jtree_ndx_dbn_inf_engine.m

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function engine = jtree_ndx_dbn_inf_engine(bnet, varargin)
% JTREE_NDX_DBN_INF_ENGINE Junction tree inference algorithm for DBNs which pre-computes indices.
% engine = jtree_ndx_dbn_inf_engine(bnet, ...)
%
% This is to jtree_dbn_inf_engine what jtree_ndx_inf_engine is to jtree_inf_engine.
%
% Optional arguments
% ndx_type - 'B', 'D', or 'SD' [ 'SD' ]

ss = length(bnet.intra);

clusters = {};
ndx_type = 'SD';

if nargin >= 2
  args = varargin;
  nargs = length(args);
  for i=1:2:nargs
    switch args{i},
     case 'clusters', clusters = args{i+1};
     case 'ndx_type', ndx_type = args{i+1};
    end
  end
end

engine.evidence = [];
engine.node_sizes = [];
engine.ndx_type = ndx_type;

[int, engine.persist, engine.transient] = compute_interface_nodes(bnet.intra, bnet.inter);
engine.persist_bitv = zeros(1, ss);
engine.persist_bitv(engine.persist) = 1;

%engine.interface = engine.persist; % WRONG!
engine.interface = int;
engine.nonint = mysetdiff(1:ss, int);

onodes = bnet.observed;
  
% Create a "1.5 slice" jtree, containing slice 1 and the interface nodes of slice 2
% To keep the node numbering the same, we simply disconnect the non-interface nodes
% from slice 2, and set their size to 1.
% We do this to speed things up, and so that the likelihood is computed correctly - we do not need to do
% this if we just want to compute marginals. 
intra15 = bnet.intra;
for i=engine.nonint(:)'
  intra15(i,:) = 0;
  intra15(:,i) = 0;
end
dag15 = [bnet.intra bnet.inter;
	 zeros(ss)    intra15];
ns = bnet.node_sizes(:);
ns(engine.nonint+ss) = 1; % disconnected nodes get size 1
obs_nodes = [onodes(:) onodes(:)+ss];
bnet15 = mk_bnet(dag15, ns, 'discrete', bnet.dnodes, 'equiv_class', bnet.equiv_class(:), ...
		 'observed', obs_nodes(:));
ns(obs_nodes) = 1;

% use unconstrained elimination,
% but force there to be a clique containing both interfaces
clusters(end+1:end+2) = {int, int+ss};
engine.jtree_engine = jtree_ndx_inf_engine(bnet15, 'clusters', clusters, 'root', int+ss, ...
					   'ndx_type', ndx_type);


engine.in_clq = clq_containing_nodes(engine.jtree_engine, int);
engine.out_clq = clq_containing_nodes(engine.jtree_engine, int+ss);
engine.jtree_struct = struct(engine.jtree_engine); % violate object privacy

cliques = engine.jtree_struct.cliques;

engine.mult_int_onto_inclq_ndx_id = add_ndx(cliques{engine.in_clq}, engine.interface, ns, ndx_type);
engine.marg_root_onto_int2_ndx_id = add_ndx(cliques{engine.jtree_struct.root_clq}, ...
					    engine.interface+ss, ns, ndx_type);

engine.marg_inclq_onto_int_ndx_id = add_ndx(cliques{engine.in_clq}, engine.interface, ns, ndx_type);
engine.marg_outclq_onto_int2_ndx_id = add_ndx(cliques{engine.out_clq}, engine.interface+ss, ns, ndx_type);
engine.mult_int2_onto_outclq_ndx_id = add_ndx(cliques{engine.out_clq}, engine.interface+ss, ns, ndx_type);
engine.mult_int_onto_int_ndx_id = add_ndx(engine.interface, engine.interface, ns, ndx_type);




% Also create an engine just for slice 1
bnet1 = mk_bnet(bnet.intra1, bnet.node_sizes_slice, 'discrete', bnet.dnodes, ...
		'equiv_class', bnet.equiv_class(:,1), 'observed', onodes);
for i=1:max(bnet1.equiv_class)
  bnet1.CPD{i} = bnet.CPD{i};
end

engine.jtree_engine1 = jtree_ndx_inf_engine(bnet1, 'clusters', {int},  'root', int, ...
					      'ndx_type', ndx_type);

engine.in_clq1 = clq_containing_nodes(engine.jtree_engine1, int);
engine.jtree_struct1 = struct(engine.jtree_engine1); % violate object privacy

cliques = engine.jtree_struct1.cliques;
engine.mult_int_onto_inclq1_ndx_id = add_ndx(cliques{engine.in_clq1}, engine.interface, ns, ndx_type);
engine.marg_inclq1_onto_int_ndx_id = add_ndx(cliques{engine.in_clq1}, engine.interface, ns, ndx_type);


% stuff needed by marginal_nodes
engine.clpot = [];
engine.T = [];
engine.maximize = [];
engine.actual_node_sizes = [];
engine.eff_node_sizes = [];

engine = class(engine, 'jtree_ndx_dbn_inf_engine', inf_engine(bnet));