diff toolboxes/FullBNT-1.0.7/bnt/learning/learn_struct_pdag_ic_star.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/learning/learn_struct_pdag_ic_star.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,155 @@
+function [pdag, G] = learn_struct_pdag_ic_star(cond_indep, n, k, varargin)
+% LEARN_STRUCT_PDAG_IC_STAR Learn a partially oriented DAG (pattern) with latent 
+% variables using the IC* algorithm
+% P = learn_struct_pdag_ic_star(cond_indep, n, k, ...)
+%
+% n is the number of nodes.
+% k is an optional upper bound on the fan-in (default: n)
+% cond_indep is a boolean function that will be called as follows:
+% feval(cond_indep, x, y, S, ...)
+% where x and y are nodes, and S is a set of nodes (positive integers),
+% and ... are any optional parameters passed to this function.
+%
+% The output P is an adjacency matrix, in which
+% P(i,j) = -1 if there is either a latent variable L such that i <-L-> j 
+% OR there is a directed edge from i->j.
+% P(i,j) = -2 if there is a marked directed i-*>j edge.
+% P(i,j) = P(j,i) = 1 if there is and undirected edge i--j
+% P(i,j) = P(j,i) = 2 if there is a latent variable L such that i<-L->j.
+%
+% The IC* algorithm learns a latent structure associated with a set of observed 
+% variables. 
+% The latent structure revealed is the projection in which every latent variable is
+% 1) a root node
+% 2) linked to exactly two observed variables.
+% Latent variables in the projection are represented using a bidirectional graph, 
+% and thus remain implicit.
+%
+% See Pearl, "Causality: Models, Reasoning, and Inference", 2000, p52 for more details.
+% Written by Tamar Kushnir, 2000
+
+sep = cell(n,n);
+ord = 0;
+done = 0;
+G = ones(n,n);
+G = setdiag(G,0);
+while ~done
+  done = 1;
+  [X,Y] = find(G); 
+  for i=1:length(X)
+    x = X(i); y = Y(i);
+    nbrs = mysetdiff(myunion(neighbors(G, x), neighbors(G,y)), [x y]);
+    if length(nbrs) >= ord & G(x,y) ~= 0
+      done = 0;
+      SS = subsets(nbrs, ord, ord); % all subsets of size ord
+      for si=1:length(SS)
+	S = SS{si};
+	if feval(cond_indep, x, y, S, varargin{:})  
+	  G(x,y) = 0;
+	  G(y,x) = 0;
+	  sep{x,y} = myunion(sep{x,y}, S);
+	  sep{y,x} = myunion(sep{y,x}, S);
+	  break; % no need to check any more subsets 
+	end
+      end
+    end
+  end
+  ord = ord + 1;
+end
+
+% Create the minimal pattern,
+% i.e., the only directed edges are V structures.
+pdag = G;
+[X, Y] = find(G);
+% We want to generate all unique triples x,y,z
+% where y is a common neighbor to x and z
+for i=1:length(X)
+  x = X(i);
+  y = Y(i);
+  Z = find(G(y,:));
+  Z = mysetdiff(Z, x);
+  for z=Z(:)'
+    if G(x,z)==0 & ~ismember(y, sep{x,z}) & ~ismember(y, sep{z,x})
+      pdag(x,y) = -1; pdag(y,x) = 0;
+      pdag(z,y) = -1; pdag(y,z) = 0;
+    end
+  end
+end
+
+% Convert the minimal pattern to a complete one using the following rules:
+% Rule 1:
+% if a and b are non-adjacent nodes with a common neighbor c,
+% if a->c and not b->c then c-*>b (marked arrow).
+% Rule 2:
+% if a and b are adjacent and there is a directed path (marked links) from a to b
+% then a->b (add arrowhead).
+%Pearl (2000)
+
+arrowin = [-1 -2 2];
+old_pdag = zeros(n);
+iter = 0;
+while ~isequal(pdag, old_pdag)
+  iter = iter + 1;
+  old_pdag = pdag;
+  % rule 1
+  [X, Y] = find(pdag);
+  for i=1:length(X)
+    x = X(i);
+    y = Y(i);
+    Z = find(pdag(y,:));
+    Z = mysetdiff(Z, x);
+    for z=Z(:)'
+      if G(x,z)==0 & ismember(pdag(x,y),arrowin) & ~ismember(pdag(z,y),arrowin)
+        pdag(y,z) = -2; pdag(z,y) = 0;
+      end
+    end
+  end
+  % rule 2
+  [X, Y] = find(G); 
+  %check all adjacent nodes because if pdag(x,y) = -1 
+  %and pdag(y,x) = 0 there could still be an bidirected edge between x & y.
+  for i=1:length(X)
+    x = X(i);
+    y = Y(i);
+    if ~ismember(pdag(x,y), arrowin) %x->y doesn't exist yet
+      %find marked path from x to y
+      add_arrow = marked_path(x,y,pdag);
+      if add_arrow 
+        if pdag(y,x)==-1 %bidirected edge
+          pdag(x,y) = 2; pdag(y,x) = 2;
+        else
+          pdag(x,y) = -1;pdag(y,x) = 0;
+        end
+      end
+    end
+  end
+end
+
+
+%%%%%%%%%%%%%
+
+function t = marked_path(x,y,L)
+% MARKED_PATH is a boolean function which returns 1 if a marked path 
+% between nodes x and y exists in the partially directed latent structure L.
+%
+% t = marked_path(x,y,L)
+%
+% x and y are the starting and ending nodes in the path, respectively.
+% L is a latent structure (partially directed graph with possible latent variables).
+%
+% Rule 2 of IC* algorithm (see Pearl, 2000)
+
+t=0;
+
+%find set of marked links from x
+marked = find(L(x,:)==-2);
+if ismember(y,marked)
+  t=1; %marked path found
+else
+  for m=marked(:)'
+    t = marked_path(m,y,L);
+    if t==1
+      break; %stop when marked path found
+    end
+  end
+end