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, 251 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m
new file mode 100644
index 00000000..93a6dcef
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m
@@ -0,0 +1,34 @@
+function CPT = CPD_to_CPT(CPD)
+% CPD_TO_CPT Convert the discrete CPD to tabular form (noisyor)
+% CPT = CPD_to_CPT(CPD)
+%
+% CPT(U1,...,Un, X) = Pr(X|U1,...,Un) where the Us are the parents (excluding leak).
+
+if ~isempty(CPD.CPT)
+  CPT = CPD.CPT; % remember to flush cache if params change (e.g., during learning)
+  return;
+end
+
+q = [CPD.leak_inhibit CPD.inhibit(:)'];
+% q(i) is the prob. that the i'th parent will be inhibited (flipped from 1 to 0).
+% q(1) is the leak inhibition probability, and length(q) = n + 1.
+
+if length(q)==1
+  CPT = [q  1-q];
+  return;
+end
+
+n = length(q);
+Bn = ind2subv(2*ones(1,n), 1:(2^n))-1;  % all n bit vectors, with the left most column toggling fastest (LSB)
+CPT = zeros(2^n, 2);
+% Pr(X=0 | U_1 .. U_n) = prod_{i: U_i = on} q_i =  prod_i q_i ^ U_i = exp(u' * log(q_i))
+% This method is problematic when q contains zeros
+
+Q = repmat(q(:)', 2^n, 1);
+Q(logical(~Bn)) = 1;
+CPT(:,1) = prod(Q,2);
+CPT(:,2) = 1-CPT(:,1);
+
+CPT = reshape(CPT(2:2:end), 2*ones(1,n)); % skip cases in which the leak is off       
+
+CPD.CPT = CPT;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m~ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m~
new file mode 100644
index 00000000..6f4cacd4
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_CPT.m~
@@ -0,0 +1,70 @@
+function CPT = CPD_to_CPT(CPD)
+% CPD_TO_CPT Convert the discrete CPD to tabular form (noisyor)
+% CPT = CPD_to_CPT(CPD)
+%
+% CPT(U1,...,Un, X) = Pr(X|U1,...,Un) where the Us are the parents (excluding leak).
+
+if ~isempty(CPD.CPT)
+  CPT = CPD.CPT; % remember to flush cache if params change (e.g., during learning)
+  return;
+end
+
+q = [CPD.leak_inhibit CPD.inhibit(:)'];
+% q(i) is the prob. that the i'th parent will be inhibited (flipped from 1 to 0).
+% q(1) is the leak inhibition probability, and length(q) = n + 1.
+
+if length(q)==1
+  CPT = [q  1-q];
+  return;
+end
+
+n = length(q);
+Bn = ind2subv(2*ones(1,n), 1:(2^n))-1;  % all n bit vectors, with the left most column toggling fastest (LSB)
+CPT = zeros(2^n, 2);
+% Pr(X=0 | U_1 .. U_n) = prod_{i: U_i = on} q_i =  prod_i q_i ^ U_i = exp(u' * log(q_i))
+% This method is problematic when q contains zeros
+
+Q = repmat(q(:)', 2^n, 1);
+Q(logical(~Bn)) = 1;
+CPT(:,1) = prod(Q,2);
+CPT(:,2) = 1-CPT(:,1);
+
+CPT = reshape(CPT(2:2:end), 2*ones(1,n)); % skip cases in which the leak is off       
+
+CPD.CPT = CPT;
+
+function CPT = CPD_to_CPT(CPD)
+% CPD_TO_CPT Convert the discrete CPD to tabular form (noisyor)
+% CPT = CPD_to_CPT(CPD)
+%
+% CPT(U1,...,Un, X) = Pr(X|U1,...,Un) where the Us are the parents (excluding leak).
+
+if ~isempty(CPD.CPT)
+  CPT = CPD.CPT; % remember to flush cache if params change (e.g., during learning)
+  return;
+end
+
+q = [CPD.leak_inhibit CPD.inhibit(:)'];
+% q(i) is the prob. that the i'th parent will be inhibited (flipped from 1 to 0).
+% q(1) is the leak inhibition probability, and length(q) = n + 1.
