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, 76 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@hhmmF_CPD/Old/hhmmF_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@hhmmF_CPD/Old/hhmmF_CPD.m
new file mode 100644
index 00000000..4fdd9bc9
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@hhmmF_CPD/Old/hhmmF_CPD.m
@@ -0,0 +1,76 @@
+function CPD = hhmmF_CPD(bnet, self, Qnodes, d, D, varargin)
+% HHMMF_CPD Make the CPD for an F node at depth D of a D-level hierarchical HMM
+% CPD = hhmmF_CPD(bnet, self, Qnodes, d, D, ...)
+%
+%    Q(d-1)
+%          \
+%           \
+%           F(d)
+%         /   |
+%        /    |
+%    Q(d)  F(d+1)
+%
+% We assume nodes are ordered (numbered) as follows:
+% Q(1), ... Q(d), F(d+1), F(d)
+%
+% F(d)=2 means level d has finished. The prob this happens depends on Q(d)
+% and optionally on Q(d-1), Q(d=1), ..., Q(1).
+% Also, level d can only finish if the level below has finished
+% (hence the F(d+1) -> F(d) arc).
+%
+% If d=D, there is no F(d+1), so F(d) is just a regular tabular_CPD.
+% If all models always finish in the same state (e.g., their last),
+% we don't need to condition on the state of parent models (Q(d-1), ...)
+%
+% optional args [defaults]
+%
+% termprob - termprob(k,i,2) = prob finishing given Q(d)=i and Q(1:d-1)=k [ finish in last state ]
+%
+% hhmmF_CPD is a subclass of tabular_CPD so we inherit inference methods like CPD_to_pot, etc.
+%
+% We create an isolated tabular_CPD with no F parent to learn termprob
+% so we can avail of e.g., entropic or Dirichlet priors.
+%
+% For details, see "Linear-time inference in hierarchical HMMs", Murphy and Paskin, NIPS'01.
+
+
+ps = parents(bnet.dag, self);
+Qps = myintersect(ps, Qnodes);
+F = mysetdiff(ps, Qps);
+CPD.Q = Qps(end); % Q(d)
+assert(CPD.Q == Qnodes(d));
+CPD.Qps = Qps(1:end-1); % all Q parents except Q(d), i.e., calling context
+
+ns = bnet.node_sizes(:);
+CPD.Qsizes = ns(Qnodes);
+CPD.d = d;
+CPD.D = D;
+
+Qsz = ns(CPD.Q);
+Qpsz = prod(ns(CPD.Qps));
+
+% set default arguments
+p = 0.9;
+%termprob(k,i,t) Might terminate if i=Qsz; will not terminate if i<Qsz
+termprob = zeros(Qpsz, Qsz, 2);
+termprob(:, Qsz, 2) = p; 
+termprob(:, Qsz, 1) = 1-p; 
+termprob(:, 1:(Qsz-1), 1) = 1; 
+    
+for i=1:2:length(varargin)
+  switch varargin{i},
+   case 'termprob', termprob = varargin{i+1}; 
+   otherwise, error(['unrecognized argument ' varargin{i}])
+  end
+end
+
+ps = [CPD.Qps CPD.Q];
+% ns(self) = 2 since this is an F node
+CPD.sub_CPD_term = mk_isolated_tabular_CPD(ps, ns([ps self]), {'CPT', termprob});
+S = struct(CPD.sub_CPD_term);
+CPD.termprob = S.CPT;
+
+CPD = class(CPD, 'hhmmF_CPD', tabular_CPD(bnet, self));
+
+CPD = update_CPT(CPD);
+