BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 52 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/KPMstats/clg_Mstep_simple.m b/sourcecodes/bnt-master/KPMstats/clg_Mstep_simple.m
new file mode 100644
index 00000000..5b66bb0e
--- /dev/null
+++ b/sourcecodes/bnt-master/KPMstats/clg_Mstep_simple.m
@@ -0,0 +1,52 @@
+function [mu, B] = clg_Mstep_simple(w, Y, YY, YTY, X, XX, XY)
+% CLG_MSTEP_SIMPLE Same as CLG_MSTEP, but doesn;t estimate Sigma,  so is slightly faster
+% function [mu, B] = clg_Mstep_simple(w, Y, YY, YTY, X, XX, XY)
+%
+% See clg_Mstep for details.
+% Unlike clg_Mstep, there are no optional arguments, which are slow to process
+% if this function is inside a tight loop.
+
+[Ysz Q] = size(Y);
+
+if isempty(X) % no regression
+  %B = [];
+  B2 = zeros(Ysz, 1, Q);
+  for i=1:Q
+    B(:,:,i) = B2(:,1:0,i); % make an empty array of size Ysz x 0 x Q
+  end
+  [mu, Sigma] = mixgauss_Mstep(w, Y, YY, YTY);
+  return;
+end
+
+N = sum(w);
+%YY = YY + cov_prior; % regularize the scatter matrix
+
+% Set any zero weights to one before dividing
+% This is valid because w(i)=0 => Y(:,i)=0, etc
+w = w + (w==0);
+
+Xsz = size(X,1);
+% Append 1 to X to get Z
+ZZ = zeros(Xsz+1, Xsz+1, Q);
+ZY = zeros(Xsz+1, Ysz, Q);
+for i=1:Q
+  ZZ(:,:,i) = [XX(:,:,i)  X(:,i);
+	       X(:,i)'    w(i)];
+  ZY(:,:,i) = [XY(:,:,i);
+	       Y(:,i)'];
+end
+
+mu = zeros(Ysz, Q);
+B = zeros(Ysz, Xsz, Q);
+for i=1:Q
+  % eqn 9
+  if rcond(ZZ(:,:,i)) < 1e-10
+    sprintf('clg_Mstep warning: ZZ(:,:,%d) is ill-conditioned', i);
+    %probably because there are too few cases for a high-dimensional input
+    ZZ(:,:,i) = ZZ(:,:,i) + 1e-5*eye(Xsz+1);
+  end
+  %A = ZY(:,:,i)' * inv(ZZ(:,:,i));
+  A = (ZZ(:,:,i) \ ZY(:,:,i))';
+  B(:,:,i) = A(:, 1:Xsz);
+  mu(:,i) = A(:, Xsz+1);
+end