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

24 files changed, 762 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries
new file mode 100644
index 00000000..b2150de3
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries
@@ -0,0 +1,7 @@
+/belprop_inf_engine.m/1.1.1.1/Tue Dec 31 19:00:06 2002//
+/enter_evidence.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/find_mpe.m/1.1.1.1/Wed Jun 19 22:08:40 2002//
+/loopy_converged.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//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries.Log
new file mode 100644
index 00000000..9c6f22e4
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Entries.Log
@@ -0,0 +1,2 @@
+A D/Old////
+A D/private////
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Repository
new file mode 100644
index 00000000..928be328
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/static/@belprop_inf_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/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/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Entries
new file mode 100644
index 00000000..06598b7b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Entries
@@ -0,0 +1,6 @@
+/belprop_gdl_inf_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/belprop_inf_engine_nostr.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/enter_evidence.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/enter_evidence1.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/marginal_domain.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/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Repository
new file mode 100644
index 00000000..f6b12595
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/static/@belprop_inf_engine/Old
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Root b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/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/Old/belprop_gdl_inf_engine.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/belprop_gdl_inf_engine.m
new file mode 100644
index 00000000..f3b84925
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/belprop_gdl_inf_engine.m
@@ -0,0 +1,67 @@
+function engine = belprop_gdl_inf_engine(gdl, varargin) 
+% BELPROP_GDL_INF_ENGINE Make a belief propagation inference engine for a GDL graph
+% engine = belprop_gdl_inf_engine(gdl_graph, ...)
+%
+% If the GDL graph is a tree, this will give exact results.
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default in brackets]
+% e.g., engine = belprop_inf_engine(gdl, 'tol', 1e-2, 'max_iter', 10)
+%
+% protocol - 'tree' means send messages up then down the tree,
+%            'parallel' means use synchronous updates ['parallel']
+% max_iter - max. num. iterations [ 2*num_nodes ]
+% momentum - weight assigned to old message in convex combination (useful for damping oscillations) [0]
+% tol - tolerance used to assess convergence [1e-3]
+% maximize - 1 means use max-product, 0 means use sum-product [0]
+
+
+engine = init_fields;
+engine = class(engine, 'belprop_gdl_inf_engine');
+
+% set default params
+N = length(gdl.G);
+engine.protocol = 'parallel';
+engine.max_iter = 2*N;
+engine.momentum = 0;
+engine.tol = 1e-3;
+engine.maximize = 0;
+
+engine = set_params(engine, varargin);
+
+engine.gdl = gdl;
+
+if strcmp(engine.protocol, 'tree')
+  % Make a rooted tree, so there is a fixed message passing order.
+  root = N;
+  [engine.tree, engine.preorder, engine.postorder, height, cyclic] = mk_rooted_tree(gdl.G, root);
+  assert(~cyclic);
+end
+
+% store results computed by enter_evidence here
+ndoms = length(gdl.doms);
+nvars = length(gdl.vars);
+engine.marginal_domains = cell(1, ndoms);
+
+% to compute the marginal on each variable, we need to know which domain to marginalize
+% and we want to choose the lightest. We compute the weight once we have seen the evidence.
