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

7 files changed, 150 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Entries
new file mode 100644
index 00000000..15bb91c3
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Entries
@@ -0,0 +1,5 @@
+/convert_to_pot.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/convert_to_table.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/prob_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/prob_node.m/1.1.1.1/Wed May 29 15:59:52 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Repository
new file mode 100644
index 00000000..df41b4fd
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@discrete_CPD/Old
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_pot.m b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_pot.m
new file mode 100644
index 00000000..3f178e1c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_pot.m
@@ -0,0 +1,44 @@
+function pot = convert_to_pot(CPD, pot_type, domain, evidence)
+% CONVERT_TO_POT Convert a tabular CPD to one or more potentials
+% pots = convert_to_pot(CPD, pot_type, domain, evidence)
+%
+% pots{i} = CPD evaluated using evidence(domain(:,i))
+% If 'domains' is a single row vector, pots will be an object, not a cell array.
+
+ncases = size(domain,2);
+assert(ncases==1); % not yet vectorized
+
+sz = dom_sizes(CPD);
+ns = zeros(1, max(domain));
+ns(domain) = sz;
+
+local_ev = evidence(domain);
+obs_bitv = ~isemptycell(local_ev);
+odom = domain(obs_bitv);
+T = convert_to_table(CPD, domain, local_ev, obs_bitv);
+
+switch pot_type
+ case 'u',
+  pot = upot(domain, sz, T, 0*myones(sz));  
+ case 'd',
+  ns(odom) = 1;
+  pot = dpot(domain, ns(domain), T);          
+ case {'c','g'},
+  % Since we want the output to be a Gaussian, the whole family must be observed.
+  % In other words, the potential is really just a constant.
+  p = T;
+  %p = prob_node(CPD, evidence(domain(end)), evidence(domain(1:end-1)));
+  ns(domain) = 0;
+  pot = cpot(domain, ns(domain), log(p));       
+ case 'cg',
+  T = T(:);
+  ns(odom) = 1;
+  can = cell(1, length(T));
+  for i=1:length(T)
+    can{i} = cpot([], [], log(T(i)));
+  end
+  pot = cgpot(domain, [], ns, can);   
+ otherwise,
+  error(['unrecognized pot type ' pot_type])
+end
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_table.m b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_table.m
new file mode 100644
index 00000000..65121122
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/convert_to_table.m
@@ -0,0 +1,23 @@
+function T = convert_to_table(CPD, domain, local_ev, obs_bitv)
+% CONVERT_TO_TABLE Convert a discrete CPD to a table
+% function T = convert_to_table(CPD, domain, local_ev, obs_bitv)
+%
+% We convert the CPD to a CPT, and then lookup the evidence on the discrete parents.
+% The resulting table can easily be converted to a potential.
+
+
+CPT = CPD_to_CPT(CPD);
+obs_child_only = ~any(obs_bitv(1:end-1)) & obs_bitv(end);
+
+if obs_child_only
+  sz = size(CPT);
+  CPT = reshape(CPT, prod(sz(1:end-1)), sz(end));
+  o = local_ev{end};
+  T = CPT(:, o);
+else
+  odom = domain(obs_bitv);  
+  vals = cat(1, local_ev{find(obs_bitv)}); % undo cell array
+  map = find_equiv_posns(odom, domain);
+  index = mk_multi_index(length(domain), map, vals);
+  T = CPT(index{:});
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_CPD.m
new file mode 100644
index 00000000..c0a79bda
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_CPD.m
@@ -0,0 +1,25 @@
+function p = prob_CPD(CPD, domain, ns, cnodes, evidence)
+% PROB_CPD Compute prob of a node given evidence on the parents (discrete)
+% p = prob_CPD(CPD, domain, ns, cnodes, evidence)
+%
+% domain is the domain of CPD.
+% node_sizes(i) is the size of node i.
+% cnodes = all the cts nodes
+% evidence{i} is the evidence on the i'th node.
+
+ps = domain(1:end-1);
+self = domain(end);
+CPT = CPD_to_CPT(CPD);
+
+if isempty(ps)
+  T = CPT;
+else
+  assert(~any(isemptycell(evidence(ps))));
+  pvals = cat(1, evidence{ps});
+  i = subv2ind(ns(ps), pvals(:)');
+  T = reshape(CPT, [prod(ns(ps)) ns(self)]);
+  T = T(i,:);
+end
+p = T(evidence{self});
+
+ 
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_node.m b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_node.m
new file mode 100644
index 00000000..1a39fc79
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@discrete_CPD/Old/prob_node.m
@@ -0,0 +1,51 @@
+function [P, p] = prob_node(CPD, self_ev, pev)
+% PROB_NODE Compute prod_m P(x(i,m)| x(pi_i,m), theta_i) for node i (discrete)
+% [P, p] = prob_node(CPD, self_ev, pev)
+%
+% self_ev(m) is the evidence on this node in case m.
+% pev(i,m) is the evidence on the i'th parent in case m (if there are any parents).
+% (These may also be cell arrays.)
+%
+% p(m) = P(x(i,m)| x(pi_i,m), theta_i) 
+% P = prod p(m)
+
+if iscell(self_ev), usecell = 1; else usecell = 0; end
+
+ncases = length(self_ev);
+sz = dom_sizes(CPD);
+
+nparents = length(sz)-1;
+if nparents == 0
+  assert(isempty(pev));
+else
+  assert(isequal(size(pev), [nparents ncases]));
+end
+
+n = length(sz);
+dom = 1:n;
+p = zeros(1, ncases);
+if nparents == 0
+  for m=1:ncases
+    if usecell
+      evidence = {self_ev{m}};
+    else
+      evidence = num2cell(self_ev(m));
+    end
+    T = convert_to_table(CPD, dom, evidence);
+    p(m) = T;
+  end
+else
+  for m=1:ncases
+    if usecell
+      evidence = cell(1,n);
+      evidence(1:n-1) = pev(:,m);
+      evidence(n) = self_ev(m);
+    else
+      evidence = num2cell([pev(:,m)', self_ev(m)]);
+    end
+    T = convert_to_table(CPD, dom, evidence);
+    p(m) = T;
+  end
+end
+P = prod(p);
+