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

19 files changed, 176 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Entries b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Entries
new file mode 100644
index 00000000..d37ad7eb
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Entries
@@ -0,0 +1,17 @@
+/approxeq_pot.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/display.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/divide_by_pot.m/1.1.1.1/Thu Aug  5 15:25:08 2004//
+/domain_pot.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/dpot.m/1.1.1.1/Tue Oct  1 19:04:44 2002//
+/dpot_to_table.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/find_most_prob_entry.m/1.1.1.1/Sun Jun 16 19:06:20 2002//
+/get_fields.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/marginalize_pot.m/1.1.1.1/Wed Aug  4 19:59:14 2004//
+/multiply_by_pot.m/1.1.1.1/Wed Aug  4 19:59:14 2004//
+/multiply_pots.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/normalize_pot.m/1.1.1.1/Wed Aug  4 15:54:48 2004//
+/pot_to_marginal.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/set_domain_pot.m/1.1.1.1/Wed May 29 15:59:58 2002//
+/subsasgn.m/1.1.1.1/Wed Apr 27 18:34:48 2005//
+/subsref.m/1.1.1.1/Wed Apr 27 18:34:48 2005//
+D
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Repository b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Repository
new file mode 100644
index 00000000..485f27df
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/potentials/@dpot
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Root b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/approxeq_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/approxeq_pot.m
new file mode 100644
index 00000000..b0f8d0ed
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/approxeq_pot.m
@@ -0,0 +1,5 @@
+function p = approxeq_pot(A, B, tol)
+
+if nargin < 3, tol = 1e-3; end
+
+p = approxeq(A.T, B.T, tol);
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/display.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/display.m
new file mode 100644
index 00000000..1b0647bb
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/display.m
@@ -0,0 +1,4 @@
+function display(pot)
+
+disp('discrete potential object');
+disp(struct(pot));
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/divide_by_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/divide_by_pot.m
new file mode 100644
index 00000000..aae4790c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/divide_by_pot.m
@@ -0,0 +1,14 @@
+function Tbig = divide_by_pot(Tbig, Tsmall)
+% DIVIDE_BY_POT Tbig /= Tsmall
+% Tbig = divide_by_pot(Tbig, Tsmall)
+%
+% Tsmall's domain must be a subset of Tbig's domain.
+
+%process sparse dpot, we do not concern only one of the two pots is sparse
+if issparse(Tbig.T) && issparse(Tsmall.T)
+   Tbig.T = divide_by_sparse_table(Tbig.T, Tbig.domain, Tbig.sizes, Tsmall.T, Tsmall.domain, Tsmall.sizes);
+else
+   Tbig.T = divide_by_table(Tbig.T, Tbig.domain, Tbig.sizes, Tsmall.T, Tsmall.domain, Tsmall.sizes);
+end
+
+
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/domain_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/domain_pot.m
new file mode 100644
index 00000000..a67cef02
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/domain_pot.m
@@ -0,0 +1,5 @@
+function dom = domain_pot(pot)
+% DOMAIN_POT Return the domain of this dpot.
+% dom = domain_pot(pot)
+
+dom = pot.domain;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot.m
new file mode 100644
index 00000000..74b5dd9e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot.m
@@ -0,0 +1,26 @@
+function pot = dpot(domain, sizes, T)
+% DPOT Make a discrete (sparse) potential.
+% pot = dpot(domain, sizes, T, spar)
+%
+% sizes(i) is the size of the i'th domain element.
+% T defaults to all 1s.
+
+%assert(length(sizes) == length(domain));
+
+pot.domain = domain(:)'; % so we can see it when we display
+if nargin < 3
+  pot.T = myones(sizes);
+  %pot.T = ones(1,prod(sizes)); % 1D vector
+else 
+   if isempty(T)
+      pot.T = [];
+   else
+      if issparse(T)
+         pot.T = T;   
+      else
+         pot.T = myreshape(T, sizes);  
+      end
+   end
+end
+pot.sizes = sizes(:)';
+pot = class(pot, 'dpot');
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot_to_table.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot_to_table.m
new file mode 100644
index 00000000..bd2d3d98
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/dpot_to_table.m
@@ -0,0 +1,3 @@
+function T = dpot_to_table(pot)
+
+T = pot.T;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/find_most_prob_entry.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/find_most_prob_entry.m
new file mode 100644
index 00000000..d30561a8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/find_most_prob_entry.m
@@ -0,0 +1,10 @@
+function [indices, pot] = find_most_prob_entry(pot)
+% function [indices, pot] = find_most_prob_entry(pot)
+% function [indices, pot] = find_most_prob_entry(pot)
+% Find the indices of the argmax, and set all other enties to 0.
