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, 79 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/noisyor_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/noisyor_CPD.m
new file mode 100644
index 00000000..aecf9b6d
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/noisyor_CPD.m
@@ -0,0 +1,79 @@
+function CPD = noisyor_CPD(bnet, self, leak_inhibit, inhibit)
+% NOISYOR_CPD Make a noisy-or CPD
+% CPD = NOISYOR_CPD(BNET, NODE_NUM, LEAK_INHIBIT, INHIBIT)
+%
+% A noisy-or node turns on if any of its parents are on, provided they are not inhibited.
+% The prob. that the i'th parent gets inhibited (flipped from 1 to 0) is inhibit(i).
+% The prob that the leak node (a dummy parent that is always on) gets inhibit is leak_inhibit.
+% These params default to random values if omitted.
+%
+% Example: suppose C has parents A and B, and the
+% link of A->C fails with prob pA and the link B->C fails with pB.
+% Then the noisy-OR gate defines the following distribution
+%
+%  A  B  P(C=0)
+%  0  0  1.0
+%  1  0  pA
+%  0  1  pB
+%  1  1  pA * PB
+%
+% Currently, learning is not supported for noisy-or nodes
+% (since the M step is somewhat complicated).
+%
+% For simple generalizations of the noisy-OR model, see e.g.,
+% - Srinivas, "A generalization of the noisy-OR model", UAI 93
+% - Meek and Heckerman, "Learning Causal interaction models", UAI 97.
+  
+
+
+if nargin==0
+  % This occurs if we are trying to load an object from a file.
+  CPD = init_fields;
+  CPD = class(CPD, 'noisyor_CPD', discrete_CPD(1, []));
+  return;
+elseif isa(bnet, 'noisyor_CPD')
+  % This might occur if we are copying an object.
+  CPD = bnet;
+  return;
+end
+CPD = init_fields;
+
+
+ps = parents(bnet.dag, self);
+fam = [ps self];
+ns = bnet.node_sizes;
+assert(all(ns(fam)==2));
+assert(isempty(myintersect(fam, bnet.cnodes)));
+
+if nargin < 3, leak_inhibit = rand(1, 1); end
+if nargin < 4, inhibit = rand(1, length(ps)); end
+
+CPD.self = self;
+CPD.inhibit = inhibit;
+CPD.leak_inhibit = leak_inhibit;
+
+
+% For BIC
+CPD.nparams = 0;
+CPD.nsamples = 0;
+
+CPD.CPT = []; % cached copy, to speed up CPD_to_CPT
+
+clamped = 1;
+CPD = class(CPD, 'noisyor_CPD', discrete_CPD(clamped, ns([ps self])));
+
+
+
+%%%%%%%%%%%
+
+function CPD = 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.)
+
+CPD.self = [];
+CPD.inhibit = [];
+CPD.leak_inhibit = [];
+CPD.nparams = [];
+CPD.nsamples = [];
+CPD.CPT = [];