+engine.dom_weight = [];
+engine.evidence = [];
+
+
+%%%%%%%%%
+
+function engine = init_fields()
+
+engine.protocol = [];
+engine.gdl = [];
+engine.max_iter = [];
+engine.momentum = [];
+engine.tol = [];
+engine.maximize = [];
+engine.marginal_domains = [];
+engine.evidence = [];
+engine.tree = [];
+engine.preorder = [];
+engine.postorder = [];
+engine.dom_weight = [];
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/belprop_inf_engine_nostr.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/belprop_inf_engine_nostr.m
new file mode 100644
index 00000000..8219a868
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/belprop_inf_engine_nostr.m
@@ -0,0 +1,31 @@
+function engine = belprop_inf_engine(fg, max_iter, momentum, tol, maximize)
+
+if nargin < 2, max_iter = length(fg.G); end
+if nargin < 3, momentum = 0; end
+if nargin < 4, tol = 1e-3; end
+if nargin < 5, maximize = 0; end
+
+engine.fgraph = fg;
+engine.max_iter = max_iter;
+engine.momentum = momentum;
+engine.tol = tol;
+engine.maximize = maximize;
+
+% store results computed by enter_evidence here
+ndoms = length(fg.doms);
+nvars = length(fg.vars);
+engine.marginal_domains = cell(1, ndoms);
+
+% to compute the marginal on each variable, we need to know which domain to marginalize
+% so we represent each domain as a bit vector, and compute its (pre-evidence) weight
+engine.dom_weight = [];
+
+% engine.dom_bitv = sparse(ndoms, nvars);
+% ns = fg.node_sizes;
+% for i=1:ndoms
+%   engine.dom_bitv(i, fg.doms{i}) = 1;
+%   engine.dom_weight(i) = prod(ns(fg.doms{i}));
+% end
+
+
+engine = class(engine, 'belprop_inf_engine');
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence.m
new file mode 100644
index 00000000..54649557
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence.m
@@ -0,0 +1,80 @@
+function engine = enter_evidence(engine, evidence)
+
+doms = engine.fg.doms;
+ndoms = length(doms);
+ns = engine.fg.node_sizes;
+obs = find(~isemptycell(evidence));
+cobs = myintersect(obs, engine.fg.cnodes);
+dobs = myintersect(obs, engine.fg.dnodes);
+ns(cobs) = 0;
+ns(dobs) = 1;
+
+% prime each local kernel with evidence (if any)
+local_kernel = cell(1, ndoms);
+for i=1:length(engine.fg.kernels_of_type)
+  u = engine.fg.kernels_of_type{i};
+  local_kernel(u) = kernel_to_dpots(engine.fg.kernels{i}, evidence, engine.fg.domains_of_type{i});
+end
+  
+% initialise all msgs to 1s
+nedges = engine.fg.nedges;
+msg = cell(1, nedges);
+for i=1:nedges
+  msg{i} = dpot(engine.fg.sepset{i}, ns(engine.fg.sepset{i}));
+end
+
+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
+  for i=1:ndoms
+    prod_of_msg{i} = dpot(doms{i}, ns(doms{i}));
+    nbrs = engine.fg.nbrs{i};
+    for j=1:length(nbrs)
+      ndx = engine.fg.edge_ndx(j,i);
+      prod_of_msg{i} = multiply_by_pot(prod_of_msg{i}, msg{ndx});
+    end
+  end
+  old_msg = msg;
+  
+  % each node computes its local belief
+  for i=1:ndoms
+    bel{i} = normalize_pot(multiply_pots(prod_of_msg{i}, local_kernel{i}));
+  end
+
+  % converged?
+  converged = 1;
+  for i=1:ndoms
+    if ~approxeq(bel{i}, old_bel{i}, engine.tol)
+      converged = 0;
+      break;
+    end
+  end
+
+  if ~converged
+    % each node sends a msg to each of its neighbors
+    for i=1:ndoms
+      nbrs = engine.fg.nbrs{i};
+      for j=1:length(nbrs)
+	% multiply all incoming msgs except from j
+	temp = prod_of_msg{i};
+	ndx = engine.fg.edge_ndx(j,i);
+	temp = divide_by_pot(temp, old_msg{ndx});
+	% send msg from i to j
+	temp = multiply_by_pot(temp, local_kernel{i});
+	ndx = engine.fg.edge_ndx(i,j);
+	msg{ndx} = normalize_pot(marginalize_pot(temp, engine.fg.sepset{ndx}));
+      end
+    end
+  end
+
+  iter = iter + 1;
+end
+
+  
+engine.marginal = bel;
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence1.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence1.m
new file mode 100644
index 00000000..b38cd3cb
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/enter_evidence1.m
@@ -0,0 +1,94 @@
+function engine = enter_evidence(engine, evidence)
+
+doms = engine.fgraph.doms;
+ndoms = length(doms);
+ns = engine.fgraph.node_sizes;
+obs = find(~isemptycell(evidence));
+cobs = myintersect(obs, engine.fgraph.cnodes);
+dobs = myintersect(obs, engine.fgraph.dnodes);
