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, 121 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Entries
new file mode 100644
index 00000000..d2a809f0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Entries
@@ -0,0 +1,6 @@
+/enter_evidence.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//
+/pearl_unrolled_dbn_inf_engine.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/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Repository
new file mode 100644
index 00000000..5c0fed50
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_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/@pearl_unrolled_dbn_inf_engine/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/enter_evidence.m
new file mode 100644
index 00000000..a9731ffd
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/enter_evidence.m
@@ -0,0 +1,41 @@
+function [engine, loglik, niter] = enter_evidence(engine, evidence, varargin)
+% ENTER_EVIDENCE Add the specified evidence to the network (loopy_unrolled_dbn)
+% [engine, loglik, niter] = 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 (not yet supported), else sum-product [0]
+% filename - as in loopy_pearl
+%
+% e.g., engine = enter_evidence(engine, ev, 'maximize', 1)
+
+maximize = 0;
+filename = engine.filename;
+
+if nargin >= 2
+  args = varargin;
+  nargs = length(args);
+  for i=1:2:nargs
+    switch args{i},
+     case 'maximize', maximize = args{i+1};
+     case 'filename', filename = args{i+1};
+    end
+  end
+end
+
+
+[ss T] = size(evidence);
+if T ~= engine.T
+  bnetT = dbn_to_bnet(bnet_from_engine(engine), T);
+  engine.unrolled_engine = pearl_inf_engine(bnetT, 'protocol', engine.protocol, ...
+					    'max_iter', engine.max_iter_per_slice * T, ...
+					    'tol', engine.tol, 'momentum', engine.momentum);
+  engine.T = T;
+end
+[engine.unrolled_engine, loglik, niter] = enter_evidence(engine.unrolled_engine, evidence(:), ...
+						  'maximize', maximize, 'filename', filename);
+
+
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/marginal_family.m
new file mode 100644
index 00000000..a40f2974
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_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/@pearl_unrolled_dbn_inf_engine/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/marginal_nodes.m
new file mode 100644
index 00000000..0fb095e5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_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/@pearl_unrolled_dbn_inf_engine/pearl_unrolled_dbn_inf_engine.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/pearl_unrolled_dbn_inf_engine.m
new file mode 100644
index 00000000..637d29c8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/pearl_unrolled_dbn_inf_engine.m
@@ -0,0 +1,39 @@
+function engine = pearl_unrolled_dbn_inf_engine(bnet, varargin)
+% LOOPY_DBN_INF_ENGINE Loopy Pearl version of forwards-backwards
+% engine = loopy_unrolld_dbn_inf_engine(bnet, ...)
+%
+% Optional arguments
+% 'max_iter' - specifies the max num. forward-backward passes to perform PER SLICE [2]
+% 'tol' - as in loopy_pearl [1e-3]
+% 'momentum' - as in loopy_pearl [0]
+% protocol - tree or parallel [parallel]
+% filename - as in pearl [ '' ]
+
+max_iter_per_slice = 2;
+tol = 1e-3;
+momentum = 0;
+protocol = 'parallel';
+filename = '';
+
+args = varargin;
+for i=1:2:length(args)
+  switch args{i},
+   case 'max_iter', max_iter_per_slice = args{i+1};
+   case 'tol', tol = args{i+1};
+   case 'momentum', momentum = args{i+1};
+   case 'protocol', protocol = args{i+1};
+   case 'filename', filename = args{i+1};
+  end
+end
+
+engine.filename = filename;
+engine.max_iter_per_slice = max_iter_per_slice;
+engine.tol = tol;
+engine.momentum = momentum;
+engine.unrolled_engine = [];
+engine.T = -1;
+engine.ss = length(bnet.intra);
+engine.protocol = protocol;
+
+engine = class(engine, 'pearl_unrolled_dbn_inf_engine', inf_engine(bnet));
+
diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/update_engine.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/update_engine.m
new file mode 100644
index 00000000..e8613a43
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@pearl_unrolled_dbn_inf_engine/update_engine.m
@@ -0,0 +1,6 @@
+function engine = update_engine(engine, newCPDs) 
+% UPDATE_ENGINE Update the engine to take into account the new parameters (pearl_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);