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

16 files changed, 116 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries
new file mode 100644
index 00000000..47f0e262
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries
@@ -0,0 +1,8 @@
+/README/1.1.1.1/Wed May 29 15:59:52 2002//
+/adjustable_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/display.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/generic_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/learn_params.m/1.1.1.1/Thu Jun 10 01:53:20 2004//
+/log_prior.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/set_clamped.m/1.1.1.1/Wed May 29 15:59:52 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log
new file mode 100644
index 00000000..24f16336
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/Old////
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository
new file mode 100644
index 00000000..19ab61e0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@generic_CPD
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m
new file mode 100644
index 00000000..a73d073b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m
@@ -0,0 +1,26 @@
+function score = BIC_score_CPD(CPD, fam, data, ns, cnodes)
+% BIC_score_CPD Compute the BIC score of a generic CPD
+% score = BIC_score_CPD(CPD, fam, data, ns, cnodes)
+%
+% We assume this node has a maximize_params method
+
+ncases = size(data, 2);
+CPD = reset_ess(CPD);
+% make a fully observed joint distribution over the family
+fmarginal.domain = fam;
+fmarginal.T = 1;
+fmarginal.mu = [];
+fmarginal.Sigma = [];
+if ~iscell(data)
+  cases = num2cell(data);
+else
+  cases = data;
+end
+for m=1:ncases
+  CPD = update_ess(CPD, fmarginal, cases(:,m), ns, cnodes);
+end
+CPD = maximize_params(CPD);
+self = fam(end);
+ps = fam(1:end-1);
+L = log_prob_node(CPD, cases(self,:), cases(ps,:));
+score = L - 0.5*CPD.nparams*log(ncases);
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m
new file mode 100644
index 00000000..47daac88
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m
@@ -0,0 +1,16 @@
+function pots = CPD_to_dpots(CPD, domain, ns, cnodes, evidence)
+% CPD_TO_DPOTS Convert the CPD to several discrete potentials, for different instantiations (generic)
+% pots = CPD_to_dpots(CPD, domain, ns, cnodes, evidence)
+%
+% domain(:,i) is the domain of the i'th instantiation of CPD.
+% node_sizes(i) is the size of node i.
+% cnodes = all the cts nodes
+% evidence{i} is the evidence on the i'th node.
+%
+% This just calls CPD_to_dpot for each domain.
+    
+nCPDs = size(domain,2);
+pots = cell(1,nCPDs);
+for i=1:nCPDs
+  pots{i} = CPD_to_dpot(CPD, domain(:,i), ns, cnodes, evidence);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries
new file mode 100644
index 00000000..505b09aa
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries
@@ -0,0 +1,3 @@
+/BIC_score_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/CPD_to_dpots.m/1.1.1.1/Wed May 29 15:59:52 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository
new file mode 100644
index 00000000..96b94fc8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@generic_CPD/Old
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README
new file mode 100644
index 00000000..7a9b164b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README
@@ -0,0 +1,2 @@
+A generic CPD implements general purpose functions like 'display',
+that subtypes can inherit.
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m
new file mode 100644
index 00000000..78feea55
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m
@@ -0,0 +1,5 @@
+function p = adjustable_CPD(CPD)
+% ADJUSTABLE_CPD Does this CPD have any adjustable params? (generic)
+% p = adjustable_CPD(CPD)
+   
+p = ~CPD.clamped;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m
new file mode 100644
index 00000000..001ab2c9
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m
@@ -0,0 +1,3 @@
+function display(CPD)
+
+disp(struct(CPD));
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m
new file mode 100644
index 00000000..66a85e6a
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m
@@ -0,0 +1,8 @@
+function CPD = generic_CPD(clamped)
+% GENERIC_CPD Virtual constructor for generic CPD
+% CPD = discrete_CPD(clamped)
+
+if nargin < 1, clamped = 0; end
+
+CPD.clamped = clamped;
+CPD = class(CPD, 'generic_CPD');
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m
new file mode 100644
index 00000000..c36eb004
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m
@@ -0,0 +1,32 @@
+function CPD = learn_params(CPD, fam, data, ns, cnodes)
+% LEARN_PARAMS Compute the maximum likelihood estimate of the params of a generic CPD given complete data
+% CPD = learn_params(CPD, fam, data, ns, cnodes)
+%
+% data(i,m) is the value of node i in case m (can be cell array).
+% We assume this node has a maximize_params method.
+
+%error('no longer supported') % KPM 1 Feb 03
+
+if 1
+ncases = size(data, 2);
+CPD = reset_ess(CPD);
+% make a fully observed joint distribution over the family
+fmarginal.domain = fam;
+fmarginal.T = 1;
+fmarginal.mu = [];
+fmarginal.Sigma = [];
+if ~iscell(data)
+  cases = num2cell(data);
+else
+  cases = data;
+end
+hidden_bitv = zeros(1, max(fam));
+for m=1:ncases
+  % specify (as a bit vector) which elements in the family domain are hidden
+  hidden_bitv = zeros(1, max(fmarginal.domain));
+  ev = cases(:,m);
+  hidden_bitv(find(isempty(evidence)))=1;
+  CPD = update_ess(CPD, fmarginal, ev, ns, cnodes, hidden_bitv);
+end
+CPD = maximize_params(CPD);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m
new file mode 100644
index 00000000..a73dcde0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m
@@ -0,0 +1,5 @@
+function L = log_prior(CPD)
+% LOG_PRIOR Return log P(theta) for a generic CPD  - we return 0
+% L = log_prior(CPD)
+
+L = 0;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m
new file mode 100644
index 00000000..5ad68037
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m
@@ -0,0 +1,3 @@
+function CPD = set_clamped(CPD, bit)
+
+CPD.clamped = bit;