0, do not change mu [1]
+% 'adj_Sigma' - if 0, do not change Sigma [1]
+%
+% If the number of mixture components differs depending on Q, just set  the trailing
+% entries of mixmat to 0, e.g., 2 components if Q=1, 3 components if Q=2,
+% then set mixmat(1,3)=0. In this case, B2(1,3,:)=1.0.
+
+if ~isstr(varargin{1}) % catch old syntax
+  error('optional arguments should be passed as string/value pairs')
+end
+
+[max_iter, thresh, verbose, cov_type,  adj_prior, adj_trans, adj_mix, adj_mu, adj_Sigma] = ...
+    process_options(varargin, 'max_iter', 10, 'thresh', 1e-4, 'verbose', 1, ...
+		    'cov_type', 'full', 'adj_prior', 1, 'adj_trans', 1, 'adj_mix', 1, ...
+		    'adj_mu', 1, 'adj_Sigma', 1);
+  
+previous_loglik = -inf;
+loglik = 0;
+converged = 0;
+num_iter = 1;
+LL = [];
+
+if ~iscell(data)
+  data = num2cell(data, [1 2]); % each elt of the 3rd dim gets its own cell
+end
+numex = length(data);
+
+
+O = size(data{1},1);
+Q = length(prior);
+if isempty(mixmat)
+  mixmat = ones(Q,1);
+end
+M = size(mixmat,2);
+if M == 1
+  adj_mix = 0;
+end
+
+while (num_iter <= max_iter) & ~converged
+  % E step
+  [loglik, exp_num_trans, exp_num_visits1, postmix, m, ip, op] = ...
+      ess_mhmm(prior, transmat, mixmat, mu, Sigma, data);
+  
+  
+  % M step
+  if adj_prior
+    prior = normalise(exp_num_visits1);
+  end
+  if adj_trans 
+    transmat = mk_stochastic(exp_num_trans);
+  end
+  if adj_mix
+    mixmat = mk_stochastic(postmix);
+  end
+  if adj_mu | adj_Sigma
+    [mu2, Sigma2] = mixgauss_Mstep(postmix, m, op, ip, 'cov_type', cov_type);
+    if adj_mu
+      mu = reshape(mu2, [O Q M]);
+    end
+    if adj_Sigma
+      Sigma = reshape(Sigma2, [O O Q M]);
+    end
+  end
+  
+  if verbose, fprintf(1, 'iteration %d, loglik = %f\n', num_iter, loglik); end
+  num_iter =  num_iter + 1;
+  converged = em_converged(loglik, previous_loglik, thresh);
+  previous_loglik = loglik;
+  LL = [LL loglik];
+end
+
+
+%%%%%%%%%
+
+function [loglik, exp_num_trans, exp_num_visits1, postmix, m, ip, op] = ...
+    ess_mhmm(prior, transmat, mixmat, mu, Sigma, data)
+% ESS_MHMM Compute the Expected Sufficient Statistics for a MOG Hidden Markov Model.
+%
+% Outputs:
+% exp_num_trans(i,j)   = sum_l sum_{t=2}^T Pr(Q(t-1) = i, Q(t) = j| Obs(l))
+% exp_num_visits1(i)   = sum_l Pr(Q(1)=i | Obs(l))
+%
+% Let w(i,k,t,l) = P(Q(t)=i, M(t)=k | Obs(l))
+% where Obs(l) = Obs(:,:,l) = O_1 .. O_T for sequence l
+% Then 
+% postmix(i,k) = sum_l sum_t w(i,k,t,l) (posterior mixing weights/ responsibilities)
+% m(:,i,k)   = sum_l sum_t w(i,k,t,l) * Obs(:,t,l)
+% ip(i,k) = sum_l sum_t w(i,k,t,l) * Obs(:,t,l)' * Obs(:,t,l)
+% op(:,:,i,k) = sum_l sum_t w(i,k,t,l) * Obs(:,t,l) * Obs(:,t,l)'
+
+
+verbose = 0;
+
+%[O T numex] = size(data);
+numex = length(data);
+O = size(data{1},1);
+Q = length(prior);
+M = size(mixmat,2);
+exp_num_trans = zeros(Q,Q);
+exp_num_visits1 = zeros(Q,1);
+postmix = zeros(Q,M);
+m = zeros(O,Q,M);
+op = zeros(O,O,Q,M);
+ip = zeros(Q,M);
+
+mix = (M>1);
+
+loglik = 0;
+if verbose, fprintf(1, 'forwards-backwards example # '); end
+for ex=1:numex
+  if verbose, fprintf(1, '%d ', ex); end
+  %obs = data(:,:,ex);
+  obs = data{ex};
+  T = size(obs,2);
+  if mix
+    [B, B2] = mixgauss_prob(obs, mu, Sigma, mixmat);
+    [alpha, beta, gamma,  current_loglik, xi, gamma2] = ...
+	fwdback(prior, transmat, B, 'obslik2', B2, 'mixmat', mixmat);
+  else
+    B = mixgauss_prob(obs, mu, Sigma);
+    [alpha, beta, gamma,  current_loglik, xi] = fwdback(prior, transmat, B);
+  end    
+  loglik = loglik +  current_loglik; 
+  if verbose, fprintf(1, 'll at ex %d = %f\n', ex, loglik); end
+
+  exp_num_trans = exp_num_trans + sum(xi,3);
+  exp_num_visits1 = exp_num_visits1 + gamma(:,1);
+  
+  if mix
+    postmix = postmix + sum(gamma2,3);
+  else
+    postmix = postmix + sum(gamma,2); 
+    gamma2 = reshape(gamma, [Q 1 T]); % gamma2(i,m,t) = gamma(i,t)
+  end
+  for i=1:Q
+    for k=1:M
+      w = reshape(gamma2(i,k,:), [1 T]); % w(t) = w(i,k,t,l)
+      wobs = obs .* repmat(w, [O 1]); % wobs(:,t) = w(t) * obs(:,t)
+      m(:,i,k) = m(:,i,k) + sum(wobs, 2); % m(:) = sum_t w(t) obs(:,t)
+      op(:,:,i,k) = op(:,:,i,k) + wobs * obs'; % op(:,:) = sum_t w(t) * obs(:,t) * obs(:,t)'
+      ip(i,k) = ip(i,k) + sum(sum(wobs .* obs, 2)); % ip = sum_t w(t) * obs(:,t)' * obs(:,t)
+    end
+  end
+end
+if verbose, fprintf(1, '\n'); end