+ns(cobs) = 0;
+ns(dobs) = 1;
+
+% recompute the weight of each domain now that we know what nodes are observed
+for i=1:ndoms
+  engine.dom_weight(i) = prod(ns(engine.fgraph.doms{i}));
+end
+
+% prime each local kernel with evidence (if any)
+local_kernel = cell(1, ndoms);
+for i=1:length(engine.fgraph.kernels_of_type)
+  u = engine.fgraph.kernels_of_type{i};
+  local_kernel(u) = kernel_to_dpots(engine.fgraph.kernels{i}, evidence, engine.fgraph.domains_of_type{i});
+end
+  
+% initialise all msgs to 1s
+msg = cell(ndoms, ndoms);
+for i=1:ndoms
+  nbrs = engine.fgraph.nbrs{i};
+  for j=nbrs(:)'
+    dom = engine.fgraph.sepset{i,j};
+    msg{i,j} = dpot(dom, ns(dom));
+  end
+end
+
+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
+  for i=1:ndoms
+    prod_of_msg{i} = dpot(doms{i}, ns(doms{i}));
+    nbrs = engine.fgraph.nbrs{i};
+    for j=nbrs(:)'
+      prod_of_msg{i} = multiply_by_pot(prod_of_msg{i}, msg{j,i});
+    end
+  end
+  
+  % each node computes its local belief
+  old_bel = bel;
+  for i=1:ndoms
+    bel{i} = normalize_pot(multiply_pots(prod_of_msg{i}, local_kernel{i}));
+  end
+
+  % converged?
+  if iter==1
+    converged = 0;
+  else
+    converged = 1;
+    for i=1:ndoms
+      belT = get_params(bel{i}, 'table');
+      old_belT = get_params(old_bel{i}, 'table');
+      if ~approxeq(belT, old_belT, 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.fgraph.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});
+	msg{i,j} = normalize_pot(marginalize_pot(temp, engine.fgraph.sepset{i,j}));
+      end
+    end
+  end
+
+  iter = iter + 1
+end
+
+engine.marginal_domains = bel;
+%for i=1:ndoms  
+  %engine.marginal_domains{i} = get_params(bel{i}, 'table');
+%end
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/marginal_domain.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/marginal_domain.m
new file mode 100644
index 00000000..49ad94c5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/Old/marginal_domain.m
@@ -0,0 +1,5 @@
+function marginal = marginal_domain(engine, i)
+% MARGINAL_DOMAIN Return the marginal on the specified domain (belprop)
+% marginal = marginal_domain(engine, i)
+
+marginal = pot_to_marginal(engine.marginal_domains{i});
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/belprop_inf_engine.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/belprop_inf_engine.m
new file mode 100644
index 00000000..839af506
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/belprop_inf_engine.m
@@ -0,0 +1,90 @@
+function engine = belprop_inf_engine(bnet, varargin) 
+% BELPROP_INF_ENGINE Make a loopy belief propagation inference engine
+% engine = belprop_inf_engine(bnet, ...)
+%
+% This is like pearl_inf_engine, except it uses potential objects,
+% instead of lambda/pi structs. Hence it is slower.
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default in brackets]
+%
+% protocol - 'tree' means send messages up then down the tree,
+%            'parallel' means use synchronous updates ['parallel']
+% max_iter - max. num. iterations [ 2*num_nodes ]
+% momentum - weight assigned to old message in convex combination (useful for damping oscillations) [0]
+% tol      - tolerance used to assess convergence [1e-3]
+% maximize - 1 means use max-product, 0 means use sum-product [0]
+% filename - name of file to write beliefs to after each iteration within enter_evidence [ [] ]
+%
+% e.g., engine = belprop_inf_engine(bnet, 'maximize', 1, 'max_iter', 10)
+
+% gdl = general distributive law
+engine.gdl = bnet_to_gdl(bnet);
+
+% set default params
+N = length(engine.gdl.G);
+engine.protocol = 'parallel';
+engine.max_iter = 2*N;
+engine.momentum = 0;
+engine.tol = 1e-3;
+engine.maximize = 0;
+engine.filename = [];
+engine.fid = [];
+
+args = varargin;
+nargs = length(args);
+for i=1:2:nargs
+  switch args{i},
+   case 'max_iter', engine.max_iter = args{i+1};
+   case 'momentum', engine.momentum = args{i+1};
+   case 'tol',      engine.tol = args{i+1};
+   case 'protocol', engine.protocol = args{i+1};
+   case 'filename', engine.filename = args{i+1};
+   otherwise,
+    error(['invalid argument name ' args{i}]);
+  end
+end
+
+
+if strcmp(engine.protocol, 'tree')
+  % Make a rooted tree, so there is a fixed message passing order.