+
+if length(q)==1
+  CPT = [q  1-q];
+  return;
+end
+
+n = length(q);
+Bn = ind2subv(2*ones(1,n), 1:(2^n))-1;  % all n bit vectors, with the left most column toggling fastest (LSB)
+CPT = zeros(2^n, 2);
+% Pr(X=0 | U_1 .. U_n) = prod_{i: U_i = on} q_i =  prod_i q_i ^ U_i = exp(u' * log(q_i))
+% This method is problematic when q contains zeros
+
+Q = repmat(q(:)', 2^n, 1);
+Q(logical(~Bn)) = 1;
+CPT(:,1) = prod(Q,2);
+CPT(:,2) = 1-CPT(:,1);
+
+CPT = reshape(CPT(2:2:end), 2*ones(1,n)); % skip cases in which the leak is off       
+
+CPD.CPT = CPT;
+
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_lambda_msg.m b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_lambda_msg.m
new file mode 100644
index 00000000..8046c860
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_lambda_msg.m
@@ -0,0 +1,19 @@
+function lam_msg = CPD_to_lambda_msg(CPD, msg_type, n, ps, msg, p, evidence)
+% CPD_TO_LAMBDA_MSG Compute lambda message (noisyor)
+% lam_msg = CPD_to_lambda_msg(CPD, msg_type, n, ps, msg, p)
+% Pearl p190 top eqn
+
+switch msg_type
+  case 'd', 
+   l0 = msg{n}.lambda(1);
+   l1 = msg{n}.lambda(2);
+   Pi = sum_prod_CPD_and_pi_msgs(CPD, n, ps, msg, p);
+   i = find(p==ps); % p is n's i'th parent
+   q = CPD.inhibit(i);
+   lam_msg = zeros(2,1);
+   for u=0:1
+     lam_msg(u+1) = l1 - (q^u)*(l1 - l0)*Pi;
+   end       
+ case 'g',
+  error('noisyor_CPD can''t create Gaussian msgs')
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_pi.m b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_pi.m
new file mode 100644
index 00000000..6955f115
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CPD_to_pi.m
@@ -0,0 +1,12 @@
+function pi = CPD_to_pi(CPD, msg_type, n, ps, msg, evidence)
+% CPD_TO_PI Compute pi vector (noisyor)
+% pi = CPD_to_pi(CPD, msg_type, n, ps, msg)
+% Pearl p188 eqn 4.57
+  
+switch msg_type
+ case 'd',
+   pi = sum_prod_CPD_and_pi_msgs(CPD, n, ps, msg);
+   pi = [pi 1-pi]';
+ case 'g', 
+  error('can''t convert noisy-or CPD to Gaussian pi')
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries
new file mode 100644
index 00000000..4cfae75b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries
@@ -0,0 +1,5 @@
+/CPD_to_CPT.m/1.1.1.1/Mon Aug  2 22:23:32 2004//
+/CPD_to_lambda_msg.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/CPD_to_pi.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/noisyor_CPD.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries.Log
new file mode 100644
index 00000000..b2cd71e0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/private////
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Repository
new file mode 100644
index 00000000..a3f1a38a
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@noisyor_CPD
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
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 = [];
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Entries
new file mode 100644
index 00000000..b56c53ed
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Entries
@@ -0,0 +1,2 @@
+/sum_prod_CPD_and_pi_msgs.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Repository
new file mode 100644
index 00000000..716dfddd
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@noisyor_CPD/private
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/sum_prod_CPD_and_pi_msgs.m b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/sum_prod_CPD_and_pi_msgs.m
new file mode 100644
index 00000000..9ca31d3c
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@noisyor_CPD/private/sum_prod_CPD_and_pi_msgs.m
@@ -0,0 +1,25 @@
+function pi = sum_prod_CPD_and_pi_msgs(CPD, n, ps, msg, except)
+% SUM_PROD_CPD_AND_PI_MSGS Compute pi = sum_{u\p} P(n|u) prod_{ui in ps\p} pi_msg(ui->n)
+% pi = sum_prod_CPD_and_pi_msgs(CPD, n, ps, msg, p)
+%
+% pi  = prod_i (qi pi_msg(ui->n) + 1 - pi_msg(ui->n)) = prod_i (1 - ci pi_msg(ui->n))
+% is the product of the endorsement withheld (Pearl p188 eqn 4.56)
+% We skip p from this product, if specified.
+
+if nargin < 5, except = -1; end
+pi = 1;
+for i=1:length(ps)
+  p = ps(i);
+  if p ~= except
+    pi_from_parent = msg{n}.pi_from_parent{i};
+    q = CPD.inhibit(i);
+    c = 1-q;
+    pi = pi * (1 - c*pi_from_parent(2));
+  end
+end
+% The pi msg that a leak node sends to its child is [0 1]
+% since its own pi is [0 1] and its lambda to self is [0 1].
+q = CPD.leak_inhibit;
+% 1 - c*pi_from_parent = 1-c*1 = q
+pi = pi * q;
+