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, 161 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/potentials/@scgpot/direct_combine_pots.m b/sourcecodes/bnt-master/BNT/potentials/@scgpot/direct_combine_pots.m
new file mode 100644
index 00000000..deeb002d
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+++ b/sourcecodes/bnt-master/BNT/potentials/@scgpot/direct_combine_pots.m
@@ -0,0 +1,161 @@
+function pot = direct_combine_pots(pot1, pot2)
+% DIRECTED_COMBINE_POTS The combination operation corresponds to ordinary composition of conditional distributions. 
+% In some sense is similar to that of forming disjoint union of set.
+% pot = direct_combine_pots(pot1, pot2)
+
+% directed combine can be performed under the conditon that the head node set of pot1 is disjoint from the domain of 
+% pot2 or vice versa. if the last conditon was satisfied we exchange the pot1 and pot2 firstly then perform the operation.
+% If neither of them was satified the directed combine is undifined.
+
+
+if isempty( myintersect(pot1.domain, pot2.cheaddom) )
+    pot1 = pot1;
+    pot2 = pot2;
+elseif  isempty( myintersect(pot2.domain, pot1.cheaddom))
+    temppot = pot1;
+    pot1 = pot2;
+    pot2 = temppot;
+else
+    assert(0);
+    return;
+end
+
+domain = myunion(pot1.domain, pot2.domain);
+nodesizes = zeros(1,max(domain));
+nodesizes(pot2.ctaildom) = pot2.ctailsizes;
+nodesizes(pot2.cheaddom) = pot2.cheadsizes;
+nodesizes(pot2.ddom) = pot2.dsizes;
+nodesizes(pot1.ctaildom) = pot1.ctailsizes;
+nodesizes(pot1.cheaddom) = pot1.cheadsizes;
+nodesizes(pot1.ddom) = pot1.dsizes;
+
+dom_u = mysetdiff(pot2.ctaildom, pot1.cheaddom);
+if ~isempty(dom_u) & ~mysubset(dom_u, pot1.ctaildom)
+    pot1 = extension_pot(pot1, [], [], dom_u, nodesizes(dom_u));
+end
+
+dom_u = myunion(pot1.cheaddom, pot1.ctaildom);
+if ~isempty(dom_u) & ~mysubset(dom_u, pot2.ctaildom)
+    pot2 = extension_pot(pot2, [], [], dom_u, nodesizes(dom_u));
+end
+
+
+cheaddom = myunion(pot1.cheaddom, pot2.cheaddom);
+ctaildom = mysetdiff(myunion(pot1.ctaildom, pot2.ctaildom), cheaddom);
+cdom = myunion(cheaddom, ctaildom);
+ddom = mysetdiff(domain, cdom);
+dsizes = nodesizes(ddom);
+dsize = prod(nodesizes(ddom));
+cheadsizes = nodesizes(cheaddom);
+cheadsize = sum(nodesizes(cheaddom));
+ctailsizes = nodesizes(ctaildom);
+ctailsize = sum(nodesizes(ctaildom));
+
+r1 = pot1.cheadsize;
+s1 = pot1.ctailsize;
+scpot = cell(1, dsize);
+mask1 = [];
+mask2 = [];
+if ~isempty(pot1.ddom)
+    mask1 = find_equiv_posns(pot1.ddom, ddom);
+end
+if ~isempty(pot2.ddom)
+    mask2 = find_equiv_posns(pot2.ddom, ddom);
+end
+cmask1 = [];
+cmask2 = [];
+if ~isempty(pot1.cheaddom)
+    cmask1 = find_equiv_posns(pot1.cheaddom, cheaddom);
+end
+if ~isempty(pot2.cheaddom)
+    cmask2 = find_equiv_posns(pot2.cheaddom, cheaddom);
+end
+
+u1 = block(cmask1, cheadsizes);
+u2 = block(cmask2, cheadsizes);
+
+fmaskh = find_equiv_posns(pot1.cheaddom, pot2.ctaildom);
+fmaskt = find_equiv_posns(pot1.ctaildom, pot2.ctaildom);
+
+fh = block(fmaskh, pot2.ctailsizes);
+ft = block(fmaskt, pot2.ctailsizes);
+
+for i=1:dsize
+    sub = ind2subv(dsizes, i);
+    sub1 = sub(mask1);
+    sub2 = sub(mask2);
+    ind1 = subv2ind(pot1.dsizes, sub1);
+    ind2 = subv2ind(pot2.dsizes, sub2);
+    
+    if isempty(ind1)
+        ind1 = 1;
+    end
+    if isempty(ind2)
+        ind2 = 1;
+    end
+    potc1 = struct(pot1.scgpotc{ind1});
+    potc2 = struct(pot2.scgpotc{ind2});
+    p = potc1.p;
+    q = potc2.p;
+    ro = p*q;
+    
+    A = potc1.A;
+    B = potc1.B;
+    C = potc1.C;
+   
+    E = potc2.A;
+    F = potc2.B;
+    G = potc2.C;
+    
+    F1 = F(:, fh);
+    F2 = F(:, ft);
+    
+    if ~isempty(F1)
+        K1 = F1*A;
+        K2 = F1*B;
+        FCF = F1*C*F1';
+        FC = F1*C;
+        CFT = C*F1';
+    else
+        K1 = zeros(size(E));
+        K2 = zeros(size(F2));
+        FCF = zeros(size(G));
+        FC = zeros(size(C, 1), size(G, 2));
+        CFT = zeros(size(G, 2), size(C, 1));
+    end
+    
+    
+    U = zeros(cheadsize,1); 
+    W = zeros(cheadsize,cheadsize);
+    V = zeros(cheadsize,ctailsize); 
+    
+    if cheadsize > 0
+        U(u1) = A;
+        U(u2) = E + K1;
+        W(u1, u1) = C;
+        W(u2, u2) = G + FCF;
+        W(u1, u2) = CFT;
+        W(u2, u1) = FC;
+    else
+        U = zeros(cheadsize,1); 
+        W = zeros(cheadsize,cheadsize); 
+    end
+    if cheadsize > 0 | ctailsize > 0
+        if ~isempty(u1)
+            V(u1, :) = B;
+        else
+            V(u1, :) = zeros(potc1.cheadsize, ctailsize);
+        end
+        if ~isempty(u2)
+            V(u2, :) = F2 + K2;
+        else
+            V(u2, :) = zeros(potc2.cheadsize, ctailsize);
+        end
+    else
+        V = zeros(cheadsize,ctailsize); 
+    end
+
+    scpot{i} = scgcpot(cheadsize, ctailsize, ro, U, V, W);
+end
+
+pot = scgpot(ddom, cheaddom, ctaildom, nodesizes, scpot);