+
+%indices = argmax(pot.T);
+[m i] = max(pot.T(:));
+indices = ind2subv(pot.sizes, i);
+pot.T = 0*myones(pot.sizes);
+pot.T(i) = m;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/get_fields.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/get_fields.m
new file mode 100644
index 00000000..2400bc99
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/get_fields.m
@@ -0,0 +1,13 @@
+function val = get_params(pot, name)
+% GET_PARAMS Accessor function for a field (dpot)
+% val = get_params(pot, name)
+%
+% e.g., get_params(pot, 'table') or 'domain'
+
+switch name
+ case 'table', val = pot.T;
+ case 'domain', val = pot.domain;
+ otherwise,
+  error(['invalid field name ' name]);
+end
+
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/marginalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/marginalize_pot.m
new file mode 100644
index 00000000..d38c5c82
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/marginalize_pot.m
@@ -0,0 +1,17 @@
+function smallpot = marginalize_pot(bigpot, onto, maximize)
+% MARGINALIZE_POT Marginalize a dpot onto a smaller domain.
+% smallpot = marginalize_pot(bigpot, onto, maximize)
+%
+% 'onto' must be in ascending order.
+
+if nargin < 3, maximize = 0; end
+
+ns = zeros(1, max(bigpot.domain));
+ns(bigpot.domain) = bigpot.sizes;
+%assert(isequal(bigpot.sizes, mysize(bigpot.T))); % may fail if there are trailing dimensions of size 1
+if issparse(bigpot.T)
+   smallT = marg_sparse_table(bigpot.T, bigpot.domain, bigpot.sizes, onto, maximize);
+else 
+   smallT = marg_table(bigpot.T, bigpot.domain, bigpot.sizes, onto, maximize);
+end
+smallpot = dpot(onto, ns(onto), smallT);
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_by_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_by_pot.m
new file mode 100644
index 00000000..ad7caaa7
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_by_pot.m
@@ -0,0 +1,13 @@
+function Tbig = multiply_by_pot(Tbig, Tsmall)
+% MULTIPLY_BY_POT Tbig *= Tsmall
+% Tbig = multiply_by_pot(Tbig, Tsmall)
+%
+% Tsmall's domain must be a subset of Tbig's domain.
+
+%process sparse dpot, we do not consider only one of the two pots is sparse
+if issparse(Tbig.T) && issparse(Tsmall.T)
+   Tbig.T = mult_by_sparse_table(Tbig.T, Tbig.domain, Tbig.sizes, Tsmall.T, Tsmall.domain, Tsmall.sizes);
+else 
+   Tbig.T = mult_by_table(Tbig.T, Tbig.domain, Tbig.sizes, Tsmall.T, Tsmall.domain, Tsmall.sizes);
+end
+
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_pots.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_pots.m
new file mode 100644
index 00000000..0188f01b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/multiply_pots.m
@@ -0,0 +1,12 @@
+function T = multiply_pots(T1, T2)
+% MULTIPLY_POTS Multiply a pair of dpots together pointwise.
+% T = multiply_pots(pots)
+
+dom = myunion(T1.domain, T2.domain);
+%ns = sparse(1, max(dom)); % causes problems in myreshape on NT
+ns = zeros(1, max(dom));
+ns(T1.domain) = T1.sizes;
+ns(T2.domain) = T2.sizes;
+T = dpot(dom, ns(dom));
+T = multiply_by_pot(T, T1);
+T = multiply_by_pot(T, T2);   
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/normalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/normalize_pot.m
new file mode 100644
index 00000000..1bc43cdb
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/normalize_pot.m
@@ -0,0 +1,12 @@
+function [pot, loglik] = normalize_pot(pot)
+% NORMALIZE_POT Convert the discrete potential Pr(X,E) into Pr(X|E) and return log Pr(E).
+% [pot, loglik] = normalize_pot(pot)
+
+if isempty(pot.T)  %add to process sparse
+   loglik = 0;
+   return;
+end
+[pot.T, lik] = normalise(pot.T);
+loglik = log(lik + (lik==0)*eps);
+
+      
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/pot_to_marginal.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/pot_to_marginal.m
new file mode 100644
index 00000000..36ed70ea
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/pot_to_marginal.m
@@ -0,0 +1,12 @@
+function m = pot_to_marginal(pot)
+% POT_TO_MARGINAL Convert a dpot to a marginal structure.
+% m = pot_to_marginal(pot)
+
+m.domain = pot.domain;
+m.T = pot.T;
+m.mu = [];
+m.Sigma = [];  
+
+%if isvector(m.T)
+%  m.T = m.T(:);
+%end
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/set_domain_pot.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/set_domain_pot.m
new file mode 100644
index 00000000..2178c51d
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/set_domain_pot.m
@@ -0,0 +1,5 @@
+function pot = set_domain_pot(pot, domain)
+% SET_DOMAIN_POT Change the domain of a potential (dpot)
+% pot = set_domain_pot(pot, domain)
+
+pot.domain = domain;
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/subsasgn.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/subsasgn.m
new file mode 100644
index 00000000..90d43d70
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/subsasgn.m
@@ -0,0 +1,3 @@
+function B = subsasgn(A, S, B)
+
+B = builtin('subsasgn', A, S, B);
diff --git a/sourcecodes/bnt-master/BNT/potentials/@dpot/subsref.m b/sourcecodes/bnt-master/BNT/potentials/@dpot/subsref.m
new file mode 100644
index 00000000..4a48bffe
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/potentials/@dpot/subsref.m
@@ -0,0 +1,3 @@
+function B = subsref(A, S)
+
+B = builtin('subsref', A, S);