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

13 files changed, 172 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries
new file mode 100644
index 00000000..45d8ee0d
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries
@@ -0,0 +1,6 @@
+/convert_to_pot.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/convert_to_table.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/get_field.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/set_fields.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/tabular_kernel.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries.Log
new file mode 100644
index 00000000..24f16336
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/Old////
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Repository
new file mode 100644
index 00000000..61f9dcd8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@tabular_kernel
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Entries
new file mode 100644
index 00000000..b6c6e11c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Entries
@@ -0,0 +1,2 @@
+/tabular_kernel.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Repository
new file mode 100644
index 00000000..d2036843
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@tabular_kernel/Old
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/tabular_kernel.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/tabular_kernel.m
new file mode 100644
index 00000000..99f74450
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/Old/tabular_kernel.m
@@ -0,0 +1,45 @@
+function K = tabular_kernel(fg, self)
+% TABULAR_KERNEL Make a table-based local kernel (discrete potential)
+% K = tabular_kernel(fg, self)
+%
+% fg is a factor graph
+% self is the number of a representative domain
+%
+% Use 'set_params_kernel' to adjust the following fields
+%   table - a q[1]xq[2]x... array, where q[i] is the number of values for i'th node
+%       in this domain [default: random values from [0,1], which need not sum to 1]
+
+
+if nargin==0
+  % This occurs if we are trying to load an object from a file.
+  K = init_fields;
+  K = class(K, 'tabular_kernel');
+  return;
+elseif isa(fg, 'tabular_kernel')
+  % This might occur if we are copying an object.
+  K = fg;
+  return;
+end
+K = init_fields;
+
+ns = fg.node_sizes;
+dom = fg.doms{self};
+% we don't store the actual domain since it may vary due to parameter tieing
+K.sz = ns(dom);
+K.table = myrand(K.sz);
+
+K = class(K, 'tabular_kernel');
+
+
+%%%%%%%
+
+
+function K = init_fields()
+% This ensures we define the fields in the same order 
+% no matter whether we load an object from a file,
+% or create it from scratch. (Matlab requires this.)
+
+K.table = [];
+K.sz = [];
+
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_pot.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_pot.m
new file mode 100644
index 00000000..8f9adff1
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_pot.m
@@ -0,0 +1,37 @@
+function pot = convert_to_pot(CPD, pot_type, domain, evidence)
+% CONVERT_TO_POT Convert a tabular CPD to one or more potentials
+% pot = convert_to_pot(CPD, pot_type, domain, evidence)
+
+% This is the same as discrete_CPD/convert_to_pot,
+% except we didn't want to the kernel to inherit methods like sample_node etc.
+
+sz = CPD.sz;
+ns = zeros(1, max(domain));
+ns(domain) = sz;
+
+odom = domain(~isemptycell(evidence(domain)));
+T = convert_to_table(CPD, domain, evidence);
+
+switch pot_type
+ case 'u',
+  pot = upot(domain, sz, T, 0*myones(sz));  
+ case 'd',
+  ns(odom) = 1;
+  pot = dpot(domain, ns(domain), T);          
+ case 'c',
+  % Since we want the output to be a Gaussian, the whole family must be observed.
+  % In other words, the potential is really just a constant.
+  p = T.p;
+  %p = prob_node(CPD, evidence(domain(end)), evidence(domain(1:end-1)));
+  ns(domain) = 0;
+  pot = cpot(domain, ns(domain), log(p));       
+ case 'cg',
+  T = T(:);
+  ns(odom) = 1;
+  can = cell(1, length(T));
+  for i=1:length(T)
+    can{i} = cpot([], [], log(T(i)));
+  end
+  pot = cgpot(domain, [], ns, can);   
+end
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_table.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_table.m
new file mode 100644
index 00000000..30703f3a
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/convert_to_table.m
@@ -0,0 +1,13 @@
+function T = convert_to_table(CPD, domain, evidence)
+% CONVERT_TO_TABLE Convert a discrete CPD to a table
+% T = convert_to_table(CPD, domain, evidence)
+%
+% We convert the CPD to a CPT, and then lookup the evidence on the discrete parents.
+% The resulting table can easily be converted to a potential.
+
+CPT = CPD.table;
+odom = domain(~isemptycell(evidence(domain)));
+vals = cat(1, evidence{odom});
+map = find_equiv_posns(odom, domain);
+index = mk_multi_index(length(domain), map, vals);
+T = CPT(index{:});               
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/get_field.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/get_field.m
new file mode 100644
index 00000000..3319eadb
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/get_field.m
@@ -0,0 +1,11 @@
+function val = get_params_kernel(K, name)
+% GET_PARAMS_KERNEL Accessor function for a field (tabular_kernel)
+% val = get_params_kernel(K, name)
+%
+% e.g., get_params_kernel(K, 'table')
+
+switch name
+ case 'table', val = K.table;
+ otherwise,
+  error(['invalid field name ' name]);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/set_fields.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/set_fields.m
new file mode 100644
index 00000000..2f7ac435
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/set_fields.m
@@ -0,0 +1,13 @@
+function K = set_params_kernel(K, name, val)
+% SET_PARAMS_KERNEL Accessor function for a field (table_kernel)
+% K = set_params_kernel(K, name, val)
+%
+% e.g., K = set_params_kernel(K, 'table', rand(2,3,2)) for a kernel on 3 nodes with 2,3,2 values each
+
+% We should check if the arguments are valid...
+
+switch name
+ case 'table', K.table = val;
+ otherwise,
+  error(['invalid field name ' name]);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/tabular_kernel.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/tabular_kernel.m
new file mode 100644
index 00000000..74a64450
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_kernel/tabular_kernel.m
@@ -0,0 +1,40 @@
+function K = tabular_kernel(sz, table)
+% TABULAR_KERNEL Make a table-based local kernel (discrete potential)
+% K = tabular_kernel(sz, table)
+%
+% sz(i) is the number of values the i'th member of this kernel can have
+% table is an optional array of size sz[1] x sz[2] x... [default: random]
+
+if nargin==0
+  % This occurs if we are trying to load an object from a file.
+  K = init_fields;
+  K = class(K, 'tabular_kernel');
+  return;
+elseif isa(sz, 'tabular_kernel')
+  % This might occur if we are copying an object.
+  K = sz;
+  return;
+end
+K = init_fields;
+
+if nargin < 2, table = myrand(sz); end
+
+K.sz = sz;
+K.table = table;
+
+K = class(K, 'tabular_kernel');
+
+
+%%%%%%%
+
+
+function K = init_fields()
+% This ensures we define the fields in the same order 
+% no matter whether we load an object from a file,
+% or create it from scratch. (Matlab requires this.)
+
+K.sz = [];
+K.table = [];
+
+
+