+  root = N;
+  [engine.tree, engine.preorder, engine.postorder, height, cyclic] = mk_rooted_tree(engine.gdl.G, root);
+  assert(~cyclic);
+end
+
+% store results computed by enter_evidence here
+engine.marginal_domains = cell(1, N);
+
+engine.niter = [];
+
+engine = class(engine, 'belprop_inf_engine', inf_engine(bnet));
+
+%%%%%%%%%
+
+function gdl = bnet_to_gdl(bnet)
+
+gdl.G = mk_undirected(bnet.dag);
+N = length(bnet.dag);
+gdl.doms = cell(1,N);
+for i=1:N
+  gdl.doms{i} = family(bnet.dag, i);
+end 
+
+% Compute a bit vector representation of the set of domains
+% dom_bitv(i,j) = 1 iff variable j occurs in domain i
+gdl.dom_bitv = zeros(N, N);
+for i=1:N
+  gdl.dom_bitv(i, gdl.doms{i}) = 1;
+end
+   
+% compute the interesection of the domains on either side of each edge (separating set)
+gdl.sepset = cell(N, N);
+gdl.nbrs = cell(1,N);
+for i=1:N
+  nbrs = neighbors(gdl.G, i);
+  gdl.nbrs{i} = nbrs;
+  for j = nbrs(:)'
+    gdl.sepset{i,j} = myintersect(gdl.doms{i}, gdl.doms{j});
+  end
+end  
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/enter_evidence.m
new file mode 100644
index 00000000..88cce18e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/enter_evidence.m
@@ -0,0 +1,86 @@
+function [engine, ll, niter] = enter_evidence(engine, evidence, varargin)
+% ENTER_EVIDENCE Propagate evidence using belief propagation
+% [engine, ll, niter] = enter_evidence(engine, evidence, ...)
+%
+% The log-likelihood is not computed; ll = 0.
+% niter contains the number of iterations used (if engine.protocol = 'parallel')
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default value in brackets]
+%
+% maximize - 1 means use max-product, 0 means use sum-product [0]
+% exclude  - list of nodes whose potential will not be included in the joint [ [] ]
+%
+% e.g., engine = enter_evidence(engine, ev, 'maximize', 1)
+
+ll = 0;
+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
+
+engine.maximize = maximize;
+
+if ~isempty(engine.filename)
+  engine.fid = fopen(engine.filename, 'w');
+  if engine.fid == 0
+    error(['can''t open ' engine.filename]);
+  end
+else
+  engine.fid = [];
+end
+
+gdl = engine.gdl;
+bnet = bnet_from_engine(engine);
+
+ndoms = length(gdl.doms);
+ns = bnet.node_sizes;
+onodes = find(~isemptycell(evidence));
+pot_type = determine_pot_type(bnet, onodes);
+
+% prime each local kernel with evidence (if any)
+local_kernel = cell(1, ndoms);
+for i=1:ndoms
+  if myismember(i, exclude)
+    local_kernel{i} =  mk_initial_pot(pot_type, gdl.doms{i}, ns, bnet.cnodes, onodes);
+  else
+    e = bnet.equiv_class(i);
+    local_kernel{i} =  convert_to_pot(bnet.CPD{e}, pot_type, gdl.doms{i}(:), evidence);
+  end
+end
+  
+% initialise all msgs to 1s
+msg = cell(ndoms, ndoms);
+for i=1:ndoms
+  nbrs = gdl.nbrs{i};
+  for j=nbrs(:)'
+    dom = gdl.sepset{i,j};
+    msg{i,j} = mk_initial_pot(pot_type, dom, ns, bnet.cnodes, onodes);
+  end
+end
+
+switch engine.protocol
+ case 'parallel', 
+   [engine.marginal_domains, niter] = parallel_protocol(engine, evidence, pot_type, local_kernel, msg);
+ case 'tree',
+  engine.marginal_domains = serial_protocol(engine, evidence, pot_type, local_kernel, msg);
+  niter = 1;
+end
+engine.niter = niter;
+
+%fprintf('just finished %d iterations of belprop\n', niter);
+
+if ~isempty(engine.filename)
+  fclose(engine.fid);
+end
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/find_mpe.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/find_mpe.m
new file mode 100644
index 00000000..73bd0abc
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/find_mpe.m
@@ -0,0 +1,49 @@
+function mpe = find_mpe(engine, evidence, varargin)
+% FIND_MPE Find the most probable explanation of the data  (belprop)
+% function mpe = find_mpe(engine, evidence,...)
