diff toolboxes/FullBNT-1.0.7/bnt/general/convert_dbn_CPDs_to_tables1.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/general/convert_dbn_CPDs_to_tables1.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,162 @@
+function CPDpot = convert_dbn_CPDs_to_tables1(bnet, evidence)
+% CONVERT_DBN_CPDS_TO_TABLES Convert CPDs of (possibly instantiated) DBN nodes to tables
+% CPDpot = convert_dbn_CPDs_to_tables(bnet, evidence)
+%
+% CPDpot{n,t} is a table containing P(n,t|pa(n,t), ev)
+% All hidden nodes are assumed to be discrete
+% We assume the observed nodes are the same in every slice
+%
+% Evaluating the conditional likelihood of the evidence can be very slow,
+% so we take pains to vectorize where possible, i.e., we try to avoid
+% calling convert_to_table
+
+[ss T] = size(evidence);
+%obs_bitv = ~isemptycell(evidence(:));
+obs_bitv = zeros(1, 2*ss);
+obs_bitv(bnet.observed) = 1;
+obs_bitv(bnet.observed+ss) = 1;
+
+ns = bnet.node_sizes(:);
+CPDpot = cell(ss,T); 
+
+for n=1:ss
+  % slice 1
+  t = 1;
+  ps = parents(bnet.dag, n);
+  e = bnet.equiv_class(n, 1);
+  if ~any(obs_bitv(ps))
+    CPDpot{n,t} = convert_CPD_to_table_hidden_ps(bnet.CPD{e}, evidence{n,t});
+  else
+    CPDpot{n,t} = convert_to_table(bnet.CPD{e}, [ps n], evidence(:,1));
+  end
+  
+  % slices 2..T
+  debug = 1;
+  if ~obs_bitv(n)
+    CPDpot = helper_hidden_child(bnet, evidence, n, CPDpot, obs_bitv, debug);
+  else
+    CPDpot = helper_obs_child(bnet, evidence, n, CPDpot, obs_bitv, debug);
+  end
+end
+
+if 0
+CPDpot2 = convert_dbn_CPDs_to_tables_slow(bnet, evidence);
+for t=1:T
+  for n=1:ss
+    if ~approxeq(CPDpot{n,t}, CPDpot2{n,t})
+      fprintf('CPDpot n=%d, t=%d\n',n,t);
+      keyboard
+    end
+  end
+end
+end
+
+
+% special cases: c=child, p=parents, d=discrete, h=hidden, 1=1slice
+% if c=h=1 then c=d=1, since hidden nodes must be discrete
+% c=h c=d p=h p=d p=1 method
+% ---------------------------
+% 1   1   1   1   -   replicate CPT
+% 0   1   1   1   1   dhmm
+% 0   0   1   1   1   ghmm
+% -   1   -   1   -   evaluate CPT on evidence
+% other               loop
+
+%%%%%%%
+function CPDpot = helper_hidden_child(bnet, evidence, n, CPDpot, obs_bitv, debug)
+
+[ss T] = size(evidence);
+self = n+ss;
+ps = parents(bnet.dag, self);
+e = bnet.equiv_class(n, 2);
+ns = bnet.node_sizes(:);
+if ~any(obs_bitv(ps)) % all parents are hidden (hence discrete)
+  if debug, fprintf('node %d is hidden, all ps are hidden\n', n); end
+  if myismember(n, bnet.dnodes) 
+    %CPT = CPD_to_CPT(bnet.CPD{e});
+    %CPT = reshape(CPT, [prod(ns(ps)) ns(self)]);
+    CPT = convert_CPD_to_table_hidden_ps(bnet.CPD{e}, []);
+    CPDpot(n,2:T) = num2cell(repmat(CPT, [1 1 T-1]), [1 2]);
+  else
+    error(['hidden cts node disallowed'])
+  end
+else % some parents are observed - slow
+  if mysubset(ps, bnet.dnodes) % all parents are discrete
+    % given CPT(p1, p2, p3, p4, c), where p1,p3 are observed
+    % we create CPT([p2 p4 c], [p1 p3]).
