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, 101 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Entries
new file mode 100644
index 00000000..1c5d76dd
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Entries
@@ -0,0 +1,6 @@
+/enter_evidence.m/1.1.1.1/Mon Jun  7 19:05:42 2004//
+/find_mpe.m/1.1.1.1/Wed Jun 19 21:56:32 2002//
+/global_joint_inf_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/marginal_family.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/marginal_nodes.m/1.1.1.1/Mon Jun  7 19:04:48 2004//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Repository
new file mode 100644
index 00000000..0c8fadf5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/static/@global_joint_inf_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/enter_evidence.m
new file mode 100644
index 00000000..105894ff
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/enter_evidence.m
@@ -0,0 +1,42 @@
+function [engine, loglik] = enter_evidence(engine, evidence, varargin)
+% ENTER_EVIDENCE Add the specified evidence to the network (global_joint)
+% [engine, loglik] = enter_evidence(engine, evidence, ...)
+%
+% evidence{i} = [] if if X(i) is hidden, and otherwise contains its observed value.
+%
+% Warning: Computing the log likelihood requires marginalizing all the nodes and can be slow.
+%
+% The list below gives optional arguments [default value in brackets].      
+%
+% exclude - list of nodes whose potential will not be included in the joint [ [] ]
+%
+% e.g., engine = enter_evidence(engine, ev, 'exclude', 3)
+
+exclude = [];
+maximize = 0;
+
+if nargin >= 3
+  args = varargin;
+  nargs = length(args);
+  for i=1:2:nargs
+    switch args{i},
+     case 'exclude', exclude = args{i+1};
+     case 'maximize', maximize = args{i+1};
+     otherwise,
+      error(['invalid argument name ' args{i}]);
+    end
+  end
+end
+  
+assert(~maximize)
+bnet = bnet_from_engine(engine);
+N = length(bnet.node_sizes);
+%[engine.jpot, loglik] = compute_joint_pot(bnet, mysetdiff(1:N, exclude), evidence, 1:N);
+[engine.jpot] = compute_joint_pot(bnet, mysetdiff(1:N, exclude), evidence, 1:N);
+% jpot should not be normalized, otherwise it gives wrong resutls for limids like asia_dt1
+if nargout == 2
+  [m] = marginal_nodes(engine, []);
+  [T, lik] = normalize(m.T);
+  loglik = log(lik);
+end     
+%[engine.jpot loglik] = normalize_pot(engine.jpot);
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/find_mpe.m b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/find_mpe.m
new file mode 100644
index 00000000..92915b6c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/find_mpe.m
@@ -0,0 +1,28 @@
+function [mpe, ll] = find_mpe(engine, evidence)
+% FIND_MPE_GLOBAL Compute the most probable explanation(s) from the global joint
+% [mpe, ll] = find_mpe(engine, evidence)
+%
+% mpe(k,i) is the most probable value of node i in the k'th global mode  (cell array)
+%
+% We assume all nodes are discrete
+
+%engine = global_joint_inf_engine(bnet);
+bnet = bnet_from_engine(engine);
+engine = enter_evidence(engine, evidence);
+S1 = struct(engine); % violate object privacy
+S2 = struct(S1.jpot); % joint potential
+prob = max(S2.T(:));
+modes = find(S2.T(:) == prob);
+
+ens = bnet.node_sizes;
+onodes = find(~isemptycell(evidence));
+ens(onodes) = 1;
+mpe = ind2subv(ens, modes);
+for k=1:length(modes)
+  for i=onodes(:)'
+    mpe(k,i) = evidence{i};
+  end
+end
+ll = log(prob);
+
+mpe = num2cell(mpe);
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/global_joint_inf_engine.m b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/global_joint_inf_engine.m
new file mode 100644
index 00000000..86bca532
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/global_joint_inf_engine.m
@@ -0,0 +1,8 @@
+function engine = global_joint_inf_engine(bnet)
+% GLOBAL_JOINT_INF_ENGINE Construct the global joint distribution as a potential
+% engine = global_joint_inf_engine(bnet)
+%
+% Warning: this has size exponential in the number of discrete hidden variables
+
+engine.jpot = [];
+engine = class(engine, 'global_joint_inf_engine', inf_engine(bnet));    
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_family.m
new file mode 100644
index 00000000..6931814c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_family.m
@@ -0,0 +1,7 @@
+function [m, pot] = marginal_family(engine, i)
+% MARGINAL_FAMILY Compute the marginal on i's family (global_inf_engine)
+% [m, pot] = marginal_family(engine, i)
+%
+
+bnet = bnet_from_engine(engine);
+[m, pot] = marginal_nodes(engine, family(bnet.dag, i));
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_nodes.m
new file mode 100644
index 00000000..223e6574
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@global_joint_inf_engine/marginal_nodes.m
@@ -0,0 +1,8 @@
+function [m, pot] = marginal_nodes(engine, query)
+% MARGINAL_NODES Compute the marginal on the specified set of nodes (global_joint)
+% [m, pot] = marginal_nodes(engine, query)
+
+pot = marginalize_pot(engine.jpot, query);
+m = pot_to_marginal(pot);
+%[m.T, lik] = normalize(m.T);
+%loglik = log(lik);