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, 172 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/GraphViz/make_layout.m b/sourcecodes/bnt-master/GraphViz/make_layout.m
new file mode 100644
index 00000000..69740b76
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/make_layout.m
@@ -0,0 +1,172 @@
+function [x, y] = make_layout(adj)
+
+%function [x, y] = layout_dag(adj)
+% MAKE_LAYOUT		Creates a layout from an adjacency matrix
+%
+%  [X, Y] = MAKE_LAYOUT(ADJ)
+%
+% Inputs :
+%	ADJ = adjacency matrix (source, sink)
+%
+% Outputs :
+%	X, Y : Positions of nodes
+%
+% Usage Example : [X, Y] = make_layout(adj);
+%
+%
+% Note	: Uses some very simple heuristics, so any other
+%         algorithm would create a nicer layout 
+%
+% See also 
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 13-Apr-2000	 8:25 PM	ATC	Created under MATLAB 5.3.1.29215a (R11.1)
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+
+N = size(adj,1);
+tps = toposort(adj);
+
+if ~isempty(tps), % is directed ?
+  level = zeros(1,N);
+  for i=tps,
+    idx = find(adj(:,i));
+    if ~isempty(idx),
+      l = max(level(idx));
+      level(i)=l+1;
+    end;
+  end;
+else
+  level = poset(adj,1)'-1;  
+end;
+
+y = (level+1)./(max(level)+2);
+y = 1-y;
+x = zeros(size(y));
+for i=0:max(level),
+  idx = find(level==i);
+  offset = (rem(i,2)-0.5)/10;
+  x(idx) = (1:length(idx))./(length(idx)+1)+offset;
+end;
+
+%%%%%%%
+
+function [depth] = poset(adj, root)
+% POSET		Identify a partial ordering among the nodes of a graph
+% 
+%  [DEPTH] = POSET(ADJ,ROOT)
+% 
+% Inputs :
+%    ADJ : Adjacency Matrix
+%    ROOT : Node to start with
+% 
+% Outputs :
+%    DEPTH : Depth of the Node
+% 
+% Usage Example : [depth] = poset(adj,12);
+% 
+% 
+% Note     : All Nodes must be connected
+% See also 
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 17-Jun-1998	12:01 PM	ATC	Created under MATLAB 5.1.0.421
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+
+adj = adj+adj';
+
+N = size(adj,1);
+depth = zeros(N,1);
+depth(root) = 1;
+queue = root;
+
+while 1,
+  if isempty(queue),
+    if all(depth), break; 
+    else
+      root = find(depth==0); 
+      root = root(1);
+      depth(root) = 1;
+      queue = root;
+    end;
+  end;
+  r = queue(1); queue(1) = [];
+  idx = find(adj(r,:));
+  idx2 = find(~depth(idx));
+  idx = idx(idx2);
+  queue = [queue idx];
+  depth(idx) = depth(r)+1;
+end;
+
+%%%%%%%%%
+
+function [seq] = toposort(adj)
+% TOPOSORT		A Topological ordering of nodes in a directed graph
+% 
+%  [SEQ] = TOPOSORT(ADJ)
+% 
+% Inputs :
+%    ADJ : Adjacency Matrix. 
+%	   ADJ(i,j)==1 ==> there exists a directed edge
+%	   from i to j
+% 
+% Outputs :
+%    SEQ : A topological ordered sequence of nodes.
+%          empty matrix if graph contains cycles.
+%
+% Usage Example : 
+%		N=5;
+%		[l,u] = lu(rand(N));
+%		adj = ~diag(ones(1,N)) & u>0.5;		
+%		seq = toposort(adj);
+% 
+% 
+% Note     :
+% See also 
+
+% Uses :
+
+% Change History :
+% Date		Time		Prog	Note
+% 18-May-1998	 4:44 PM	ATC	Created under MATLAB 5.1.0.421
+
+% ATC = Ali Taylan Cemgil,
+% SNN - University of Nijmegen, Department of Medical Physics and Biophysics
+% e-mail : cemgil@mbfys.kun.nl 
+ 
+N = size(adj);
+indeg = sum(adj,1);
+outdeg = sum(adj,2);
+seq = [];
+
+for i=1:N,
+  % Find nodes with indegree 0
+  idx = find(indeg==0);
+  % If can't find than graph contains a cycle
+  if isempty(idx), 
+    seq = [];
+    break;
+  end;
+  % Remove the node with the max number of connections
+  [dummy idx2] = max(outdeg(idx));
+  indx = idx(idx2);
+  seq = [seq, indx];
+  indeg(indx)=-1;
+  idx = find(adj(indx,:));
+  indeg(idx) = indeg(idx)-1;
+end;
+
+
+
+