+    % We then convert all observed p1,p3 into indices ndx
+    % and return CPT(:, ndx)
+    CPT = CPD_to_CPT(bnet.CPD{e});
+    domain = [ps self];
+    % if dom is [3 7 8] and 3,8 are observed, odom_rel = [1 3], hdom_rel = 2,
+    % odom = [3 8], hdom = 7
+    odom_rel = find(obs_bitv(domain));
+    hdom_rel = find(~obs_bitv(domain));
+    odom = domain(odom_rel);
+    hdom = domain(hdom_rel);
+    CPT = permute(CPT, [hdom_rel odom_rel]);
+    CPT = reshape(CPT, prod(ns(hdom)), prod(ns(odom)));
+    parents_in_same_slice = all(ps > ss);
+    if parents_in_same_slice
+      if debug, fprintf('node %d is hidden, some ps are obs, all ps discrete, 1 slice\n', n); end
+      data = cell2num(evidence(odom-ss,2:T)); %data(i,t) = val of i'th obs parent at t+1
+    else
+      if debug, fprintf('node %d is hidden, some ps are obs, all ps discrete, 2 slice\n', n); end
+      data = zeros(length(odom), T-1);
+      for t=2:T
+	ev = evidence(:,t-1:t);
+	data(:,t-1) = cell2num(ev(odom));
+      end
+    end
+    ndx = subv2ind(ns(odom), data'); % ndx(t) encodes data(:,t)
+    CPDpot(n,2:T) = num2cell(CPT(:, ndx), [1 2]);
+  else % some parents are cts - v slow
+    if debug, fprintf('node %d is hidden, some ps are obs, some ps cts\n', n); end
+    for t=2:T
+      CPDpot{n,t} = convert_to_table(bnet.CPD{e}, [ps self], evidence(:,t-1:t));
+    end
+  end
+end
+  
+%%%%%%%
+function CPDpot = helper_obs_child(bnet, evidence, n, CPDpot, obs_bitv, debug)
+
+[ss T] = size(evidence);
+self = n+ss;
+ps = parents(bnet.dag, self);
+e = bnet.equiv_class(n, 2);
+ns = bnet.node_sizes(:);
+if ~any(obs_bitv(ps)) % all parents are hidden
+  parents_in_same_slice = all(ps > ss);
+  if parents_in_same_slice
+    if debug, fprintf('node %d is obs, all ps are hidden, 1 slice\n', n); end
+    ps1 = ps - ss;
+    if myismember(n, bnet.dnodes) 
+      CPT = CPD_to_CPT(bnet.CPD{e});
+      CPT = reshape(CPT, [prod(ns(ps)) ns(self)]); % what if no parents?
+      obslik = eval_pdf_cond_multinomial(cell2num(evidence(n,2:T)), CPT);
+      CPDpot(n,2:T) = num2cell(obslik, 1);
+    else
+      S = struct(bnet.CPD{e}); 
+      obslik = eval_pdf_cond_gauss(cell2num(evidence(n,2:T)), S.mean, S.cov);
+      CPDpot(n,2:T) = num2cell(obslik, 1);
+    end
+  else % parents span 2 slices - slow
+    if debug, fprintf('node %d is obs, all ps are hidden , 2 slice\n', n); end
+    for t=2:T
+      CPDpot{n,t} = convert_to_table(bnet.CPD{e}, [ps self], evidence(:,t-1:t));
+    end
+  end
+else 
+  if isempty(ps) % observed root
+    if debug, fprintf('node %d is obs, no ps\n', n); end
+    CPT = CPD_to_CPT(bnet.CPD{e});
+    data = cell2num(evidence(n,2:T));
+    CPDpot(n,2:T) = CPT(data);
+  else  % some parents are observed  - slow
+    if debug, fprintf('node %d is obs, some ps are obs\n', n); end
+    for t=2:T
+      CPDpot{n,t} = convert_to_table(bnet.CPD{e}, [ps self], evidence(:,t-1:t));
+    end
+  end
+end