diff toolboxes/FullBNT-1.0.7/bnt/inference/static/@jtree_inf_engine/jtree_inf_engine.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/FullBNT-1.0.7/bnt/inference/static/@jtree_inf_engine/jtree_inf_engine.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,141 @@
+function engine = jtree_inf_engine(bnet, varargin)
+% JTREE_INF_ENGINE Junction tree inference engine
+% engine = jtree_inf_engine(bnet, ...)
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+% [default value in brackets]
+%
+% clusters  - a cell array of sets of nodes we want to ensure are in the same clique (in addition to families) [ {} ]
+% root      - the root of the junction tree will be a clique that contains this set of nodes [N]
+% stages    - stages{t} is a set of nodes we want to eliminate before stages{t+1}, ... [ {1:N} ]
+%
+% e.g., engine = jtree_inf_engine(bnet, 'maximize', 1);
+%
+% For more details on the junction tree algorithm, see
+% - "Probabilistic networks and expert systems", Cowell, Dawid, Lauritzen and Spiegelhalter, Springer, 1999
+% - "Inference in Belief Networks: A procedural guide", C. Huang and A. Darwiche, 
+%      Intl. J. Approximate Reasoning, 15(3):225-263, 1996.
+
+
+% set default params
+N = length(bnet.dag);
+clusters = {};
+root = N;
+stages = { 1:N };
+maximize = 0;
+
+if nargin >= 2
+  args = varargin;
+  nargs = length(args);
+  if ~isstr(args{1})
+    error('the interface to jtree has changed; now, onodes is not allowed and all optional params must be passed by name')
+  end
+  for i=1:2:nargs
+    switch args{i},
+     case 'clusters', clusters = args{i+1}; 
+     case 'root',     root = args{i+1}; 
+     case 'stages',   stages = args{i+1}; 
+     case 'maximize', maximize = args{i+1};
+     otherwise,  
+      error(['invalid argument name ' args{i}]);       
+    end
+  end
+end
+
+engine = init_fields;
+engine = class(engine, 'jtree_inf_engine', inf_engine(bnet));
+
+engine.maximize = maximize;
+
+onodes = bnet.observed;
+
+%[engine.jtree, dummy, engine.cliques, B, w, elim_order, moral_edges, fill_in_edges, strong] = ...
+%    dag_to_jtree(bnet, onodes, stages, clusters);
+
+porder = determine_elim_constraints(bnet, onodes);
+strong = ~isempty(porder);
+ns = bnet.node_sizes(:);
+ns(onodes) = 1; % observed nodes have only 1 possible value
+[engine.jtree, root2, engine.cliques, B, w] = ...
+    graph_to_jtree(moralize(bnet.dag), ns, porder, stages, clusters);
+
+
+engine.cliques_bitv = B;
+engine.clique_weight = w;
+C = length(engine.cliques);
+engine.clpot = cell(1,C);
+
+% Compute the separators between connected cliques.
+[is,js] = find(engine.jtree > 0);
+engine.separator = cell(C,C);
+for k=1:length(is)
+  i = is(k); j = js(k);
+  engine.separator{i,j} = find(B(i,:) & B(j,:)); % intersect(cliques{i}, cliques{j});
+end
+
+% A node can be a member of many cliques, but is assigned to exactly one, to avoid
+% double-counting its CPD. We assign node i to clique c if c is the "lightest" clique that
+% contains i's family, so it can accomodate its CPD.
+
+engine.clq_ass_to_node = zeros(1, N);
+for i=1:N
+  %c = clq_containing_nodes(engine, family(bnet.dag, i));
+  clqs_containing_family = find(all(B(:,family(bnet.dag, i)), 2)); % all selected columns must be 1
+  c = clqs_containing_family(argmin(w(clqs_containing_family)));  
+  engine.clq_ass_to_node(i) = c; 
+end
+
+% Make the jtree rooted, so there is a fixed message passing order.
+if strong
+  % the last clique is guaranteed to be a strong root
+  % engine.root_clq = length(engine.cliques);
+  
+  % --- 4/17/2010, by Wei Sun (George Mason University):
+  % It has been proved that the last clique is not necessary to be the  
+  % strong root, instead, a clique called interface clique, that contains
+  % all discrete parents and at least one continuous node from a connected
+  % continuous component in a CLG, is guaranteed to be a strong root.
+  engine.root_clq = findroot(bnet, engine.cliques) ;
+else
+  % jtree_dbn_inf_engine requires the root to contain the interface.
+  % This may conflict with the strong root requirement! *********** BUG *************
+  engine.root_clq = clq_containing_nodes(engine, root);
+  if engine.root_clq <= 0
+    error(['no clique contains ' num2str(root)]);
+  end
+end  
+
+[engine.jtree, engine.preorder, engine.postorder] = mk_rooted_tree(engine.jtree, engine.root_clq);
+
+% collect 
+engine.postorder_parents = cell(1,length(engine.postorder));
+for n=engine.postorder(:)'
+  engine.postorder_parents{n} = parents(engine.jtree, n);
+end
+% distribute
+engine.preorder_children = cell(1,length(engine.preorder));
+for n=engine.preorder(:)'
+  engine.preorder_children{n} = children(engine.jtree, n);
+end
+
+  
+
+%%%%%%%%
+
+function engine = init_fields()
+
+engine.jtree = [];
+engine.cliques = [];
+engine.separator = [];
+engine.cliques_bitv = [];
+engine.clique_weight = [];
+engine.clpot = [];
+engine.clq_ass_to_node = [];
+engine.root_clq = [];
+engine.preorder = [];
+engine.postorder = [];
+engine.preorder_children = [];
+engine.postorder_parents = [];
+engine.maximize = [];
+engine.evidence = [];
+