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

8 files changed, 156 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CPD_to_CPT.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CPD_to_CPT.m
new file mode 100644
index 00000000..1942f60f
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CPD_to_CPT.m
@@ -0,0 +1,35 @@
+function CPT = CPD_to_CPT(CPD)
+% Compute the big CPT for an HHMM Q node (including F parents)
+% by combining internal transprob and startprob
+% function CPT = CPD_to_CPT(CPD)
+
+Qsz = CPD.Qsz;
+
+if ~isempty(CPD.Fbelow_ndx)
+  if ~isempty(CPD.Fself_ndx) % general case
+    error('not implemented')
+  else % no F from self, hence no startprob (top level)
+    nps = length(CPD.dom_sz)-1; % num parents
+    CPT = 0*myones(CPD.dom_sz);
+    % when Fself=1, the CPT(i,j) = delta(i,j) for all k
+    for k=1:prod(CPD.Qpsizes)
+      Qps_vals = ind2subv(CPD.Qpsizes, k);
+      ndx = mk_multi_index(nps+1, [CPD.Fbelow_ndx CPD.Qps_ndx], [1 Qps_vals]);
+      CPT(ndx{:}) = eye(Qsz); % CPT(:,2,k,:) or CPT(:,k,2,:) etc
+    end
+    ndx = mk_multi_index(nps+1, CPD.Fbelow_ndx, 2);
+    CPT(ndx{:}) = CPD.transprob; % we assume transprob is in topo order
+  end
+else % no F signal from below
+  if ~isempty(CPD.Fself_ndx) % bottom level
+    nps = length(CPD.dom_sz)-1; % num parents
+    CPT = 0*myones(CPD.dom_sz);
+    ndx = mk_multi_index(nps+1, CPD.Fself_ndx, 1);
+    CPT(ndx{:}) = CPD.transprob;
+    ndx = mk_multi_index(nps+1, CPD.Fself_ndx, 2);
+    CPT(ndx{:}) = CPD.startprob;
+  else % no F from self
+    error('An hhmmQ node without any F parents is just a tabular_CPD')
+  end
+end
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Entries
new file mode 100644
index 00000000..5e60dca6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Entries
@@ -0,0 +1,6 @@
+/CPD_to_CPT.m/1.1.1.1/Tue Sep 24 12:46:46 2002//
+/hhmm2Q_CPD.m/1.1.1.1/Tue Sep 24 22:34:40 2002//
+/maximize_params.m/1.1.1.1/Tue Sep 24 22:44:36 2002//
+/reset_ess.m/1.1.1.1/Tue Sep 24 22:36:16 2002//
+/update_ess.m/1.1.1.1/Tue Sep 24 22:43:30 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Repository
new file mode 100644
index 00000000..f66442c4
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@hhmm2Q_CPD
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/hhmm2Q_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/hhmm2Q_CPD.m
new file mode 100644
index 00000000..c1a0cc20
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/hhmm2Q_CPD.m
@@ -0,0 +1,65 @@
+function CPD = hhmm2Q_CPD(bnet, self, varargin)
+% HHMMQ_CPD Make the CPD for a Q node in a 2 level hierarchical HMM
+% CPD = hhmmQ_CPD(bnet, self, ...)
+%
+%  Fself(t-1)   Qps
+%           \    |
+%            \   v
+%  Qold(t-1) ->  Q(t)
+%            /
+%           /
+%  Fbelow(t-1) 
+%
+%
+% optional args [defaults]
+%
+% Fself - node number <= ss
+% Fbelow  - node number  <= ss
+% Qps - node numbers (all <= 2*ss) - uses 2TBN indexing
+% transprob - CPT for when Fbelow=2 and Fself=1
+% startprob - CPT for when Fbelow=2 and Fself=2
+% If Fbelow=1, we cannot change state.
