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

15 files changed, 111 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries
new file mode 100644
index 00000000..a5ebeece
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries
@@ -0,0 +1,7 @@
+/bnet_from_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/get_field.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/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//
+/set_fields.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/update_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries.Log
new file mode 100644
index 00000000..24f16336
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/Old////
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Repository
new file mode 100644
index 00000000..07b838d4
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/@inf_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Entries
new file mode 100644
index 00000000..ce1f8c1e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Entries
@@ -0,0 +1,3 @@
+/marginal_family_pot.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/observed_nodes.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Repository
new file mode 100644
index 00000000..de36d64e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/@inf_engine/Old
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Root b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/marginal_family_pot.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/marginal_family_pot.m
new file mode 100644
index 00000000..c1e63710
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/marginal_family_pot.m
@@ -0,0 +1,14 @@
+function pot = marginal_family_pot(engine, i)
+% MARGINAL_FAMILY_POT Compute the marginal on i's family and return as a potentila (inf_engine)
+% function pot = marginal_family_pot(engine,i)
+
+% This function is only called by solve_limid.
+% It requires that engine's marginal_family function return a potential.
+% This is true for jtree_inf_engine, but not for, say, jtree_ndx_inf_engine.
+% All limids must be solved using potentials,
+% but this is not true for bnets.
+
+%[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/@inf_engine/Old/observed_nodes.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/observed_nodes.m
new file mode 100644
index 00000000..97fccdb3
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/Old/observed_nodes.m
@@ -0,0 +1,5 @@
+function onodes = observed_nodes(engine)
+% OBSERVED_NODES  Return nodes that are guaranteed to be observed, indep of evidence (generic inf_engine)
+% onodes = observed_nodes(engine)
+
+onodes = [];
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/bnet_from_engine.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/bnet_from_engine.m
new file mode 100644
index 00000000..cf579fb0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/bnet_from_engine.m
@@ -0,0 +1,12 @@
+function bnet = bnet_from_engine(engine)
+% BNET_FROM_ENGINE Return the bnet structure stored inside the engine (inf_engine)
+% bnet = bnet_from_engine(engine)
+
+bnet = engine.bnet;
+
+% We cannot write 'engine.bnet' without writing a 'subsref' function,
+% since engine is an object with private parts.
+% The bnet field should be the only thing external users of the engine should need access to.
+% We do not pass bnet as a separate argument, since it could get out of synch with the one
+% encoded inside the engine.
+       
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/get_field.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/get_field.m
new file mode 100644
index 00000000..a1d16335
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/get_field.m
@@ -0,0 +1,15 @@
+function val = get_field(engine, name)
+% GET_FIELD Get the value of a named field from a generic engine
+% val = get_field(engine, name)
+%
+% The following fields can be accessed
+%
+% bnet
+%
+% e.g., bnet = get_field(engine, 'bnet')
+
+switch name
+ case 'bnet',      val = engine.bnet;
+ otherwise,
+  error(['invalid argument name ' name]);
+end                                  
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/inf_engine.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/inf_engine.m
new file mode 100644
index 00000000..f08e2438
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/inf_engine.m
@@ -0,0 +1,6 @@
+function engine = inf_engine(bnet)
+
+engine.bnet = bnet;
+engine = class(engine, 'inf_engine');
+
+
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/marginal_family.m
new file mode 100644
index 00000000..0107f1d3
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/marginal_family.m
@@ -0,0 +1,24 @@
+function m = marginal_family(engine, i, t)
+% MARGINAL_FAMILY Compute the marginal on i's family (inf_engine)
+% m = marginal_family(engine, i, t)
+%
+% t defaults to 1.
+
+if nargin < 3, t = 1; end
+
+bnet = bnet_from_engine(engine);
+if t==1
+  m = marginal_nodes(engine, family(bnet.dag, i));
+else
+  ss = length(bnet.intra);
+  fam = family(bnet.dag, i+ss);
+  if any(fam<=ss)
+    % i has a parent in the preceeding slice
+    % Hence the lowest numbered slice containing the family is t-1
+    m = marginal_nodes(engine, fam, t-1);
+  else
+    % The family all fits inside slice t
+    % Hence shift the indexes back to slice 1
+    m = marginal_nodes(engine, fam-ss, t);
+  end
+end     
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/set_fields.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/set_fields.m
new file mode 100644
index 00000000..e75cfa45
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/set_fields.m
@@ -0,0 +1,13 @@
+function engine = set_fields(engine, varargin)
+% SET_FIELDS Set the fields for a generic engine
+% engine = set_fields(engine, name/value pairs)
+%
+% e.g., engine = set_fields(engine, 'maximize', 1)
+
+args = varargin;
+nargs = length(args);
+for i=1:2:nargs
+  switch args{i},
+   case 'maximize', engine.maximize = args{i+1};
+  end
+end
diff --git a/sourcecodes/bnt-master/BNT/inference/@inf_engine/update_engine.m b/sourcecodes/bnt-master/BNT/inference/@inf_engine/update_engine.m
new file mode 100644
index 00000000..afafdeb9
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/@inf_engine/update_engine.m
@@ -0,0 +1,7 @@
+function engine = update_engine(engine, newCPDs)
+% UPDATE_ENGINE Update the engine to take into account the new parameters (inf_engine).
+% engine = update_engine(engine, newCPDs)
+%
+% This generic method is suitable for engines that do not process the parameters until 'enter_evidence'.
+
+engine.bnet.CPD = newCPDs;