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

13 files changed, 175 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Entries
new file mode 100644
index 00000000..2809c39f
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Entries
@@ -0,0 +1,6 @@
+/enter_evidence.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/jtree_unrolled_dbn_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/Wed May 29 15:59:56 2002//
+/update_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D/Old////
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Repository
new file mode 100644
index 00000000..e9fd6fe5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Entries
new file mode 100644
index 00000000..eafb1997
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Entries
@@ -0,0 +1,3 @@
+/marginal_family.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/marginal_nodes.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Repository
new file mode 100644
index 00000000..2ad645e2
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Root b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_family.m
new file mode 100644
index 00000000..efb38b26
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_family.m
@@ -0,0 +1,10 @@
+function marginal = marginal_family(engine, i, t)
+% MARGINAL_FAMILY Compute the marginal on the specified family (jtree_unrolled_dbn)
+% marginal = marginal_family(engine, i, t)
+
+if nargin < 3, t = 1; end
+
+bnet = bnet_from_engine(engine);
+ss = length(bnet.intra);
+marginal = marginal_family(engine.sub_engine, i + (t-1)*ss);
+ 
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_nodes.m
new file mode 100644
index 00000000..b0cfb04e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/Old/marginal_nodes.m
@@ -0,0 +1,18 @@
+function marginal = marginal_nodes(engine, nodes, t)
+% MARGINAL_NODES Compute the marginal on the specified query nodes (jtree_unrolled_dbn)
+% marginal = marginal_nodes(engine, nodes, t)
+%
+% 't' specifies the time slice of the earliest node in 'nodes'.
+% 'nodes' must occur in some clique.
+%
+% Example:
+% Consider a DBN with 2 nodes per slice.
+% Then t=2, nodes=[1 3] refers to node 1 in slice 2 and node 1 in slice 3,
+% i.e., nodes 3 and 5 in the unrolled network,
+
+if nargin < 3, t = 1; end
+
+bnet = bnet_from_engine(engine);
+ss = length(bnet.intra);
+query = nodes + (t-1)*ss;
+marginal = marginal_nodes(engine.sub_engine, query);    
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/enter_evidence.m
new file mode 100644
index 00000000..48b230c9
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/enter_evidence.m
@@ -0,0 +1,43 @@
+function [engine, loglik] = enter_evidence(engine, evidence, varargin)
+% ENTER_EVIDENCE Add the specified evidence to the network (jtree_unrolled_dbn)
+% [engine, loglik] = enter_evidence(engine, evidence, ...)
+%
+% evidence{i,t} = [] if if X(i,t) is hidden, and otherwise contains its observed value (scalar or column vector)
+% 
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default value in brackets]
+%
+% maximize - if 1, does max-product instead of sum-product [0]
+% filter   - if 1, does filtering (not supported), else smoothing [0]
+%
+% e.g., engine = enter_evidence(engine, ev, 'maximize', 1)
+
+maximize = 0;
+filter = 0;
+
+% parse optional params
+args = varargin;
+nargs = length(args);
+if nargs > 0
+  for i=1:2:nargs
+    switch args{i},
+     case 'maximize', maximize = args{i+1}; 
+     case 'filter',  filter = args{i+1}; 
+     otherwise,  
+      error(['invalid argument name ' args{i}]);       
+    end
+  end
+end
+
+if filter
+  error('jtree_unrolled_dbn does not support filtering')
+end
+
+if size(evidence,2) ~= engine.nslices
+  error(['engine was created assuming there are ' num2str(engine.nslices) ...
+	 ' slices, but evidence has ' num2str(size(evidence,2))])
+end
+
+[engine.unrolled_engine, loglik] = enter_evidence(engine.unrolled_engine, evidence, 'maximize', maximize);
+
+
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/jtree_unrolled_dbn_inf_engine.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/jtree_unrolled_dbn_inf_engine.m
new file mode 100644
index 00000000..156c6ee2
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/jtree_unrolled_dbn_inf_engine.m
@@ -0,0 +1,57 @@
+function engine = jtree_unrolled_dbn_inf_engine(bnet, T, varargin)
+% JTREE_UNROLLED_DBN_INF_ENGINE Unroll the DBN for T time-slices and apply jtree to the resulting static net
+% engine = jtree_unrolled_dbn_inf_engine(bnet, T, ...)
