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

1 files changed, 168 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/graph/trees.txt b/sourcecodes/bnt-master/graph/trees.txt
new file mode 100644
index 00000000..f5475aac
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+++ b/sourcecodes/bnt-master/graph/trees.txt
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+
+% make undirected adjacency matrix of graph/tree
+% e.g.,
+%  1 
+% / \
+% 2  3
+T = zeros(3,3);
+T(1,2) = 1; T(2,1)=1;
+T(1,3)=1; T(3,1) = 1;
+
+root = 1;
+[T, preorder, postorder] =  mk_rooted_tree(T, root);
+
+% bottom up message passing leaves to root
+for n=postorder(:)'
+  for p	= parents(T, n)
+     % p is parent of n
+   end
+end
+
+% top down, root to leaves
+for n=preorder(:)'
+  for c= children(T,n)
+    % c is child of n
+  end
+end
+
+
+%%%%%%%%%%%%%
+
+function ps = parents(adj_mat, i)
+% PARENTS Return the list of parents of node i
+% ps = parents(adj_mat, i)
+
+ps = find(adj_mat(:,i))';
+
+
+%%%%%%%%%%%%
+
+function cs = children(adj_mat, i, t)
+% CHILDREN Return the indices of a node's children in sorted order
+% c = children(adj_mat, i, t)
+%
+% t is an optional argument: if present, dag is assumed to be a 2-slice DBN
+
+if nargin < 3 
+  cs = find(adj_mat(i,:));
+else
+  if t==1
+    cs = find(adj_mat(i,:));
+  else
+    ss = length(adj_mat)/2;
+    j = i+ss;
+    cs = find(adj_mat(j,:)) + (t-2)*ss;
+  end
+end
+
+%%%%%%%%%%%
+
+function [T, pre, post, cycle] = mk_rooted_tree(G, root)
+% MK_ROOTED_TREE Make a directed, rooted tree out of an undirected tree.
+% [T, pre, post, cycle] = mk_rooted_tree(G, root)
+
+n = length(G);
+T = sparse(n,n); % not the same as T = sparse(n) !
+directed = 0;
+[d, pre, post, cycle, f, pred] = dfs(G, root, directed);
+for i=1:length(pred)
+  if pred(i)>0
+    T(pred(i),i)=1;
+  end
+end
+
+
+%%%%%%%%%%%
+
+function [d, pre, post, cycle, f, pred] = dfs(adj_mat, start, directed)
+% DFS Perform a depth-first search of the graph starting from 'start'.
+% [d, pre, post, cycle, f, pred] = dfs(adj_mat, start, directed)
+%
+% Input:
+% adj_mat(i,j)=1 iff i is connected to j.
+% start is the root vertex of the dfs tree; if [], all nodes are searched
+% directed = 1 if the graph is directed
+%
+% Output:
+% d(i) is the time at which node i is first discovered.
+% pre is a list of the nodes in the order in which they are first encountered (opened).
+% post is a list of the nodes in the order in which they are last encountered (closed).
+% 'cycle' is true iff a (directed) cycle is found.
+% f(i) is the time at which node i is finished.
+% pred(i) is the predecessor of i in the dfs tree.
+%
+% If the graph is a tree, preorder is parents before children,
+% and postorder is children before parents.
+% For a DAG, topological order = reverse(postorder).
+%
+% See Cormen, Leiserson and Rivest, "An intro. to algorithms" 1994, p478.
+
+n = length(adj_mat);
+
+global white gray black color
+white = 0; gray = 1; black = 2;
+color = white*ones(1,n);
+
+global time_stamp
+time_stamp = 0;
+
+global d f
+d = zeros(1,n);
+f = zeros(1,n);
+
+global pred
+pred = zeros(1,n);
+
+global cycle
+cycle = 0;
+
+global pre post
+pre = [];
+post = [];
+
+if ~isempty(start)
+  dfs_visit(start, adj_mat, directed);
+else
+  for u=1:n
+    if color(u)==white
+      dfs_visit(u, adj_mat, directed);
+    end
+  end
+end
+
+
+%%%%%%%%%%
+
+function dfs_visit(u, adj_mat, directed)
+
+global white gray black color time_stamp d f pred cycle  pre post
+
+pre = [pre u];
+color(u) = gray;
+time_stamp = time_stamp + 1;
+d(u) = time_stamp;
+if directed
+  ns = children(adj_mat, u);
+else
+  ns = neighbors(adj_mat, u);
+  ns = mysetdiff(ns, pred(u)); % don't go back to visit the guy who called you!
+end
+for v=ns(:)'
+  %fprintf('u=%d, v=%d, color(v)=%d\n', u, v, color(v))
+  switch color(v)
+    case white, % not visited v before (tree edge)
+     pred(v)=u;
+     dfs_visit(v, adj_mat, directed);
+   case gray, % back edge - v has been visited, but is still open
+    cycle = 1;
+    %fprintf('cycle: back edge from v=%d to u=%d\n', v, u);
+   case black, % v has been visited, but is closed
+    % no-op
+  end
+end
+color(u) = black;
+post = [post u];
+time_stamp = time_stamp + 1;
+f(u) = time_stamp;
+
+