diff toolboxes/FullBNT-1.0.7/netlabKPM/gmmem2.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/netlabKPM/gmmem2.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,186 @@
+function [mix, num_iter, ll] = gmmem_kpm(mix, x, varargin)
+%GMMEM_KPM Like GMMEM, but with additional optional arguments
+% function [mix, num_iter, ll] = gmmem_kpm(mix, x, varargin)
+%
+% Input:
+% mix - structure created by gmminit or gmmem_multi_restart
+% data - each row is an example
+%
+% Output:
+% mix - modified structure
+% num_iter - number of iterations needed to reach convergence
+% ll - final log likelihood
+%
+% [ ... ] = gmmem_kpm(..., 'param1',val1, 'param2',val2, ...) allows you to
+% specify optional parameter name/value pairs.
+% Parameters are below [default value in brackets]
+%
+% 'max_iter' - maximum number of EM iterations [10]
+% 'll_thresh' - change in log-likelihood threshold for convergence [1e-2]
+% 'verbose' - 1 means display output while running [0]
+% 'prior_cov' - this will be added to each estimated covariance
+%               to prevent singularities  [1e-3*eye(d)]
+% 'fn'        - this function, if non-empty,  will be called at every iteration
+%               (e.g., to display the parameters as they evolve) [ [] ]
+%               The fn is called as fn(mix, x, iter_num, fnargs).
+%               It is also called before the iteration starts as
+%               fn(mix, x, -1, fnargs), which can be used to initialize things.
+% 'fnargs'    - additional arguments to be passed to fn [ {} ]
+%
+% Modified by Kevin P Murphy, 29 Dec 2002
+
+
+% Check that inputs are consistent
+errstring = consist(mix, 'gmm', x);
+if ~isempty(errstring)
+  error(errstring);
+end
+
+[ndata, xdim] = size(x);
+
+[max_iter, ll_thresh, verbose, prior_cov, fn, fnargs] = ...
+    process_options(varargin, ...
+	'max_iter', 10, 'll_thresh', 1e-2, 'verbose', 1, ...
+	'prior_cov', 1e-3*eye(xdim), 'fn', [], 'fnargs', {});
+
+options = foptions;
+if verbose, options(1)=1; else options(1)=-1; end
+options(14) = max_iter;
+options(3) = ll_thresh;
+
+
+% Sort out the options
+if (options(14))
+  niters = options(14);
+else
+  niters = 100;
+end
+
+display = options(1);
+test = 0;
+if options(3) > 0.0
+  test = 1;	% Test log likelihood for termination
+end
+
+check_covars = 0;
+if options(5) >= 1
+  if display >= 0
+    disp('check_covars is on');
+  end
+  check_covars = 1;	% Ensure that covariances don't collapse
+  MIN_COVAR = eps;	% Minimum singular value of covariance matrix
+  init_covars = mix.covars;
+end
+
+mix0 = mix; % save init values for debugging
+
+if ~isempty(fn)
+  feval(fn, mix, x, -1, fnargs{:});
+end
+
+% Main loop of algorithm
+for n = 1:niters
+  
+  % Calculate posteriors based on old parameters
+  [post, act] = gmmpost(mix, x);
+  
+  % Calculate error value if needed
+  if (display |  test)
+    prob = act*(mix.priors)';
+    % Error value is negative log likelihood of data
+    e = - sum(log(prob + eps));
+    if display > 0
+      fprintf(1, 'Cycle %4d  Error %11.6f\n', n, e);
+    end
+    if test
+      if (n > 1 & abs(e - eold) < options(3))
+        options(8) = e;
+	ll = -e;
+	num_iter = n;
+        return; %%%%%%%%%%%%%%%% Exit here if converged
+      else
+        eold = e;
+      end
+    end
+  end
+
+  if ~isempty(fn)
+    feval(fn, mix, x, n, fnargs{:});
+  end
+
+  % Adjust the new estimates for the parameters
+  new_pr = sum(post, 1);
+  new_c = post' * x;
+  
+  % Now move new estimates to old parameter vectors
+  mix.priors = new_pr ./ ndata;
+  
+  mix.centres = new_c ./ (new_pr' * ones(1, mix.nin));
+  
+  switch mix.covar_type
+  case 'spherical'
+    n2 = dist2(x, mix.centres);
+    for j = 1:mix.ncentres
+      v(j) = (post(:,j)'*n2(:,j));
+    end
+    mix.covars = ((v./new_pr) + sum(diag(prior_cov)))./mix.nin;
+    if check_covars
+      % Ensure that no covariance is too small
+      for j = 1:mix.ncentres
+        if mix.covars(j) < MIN_COVAR
+          mix.covars(j) = init_covars(j);
+        end
+      end
+    end
+  case 'diag'
+    for j = 1:mix.ncentres
+      diffs = x - (ones(ndata, 1) * mix.centres(j,:));
+      wts = (post(:,j)*ones(1, mix.nin));
+      mix.covars(j,:) = sum((diffs.*diffs).*wts + prior_cov, 1)./new_pr(j);
+    end
+    if check_covars
+      % Ensure that no covariance is too small
+      for j = 1:mix.ncentres
+        if min(mix.covars(j,:)) < MIN_COVAR
+          mix.covars(j,:) = init_covars(j,:);
+        end
+      end
+    end
+  case 'full'
+    for j = 1:mix.ncentres
+      diffs = x - (ones(ndata, 1) * mix.centres(j,:));
+      diffs = diffs.*(sqrt(post(:,j))*ones(1, mix.nin));
+      mix.covars(:,:,j) = (diffs'*diffs + prior_cov)/new_pr(j);
+    end
+    if check_covars
+      % Ensure that no covariance is too small
+      for j = 1:mix.ncentres
+        if min(svd(mix.covars(:,:,j))) < MIN_COVAR
+          mix.covars(:,:,j) = init_covars(:,:,j);
+        end
+      end
+    end
+  case 'ppca'
+    for j = 1:mix.ncentres
+      diffs = x - (ones(ndata, 1) * mix.centres(j,:));
+      diffs = diffs.*(sqrt(post(:,j))*ones(1, mix.nin));
+      [mix.covars(j), mix.U(:,:,j), mix.lambda(j,:)] = ...
+        ppca((diffs'*diffs)/new_pr(j), mix.ppca_dim);
+    end
+    if check_covars
+      if mix.covars(j) < MIN_COVAR
+        mix.covars(j) = init_covars(j);
+      end
+    end
+    otherwise
+      error(['Unknown covariance type ', mix.covar_type]);               
+  end
+end
+
+ll = sum(log(gmmprob(mix, x)));
+num_iter = n;
+
+%if (display >= 0)
+%  disp('Warning: Maximum number of iterations has been exceeded');
+%end
+