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

8 files changed, 107 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Entries b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Entries
new file mode 100644
index 00000000..d5b4bd91
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Entries
@@ -0,0 +1,6 @@
+/marginalize_pot.m/1.1.1.1/Sun May 19 22:11:08 2002//
+/normalize_pot.m/1.1.1.1/Sun May 19 22:11:08 2002//
+/reduce_pot.m/1.1.1.1/Tue Mar 11 17:37:02 2003//
+/rescale_pot.m/1.1.1.1/Sun May 19 22:11:08 2002//
+/scgcpot.m/1.1.1.1/Sun May 19 22:11:08 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Repository b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Repository
new file mode 100644
index 00000000..18dc4d80
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/potentials/@scgcpot
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Root b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/marginalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/marginalize_pot.m
new file mode 100644
index 00000000..c4ca9b68
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/marginalize_pot.m
@@ -0,0 +1,7 @@
+function smallpot = marginalize_pot(bigpot, keepdom, sumoverdom, nodesizes)
+% MARGINALIZE_POT Marginalize a mpot onto a smaller domain.
+% smallpot = marginalize_pot(bigpot, keep)
+
+keepsize = sum(nodesizes(keepdom));
+[A1, A2, B1, B2, C11, C12, C21, C22] = partition_matrix_vec_3(bigpot.A, bigpot.B, bigpot.C, keepdom, sumoverdom, nodesizes);
+smallpot = scgcpot(keepsize, bigpot.ctailsize, bigpot.p, A1, B1, C11);
\ No newline at end of file
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/normalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/normalize_pot.m
new file mode 100644
index 00000000..8900c66e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/normalize_pot.m
@@ -0,0 +1,6 @@
+function [pot, loglik] = normalize_pot(pot)
+% NORMALIZE_POT Convert the element of stable conditional gaussian potential Pr(X,E) into Pr(X|E) and return log Pr(E).
+% [pot, loglik] = normalize_pot(pot)
+
+loglik = log(pot.p);
+pot.p = 1;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/reduce_pot.m b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/reduce_pot.m
new file mode 100644
index 00000000..466a7a72
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/reduce_pot.m
@@ -0,0 +1,32 @@
+function [reduced_pot,successful] = reduce(pot,tailnodes)
+% Executes the reduce operation defined in 
+% Stable Local Computation with Conditional Gaussian Distributions
+% Steffen L. Lauritzen
+% Frank Jensen
+% September 1999
+% The potential pot is reduced if B contains any zero columns 
+% The test are restricted to the positions in tailnodes.
+% Any columns successfully deleted are entered in the array successful
+
+if nargin < 2
+    tailnodes = 1:pot.ctailsize;
+end
+
+successful = [];
+
+% Look for all columns beeing equal to zero
+for i = tailnodes
+    if ~any(pot.B(:,i))
+        successful = [successful i]; 
+    end
+end
+
+remain = mysetdiff(1:pot.ctailsize,successful);
+
+% Erase the zero-columns and decrease the tailsize
+pot.B = pot.B(:,remain);
+pot.ctailsize = pot.ctailsize - length(successful);
+
+% Return the reduced potential
+reduced_pot = pot;
+  
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/rescale_pot.m b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/rescale_pot.m
new file mode 100644
index 00000000..996a6351
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/rescale_pot.m
@@ -0,0 +1,5 @@
+function pot = rescale_pot(pot, s)
+% RESCALE_POT Add a constant to the mpot scale factor.
+% pot = rescale_pot(pot, s)
+
+pot.p = pot.p*s;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgcpot/scgcpot.m b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/scgcpot.m
new file mode 100644
index 00000000..6d53a16f
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@scgcpot/scgcpot.m
@@ -0,0 +1,49 @@
+function pot = scgcpot(cheadsize, ctailsize, p, A, B, C)
+% SCGCPOT Make a base object of stable conditional gaussian potential.
+% pot = scgcpot(cheadsize, ctailsize, p, A, B, C)
+%
+% cheadsize is the demension of head nodes.
+% ctailsize is the demension of tail nodes.
+% r = cheadsize, s = ctailsize
+% p is discrete probability.
+% A is table of r*1 vectors;
+% B is r*s matrices
+% C is r*r positive semidefinite symmetric matrices
+
+if nargin < 3
+    p = 1; 
+end
+if nargin < 4
+    A = zeros(cheadsize,1); 
+end
+if nargin < 5
+    B = zeros(cheadsize,ctailsize); 
+end
+if nargin < 6
+    C = zeros(cheadsize,cheadsize); 
+end
+
+if isempty(A)
+    A = zeros(cheadsize,1); 
+end
+if isempty(B)
+    B = zeros(cheadsize,ctailsize); 
+end
+if isempty(C)
+    C = zeros(cheadsize,cheadsize); 
+end
+  
+pot.cheadsize = cheadsize;
+pot.ctailsize = ctailsize;
+
+pot.p = p;
+pot.A = A;
+pot.B = B;
+pot.C = C;
+%if cheadsize == 0
+%   pot.A = [];
+%end
+%if ctailsize == 0
+%    pot.B = [];
+%end
+pot = class(pot, 'scgcpot');