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default value in brackets]
+%
+% useC      - 1 means use jtree_C_inf_engine instead of jtree_inf_engine [0]
+% constrained - 1 means we constrain ourselves to eliminate slice t before t+1 [1]
+%
+% e.g., engine = jtree_unrolled_inf_engine(bnet, 'useC', 1);
+
+% set default params
+N = length(bnet.intra);
+useC = 0;
+constrained = 1;
+
+if nargin >= 3
+  args = varargin;
+  nargs = length(args);
+  if isstr(args{1})
+    for i=1:2:nargs
+      switch args{i},
+       case 'useC',   useC = args{i+1};
+       case 'constrained',  constrained = args{i+1};
+       otherwise,  
+	error(['invalid argument name ' args{i}]);       
+      end
+    end
+  else
+    error(['invalid argument name ' args{1}]);       
+  end
+end
+
+bnet2 = dbn_to_bnet(bnet, T);
+ss = length(bnet.intra);
+engine.ss = ss;
+
+% If constrained_order = 1 we constrain ourselves to eliminate slice t before t+1.
+% This prevents cliques containing nodes from far-apart time-slices.
+if constrained
+  stages = num2cell(unroll_set(1:ss, ss, T), 1);
+else
+  stages = { 1:length(bnet2.dag) };
+end
+if useC
+  jengine = jtree_C_inf_engine(bnet2, 'stages', stages);
+else
+  jengine = jtree_inf_engine(bnet2, 'stages', stages);
+end
+
+engine.unrolled_engine = jengine;
+% we don't inherit from jtree_inf_engine, because that would only store bnet2,
+% and we would lose access to the DBN-specific fields like intra/inter
+
+engine.nslices = T;
+engine = class(engine, 'jtree_unrolled_dbn_inf_engine', inf_engine(bnet));
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_family.m
new file mode 100644
index 00000000..a40f2974
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_family.m
@@ -0,0 +1,11 @@
+function marginal = marginal_family(engine, i, t, add_ev)
+% MARGINAL_FAMILY Compute the marginal on the specified family (jtree_unrolled_dbn)
+% marginal = marginal_family(engine, i, t)
+
+if nargin < 3, t = 1; end
+if nargin < 4, add_ev = 0; end
+assert(~add_ev);
+
+%marginal = marginal_family(engine.unrolled_engine, i + (t-1)*engine.ss, add_ev);
+marginal = marginal_family(engine.unrolled_engine, i + (t-1)*engine.ss);
+              
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_nodes.m
new file mode 100644
index 00000000..0fb095e5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/marginal_nodes.m
@@ -0,0 +1,16 @@
+function marginal = marginal_nodes(engine, nodes, t, add_ev)
+% MARGINAL_NODES Compute the marginal on the specified query nodes (loopy_unrolled_dbn)
+% marginal = marginal_nodes(engine, nodes, t)
+%
+% 't' specifies the time slice of the earliest node in 'nodes'.
+% 'nodes' must occur in some clique.
+%
+% Example:
+% Consider a DBN with 2 nodes per slice.
+% Then t=2, nodes=[1 3] refers to node 1 in slice 2 and node 1 in slice 3,
+% i.e., nodes 3 and 5 in the unrolled network,
+
+if nargin < 3, t = 1; end
+if nargin < 4, add_ev = 0; end
+
+marginal = marginal_nodes(engine.unrolled_engine, nodes + (t-1)*engine.ss, add_ev);
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/update_engine.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_inf_engine/update_engine.m
new file mode 100644
index 00000000..5c42d4f6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@jtree_unrolled_dbn_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 (jtree_unrolled_dbn)
+% engine = update_engine(engine, newCPDs)
+
+engine.inf_engine = update_engine(engine.inf_engine, newCPDs);
+engine.unrolled_engine = update_engine(engine.unrolled_engine, newCPDs);
+