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

6 files changed, 125 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Entries
new file mode 100644
index 00000000..680a9046
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Entries
@@ -0,0 +1,4 @@
+/normalize_pot.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/set_domain_pot.m/1.1.1.1/Wed Jul 30 13:38:08 2003//
+/simple_marginalize_pot.m/1.1.1.1/Wed May 29 15:59:58 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Repository
new file mode 100644
index 00000000..7feb051e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/potentials/@cgpot/Old
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Root b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/normalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/normalize_pot.m
new file mode 100644
index 00000000..1debd5bc
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/normalize_pot.m
@@ -0,0 +1,24 @@
+function [pot, loglik] = normalize_pot(pot)
+% NORMALIZE_POT Convert the CG potential Pr(X,E) into Pr(X|E) and return log Pr(E).
+% [pot, loglik] = normalize_pot(pot)
+
+% Marginalize down to [], so that the normalizing constant becomes Pr(E)
+temp = marginalize_pot(cg_can_to_mom(pot), []); 
+%loglik = temp.mom{1}.logp;
+[temp2, loglik] = normalize_pot(temp.mom{1});
+  
+% Adjust scale factor to reflect the fact that the pot now represents Pr(X | E) instead of Pr(X,E).
+
+scale = -loglik;
+if 1
+switch pot.subtype
+  case 'm'
+    for i=1:pot.dsize
+      pot.mom{i} = rescale_pot(pot.mom{i}, scale);
+    end
+  case 'c'
+    for i=1:pot.dsize
+      pot.can{i} = rescale_pot(pot.can{i}, scale);
+    end
+end        
+end
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/set_domain_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/set_domain_pot.m
new file mode 100644
index 00000000..f0df6ea7
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/set_domain_pot.m
@@ -0,0 +1,9 @@
+function pot = set_domain_pot(pot, domain)
+% SET_DOMAIN_POT Change the domain of a potential (cgpot)
+% pot = set_domain_pot(pot, domain)
+
+delta = domain(1) - pot.domain(1);
+assert(all(domain == pot.domain + delta));
+pot.domain = pot.domain + delta;
+pot.ddom = pot.ddom + delta;
+pot.cdom = pot.cdom + delta;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/simple_marginalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/simple_marginalize_pot.m
new file mode 100644
index 00000000..a2774636
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@cgpot/Old/simple_marginalize_pot.m
@@ -0,0 +1,86 @@
+function smallpot = marginalize_pot(bigpot, keep)
+% MARGINALIZE_POT Marginalize a cgpot onto a smaller domain.
+% smallpot = marginalize_pot(bigpot, keep)
+
+sumover = mysetdiff(bigpot.domain, keep);
+csumover = myintersect(sumover, bigpot.cdom);
+dsumover = myintersect(sumover, bigpot.ddom);
+dkeep = myintersect(keep, bigpot.ddom);
+ckeep = myintersect(keep, bigpot.cdom);
+%ns = sparse(1, max(bigpot.domain)); % must be full, so I is an integer
+ns = zeros(1, max(bigpot.domain));
+ns(bigpot.ddom) = bigpot.dsizes;
+ns(bigpot.cdom) = bigpot.csizes;
+
+% sum(ns(csumover))==0 is like isempty(csumover) but handles observed nodes.
+% Similarly, prod(ns(dsumover))==1 is like isempty(dsumover)
+
+% Marginalize the cts parts.
+% If we are in canonical form, we stay that way, since moment form might not exist.
+% Besides, we would like to minimize the number of conversions.
+if sum(ns(csumover)) > 0
+  if bigpot.subtype == 'm'
+    for i=1:bigpot.dsize
+      bigpot.mom{i} = marginalize_pot(bigpot.mom{i}, ckeep);
+    end
+  else
+    for i=1:bigpot.dsize
+      bigpot.can{i} = marginalize_pot(bigpot.can{i}, ckeep);
+    end
+  end
+end
+
+% If we are not marginalizing over any discrete nodes, we are done.
+if prod(ns(dsumover))==1
+  smallpot = cgpot(dkeep, ckeep, ns, bigpot.can, bigpot.mom, bigpot.subtype);
+  return;
+end
+
+% To marginalize the discrete parts, we must be in moment form.
+bigpot = cg_can_to_mom(bigpot);
+
+I = prod(ns(dkeep));
+J = prod(ns(dsumover));
+C = sum(ns(ckeep));
+
+% Reshape bigpot into the form mu1(:,j,i), where i is in dkeep, j is in dsumover
+T1 = zeros(I,J);
+mu1 = zeros(C,J,I);
+Sigma1 = zeros(C,C,J,I);
+sum_map = find_equiv_posns(dsumover, bigpot.ddom);
+keep_map = find_equiv_posns(dkeep, bigpot.ddom);
+iv = zeros(1, length(bigpot.ddom)); % index vector
+for i=1:I
+  keep_iv = ind2subv(ns(dkeep), i);
+  iv(keep_map) = keep_iv;
+  for j=1:J
+    sum_iv = ind2subv(ns(dsumover), j);
+    iv(sum_map) = sum_iv;
+    k = subv2ind(ns(bigpot.ddom), iv);
+    mom = struct(bigpot.mom{k}); % violate object privacy
+    T1(i,j) = exp(mom.logp);
+    if C > 0 % so mu1 and Sigma1 are non-empty
+      mu1(:,j,i) = mom.mu;
+      Sigma1(:,:,j,i) = mom.Sigma;
+    end
+  end
+end
+
+% Collapse the mixture of Gaussians
+coef = mk_stochastic(T1); % coef must be convex combination
+T2 = sum(T1,2);
+T2 = T2 + (T2==0)*eps;
+%if C > 0, disp('collapsing onto '); disp(leep); end
+mu = [];
+Sigma = [];
+mom = cell(1,I);
+for i=1:I
+  if C > 0
+    [mu, Sigma] = collapse_mog(mu1(:,:,i), Sigma1(:,:,:,i), coef(i,:));
+  end
+  logp = log(T2(i));
+  mom{i} = mpot(ckeep, ns(ckeep), logp, mu, Sigma);
+end
+
+smallpot = cgpot(dkeep, ckeep, ns, [], mom, 'm');
+