From 8070dc963753142bb86c4ed698d91fd623ed28e7 Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Thu, 28 Sep 2017 15:04:40 -0500
Subject: 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
---
 .../static/@belprop_inf_engine/private/CVS/Entries |  4 +
 .../@belprop_inf_engine/private/CVS/Repository     |  1 +
 .../static/@belprop_inf_engine/private/CVS/Root    |  1 +
 .../static/@belprop_inf_engine/private/junk        | 68 +++++++++++++++++
 .../private/parallel_protocol.m                    | 86 ++++++++++++++++++++++
 .../@belprop_inf_engine/private/tree_protocol.m    | 48 ++++++++++++
 6 files changed, 208 insertions(+)
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Entries
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Repository
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Root
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/junk
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/parallel_protocol.m
 create mode 100644 sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/tree_protocol.m

(limited to 'sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private')

diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Entries
new file mode 100644
index 00000000..938d9867
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Entries
@@ -0,0 +1,4 @@
+/junk/1.1.1.1/Wed May 29 15:59:56 2002//
+/parallel_protocol.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/tree_protocol.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Repository
new file mode 100644
index 00000000..9681913e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/static/@belprop_inf_engine/private
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Root b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/junk b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/junk
new file mode 100644
index 00000000..11438db0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/junk
@@ -0,0 +1,68 @@
+fgraph
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diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/parallel_protocol.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/parallel_protocol.m
new file mode 100644
index 00000000..3e702f7b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/parallel_protocol.m
@@ -0,0 +1,86 @@
+function [bel, niter] = parallel_protocol(engine, evidence, pot_type, local_kernel, msg)
+
+bnet = bnet_from_engine(engine);
+ns = bnet.node_sizes;
+onodes = find(~isemptycell(evidence));
+
+ndoms = length(engine.gdl.doms);
+prod_of_msg = cell(1, ndoms);
+bel = cell(1, ndoms);
+old_bel = cell(1, ndoms);
+
+converged = 0;
+iter = 1;
+while ~converged && (iter <= engine.max_iter)
+  
+  % each node multiplies all its incoming msgs and computes its local belief
+  old_bel = bel;
+  for i=1:ndoms
+    prod_of_msg{i} = mk_initial_pot(pot_type, engine.gdl.doms{i}, ns, bnet.cnodes, onodes);
+    nbrs = engine.gdl.nbrs{i};
+    for j=nbrs(:)'
+      prod_of_msg{i} = multiply_by_pot(prod_of_msg{i}, msg{j,i});
+    end
+    bel{i} = normalize_pot(multiply_by_pot(local_kernel{i}, prod_of_msg{i}));
+  end
+
+  if ~isempty(engine.fid)
+    for i=1:ndoms
+      tmp = pot_to_marginal(bel{i});
+      %fprintf(engine.fid, '%9.7f ', tmp.T(1));
+      fprintf(engine.fid, '%9.7f ', tmp.U(1));
+    end
+    %fprintf(engine.fid, '  U ');
+    %for i=1:ndoms
+    %  tmp = pot_to_marginal(bel{i});
+    %  fprintf(engine.fid, '%9.7f ', tmp.U(1));
+    %end
+    fprintf(engine.fid, '\n');
+  end
+
+  % converged?
+  if iter==1
+    converged = 0;
+  else
+    converged = 1;
+    for i=1:ndoms
+      if ~approxeq_pot(bel{i}, old_bel{i}, engine.tol)
+	converged = 0;
+	break;
+      end
+    end
+  end
+
+  if ~converged
+    old_msg = msg;
+    % each node sends a msg to each of its neighbors
+    for i=1:ndoms
+      nbrs = engine.gdl.nbrs{i};
+      for j=nbrs(:)'
+	% multiply all incoming msgs except from j
+	temp = prod_of_msg{i};
+	temp = divide_by_pot(temp, old_msg{j,i});
+	% send msg from i to j
+	temp = multiply_by_pot(temp, local_kernel{i});
+	temp2 = marginalize_pot(temp, engine.gdl.sepset{i,j}, engine.maximize);
+	msg{i,j} = normalize_pot(temp2);
+      end
+    end
+  end
+
+  iter = iter + 1;
+end
+
+
+niter = iter-1;
+
+if 0
+for i=1:ndoms
+  prod_of_msg{i} = mk_initial_pot(pot_type, engine.gdl.doms{i}, ns, bnet.cnodes, onodes);
+  nbrs = engine.gdl.nbrs{i};
+  for j=nbrs(:)'
+    prod_of_msg{i} = multiply_by_pot(prod_of_msg{i}, msg{j,i});
+  end
+  bel{i} = normalize_pot(multiply_by_pot(local_kernel{i}, prod_of_msg{i}));
+end
+end
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/tree_protocol.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/tree_protocol.m
new file mode 100644
index 00000000..940e74ae
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/private/tree_protocol.m
@@ -0,0 +1,48 @@
+function bel = tree_protocol(engine, evidence, pot_type, local_kernel, msg)
+
+bnet = bnet_from_engine(engine);
+ns = bnet.node_sizes;
+onodes = find(~isemptycell(evidence));
+
+ndoms = length(engine.gdl.doms);
+prod_of_msg = cell(1, ndoms);
+bel = cell(1, ndoms);
+  
+% collect to root (node to parents)
+for n=engine.postorder
+  % absorb msgs from children
+  prod_of_msg{n} = mk_initial_pot(pot_type, engine.gdl.doms{n}, ns, bnet.cnodes, onodes);
+  for c=children(engine.tree, n)
+    prod_of_msg{n} = multiply_by_pot(prod_of_msg{n}, msg{c,n});
+  end
+  % send msg to parents
+  for p=parents(engine.tree, n)
+    if iter==1
+      temp = prod_of_msg{n};
+    else
+      temp = divide_by_pot(prod_of_msg{n}, old_msg{p,n});
+    end
+    temp = multiply_by_pot(temp, local_kernel{n});
+    temp2 = marginalize_pot(temp, engine.gdl.sepset{n,p}, engine.maximize);
+    %fprintf('%d sends %d\n', n, p);
+    msg{n,p} = normalize_pot(temp2);
+  end
+end
+
+% distribute from root (node to children)
+for n=engine.preorder
+  % absorb from parents
+  %prod_of_msg{n} = mk_initial_pot(pot_type, doms{n}, ns, cnodes, onodes);
+  for p=parents(engine.tree, n)
+    prod_of_msg{n} = multiply_by_pot(prod_of_msg{n}, msg{p,n});
+  end
+  bel{n} = normalize_pot(multiply_pots(prod_of_msg{n}, local_kernel{n}));
+  % send msg to children
+  for c=children(engine.tree, n)
+    temp = divide_by_pot(prod_of_msg{n}, msg{c,n});
+    temp = multiply_by_pot(temp, local_kernel{n});
+    temp2 = marginalize_pot(temp, engine.gdl.sepset{n,c}, engine.maximize);
+    %fprintf('%d sends %d\n', n, c);
+    msg{n,c} = normalize_pot(temp2);
+  end
+end
-- 
cgit 1.4.1