+
+ss = bnet.nnodes_per_slice;
+ns = bnet.node_sizes(:);
+
+% set default arguments
+Fself = [];
+Fbelow = [];
+Qps = [];
+startprob = [];
+transprob = [];
+
+for i=1:2:length(varargin)
+  switch varargin{i},
+   case 'Fself', Fself = varargin{i+1};
+   case 'Fbelow', Fbelow = varargin{i+1};
+   case 'Qps', Qps = varargin{i+1};
+   case 'transprob', transprob = varargin{i+1}; 
+   case 'startprob',  startprob = varargin{i+1}; 
+  end
+end
+
+ps = parents(bnet.dag, self);
+old_self = self-ss;
+ndsz = ns(:)';
+CPD.dom_sz = [ndsz(ps) ns(self)];
+CPD.Fself_ndx = find_equiv_posns(Fself, ps);
+CPD.Fbelow_ndx = find_equiv_posns(Fbelow, ps);
+Qps = mysetdiff(ps, [Fself Fbelow old_self]);
+CPD.Qps_ndx = find_equiv_posns(Qps, ps);
+CPD.old_self_ndx = find_equiv_posns(old_self, ps);
+
+Qps = ps(CPD.Qps_ndx);
+CPD.Qsz = ns(self);
+CPD.Qpsizes = ns(Qps);
+
+CPD.transprob = transprob;
+CPD.startprob = startprob;
+CPD.start_counts = [];
+CPD.trans_counts = [];
+
+CPD = class(CPD, 'hhmm2Q_CPD', discrete_CPD(0, CPD.dom_sz));
+
+
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/maximize_params.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/maximize_params.m
new file mode 100644
index 00000000..9fe4d0ac
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/maximize_params.m
@@ -0,0 +1,10 @@
+function CPD = maximize_params(CPD, temp)
+% MAXIMIZE_PARAMS Set the params of a hhmmQ node to their ML/MAP values.
+% CPD = maximize_params(CPD, temperature)
+
+if sum(CPD.start_counts(:)) > 0
+  CPD.startprob = mk_stochastic(CPD.start_counts);
+end
+if sum(CPD.trans_counts(:)) > 0
+  CPD.transprob = mk_stochastic(CPD.trans_counts);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/reset_ess.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/reset_ess.m
new file mode 100644
index 00000000..8204c167
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/reset_ess.m
@@ -0,0 +1,12 @@
+function CPD = reset_ess(CPD)
+% RESET_ESS Reset the Expected Sufficient Statistics of a hhmm2 Q node.
+% CPD = reset_ess(CPD)
+
+domsz = CPD.dom_sz;
+domsz(CPD.Fself_ndx) = 1;
+domsz(CPD.Fbelow_ndx) = 1;
+Qdom_sz = domsz;
+Qdom_sz(Qdom_sz==1)=[]; % get rid of dimensions of size 1
+
+CPD.start_counts = zeros(Qdom_sz);
+CPD.trans_counts = zeros(Qdom_sz);
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/update_ess.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/update_ess.m
new file mode 100644
index 00000000..1a15d26c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmm2Q_CPD/update_ess.m
@@ -0,0 +1,26 @@
+function CPD = update_ess(CPD, fmarginal, evidence, ns, cnodes, hidden_bitv)
+
+marg = add_ev_to_dmarginal(fmarginal, evidence,  ns);
+
+nps = length(CPD.dom_sz)-1; % num parents
+
+if ~isempty(CPD.Fbelow_ndx)
+  if ~isempty(CPD.Fself_ndx) % general case
+    ndx = mk_multi_index(nps+1, [CPD.Fbelow_ndx CPD.Fself_ndx], [2 1]);
+    CPD.trans_counts = CPD.trans_counts + squeeze(marg.T(ndx{:}));
+    ndx = mk_multi_index(nps+1, [CPD.Fbelow_ndx CPD.Fself_ndx], [2 2]);
+    CPD.start_counts = CPD.start_counts + squeeze(marg.T(ndx{:}));
+  else % no F from self, hence no startprob (top level)
+    ndx = mk_multi_index(nps+1, CPD.Fbelow_ndx, 2);
+    CPD.trans_counts = CPD.trans_counts + squeeze(marg.T(ndx{:}));
+  end
+else % no F signal from below
+  if ~isempty(CPD.Fself_ndx) % self F (bottom level)
+    ndx = mk_multi_index(nps+1, CPD.Fself_ndx, 1);
+    CPD.trans_counts = CPD.trans_counts + squeeze(marg.T(ndx{:}));
+    ndx = mk_multi_index(nps+1, CPD.Fself_ndx, 2);
+    CPD.start_counts = CPD.start_counts + squeeze(marg.T(ndx{:}));
+  else % no F from self or below
+    error('no F signal')
+  end
+end