+%
+% evidence{i} = [] if X(i) is hidden, and otherwise contains its observed value (scalar or column vector).
+%
+% This finds the marginally most likely value for each hidden node,
+% and may give the wrong results even if the graph is acyclic,
+% unless you set break_ties = 1.
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default value in brackets]
+%
+% break_ties is optional. If 1, we will force ties to be broken consistently
+%  by calling enter_evidence N times. (see Jensen96, p106) Default = 1.
+
+break_ties = 1;
+
+% parse optional params
+args = varargin;
+nargs = length(args);
+for i=1:2:nargs
+  switch args{i},
+   case 'break_ties',    break_ties = args{i+1}; 
+   otherwise,  
+    error(['invalid argument name ' args{i}]);       
+  end
+end
+
+engine = enter_evidence(engine, evidence, 'maximize', 1);
+
+observed = ~isemptycell(evidence);
+evidence = evidence(:); % hack to handle unrolled DBNs
+N = length(evidence);
+mpe = cell(1,N);
+for i=1:N
+  m = marginal_nodes(engine, i);
+  % observed nodes are all set to 1 inside the inference engine, so we must undo this
+  if observed(i)
+    mpe{i} = evidence{i};
+  else
+    mpe{i} = argmax(m.T);
+    if break_ties
+      evidence{i} = mpe{i};                             
+      [engine, ll] = enter_evidence(engine, evidence, 'maximize', 1);  
+    end
+  end
+end
+
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/loopy_converged.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/loopy_converged.m
new file mode 100644
index 00000000..fba4f2fd
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/loopy_converged.m
@@ -0,0 +1,13 @@
+function niter = loopy_converged(engine)
+% LOOPY_CONVERGED Did loopy belief propagation converge? 0 means no, eles we return the num. iterations.
+% function niter = loopy_converged(engine)
+%
+% We use a simple heuristic: we say convergence occurred if the number of iterations
+% used was less than the maximum allowed.
+
+if engine.niter == engine.max_iter
+  niter = 0;
+else
+  niter = engine.niter;
+end
+%conv = (strcmp(engine.protocol, 'tree') | (engine.niter < engine.max_iter));
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_family.m
new file mode 100644
index 00000000..afe404a8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_family.m
@@ -0,0 +1,6 @@
+function [marginal, pot] = marginal_family(engine, query)
+% MARGINAL_NODES Compute the marginal on the family of the specified query node (belprop)
+% [marginal, pot] = marginal_family(engine, query)
+
+pot = engine.marginal_domains{query};
+marginal = pot_to_marginal(pot);
diff --git a/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_nodes.m
new file mode 100644
index 00000000..0c2b5d94
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/static/@belprop_inf_engine/marginal_nodes.m
@@ -0,0 +1,14 @@
+function [marginal, pot] = marginal_nodes(engine, query)
+% MARGINAL_NODES Compute the marginal on the specified query nodes (belprop)
+% [marginal, pot] = marginal_nodes(engine, query)
+%
+% query must be a subset of a family
+
+if isempty(query)
+  big_pot = engine.marginal_domains{1}; % pick an arbitrary domain
+else
+  big_pot = engine.marginal_domains{query(end)};   
+end
+pot = marginalize_pot(big_pot, query);
+marginal = pot_to_marginal(pot);
+ 
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 @@
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+fgraphofgraphnfgraphofgraphdfgraphefgraphsfgraph fgraph=fgraph fgraphffgraphifgraphnfgraphdfgraph(fgraph~fgraphifgraphsfgraphefgraphmfgraphpfgraphtfgraphyfgraphcfgraphefgraphlfgraphlfgraph(fgraphefgraphvfgraphifgraphdfgraphefgraphnfgraphcfgraphefgraph)fgraph)fgraph;fgraph
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+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