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

10 files changed, 99 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Entries
new file mode 100644
index 00000000..d9c315a5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Entries
@@ -0,0 +1,8 @@
+/bnet_from_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/enter_evidence.m/1.1.1.1/Mon Jun 17 23:46:46 2002//
+/find_mpe.m/1.1.1.1/Mon Jun 17 23:50:16 2002//
+/marginal_family.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/marginal_nodes.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/smoother_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+/update_engine.m/1.1.1.1/Wed May 29 15:59:56 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Repository
new file mode 100644
index 00000000..a10f8a08
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/inference/online/@smoother_engine
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Root b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/bnet_from_engine.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/bnet_from_engine.m
new file mode 100644
index 00000000..b57ee5f4
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/bnet_from_engine.m
@@ -0,0 +1,5 @@
+function bnet = bnet_from_engine(engine)
+% BNET_FROM_ENGINE Return the bnet structure stored inside the engine (smoother_engine)
+% bnet = bnet_from_engine(engine)
+
+bnet = bnet_from_engine(engine.tbn_engine);
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/enter_evidence.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/enter_evidence.m
new file mode 100644
index 00000000..299c2331
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/enter_evidence.m
@@ -0,0 +1,21 @@
+function [engine, LL] = enter_evidence(engine, ev)
+% ENTER_EVIDENCE Call the offline smoother
+% [engine, loglik] = enter_evidence(engine, evidence, ...)
+%
+% evidence{i,t} = [] if if X(i,t) is hidden, and otherwise contains its observed value (scalar or column vector)
+%
+
+T = size(ev, 2);
+f = cell(1,T);
+b = cell(1,T); % b{t}.clpot{c}
+ll = zeros(1,T);
+[f{1}, ll(1)] = fwd1(engine.tbn_engine, ev(:,1), 1);
+for t=2:T
+  [f{t}, ll(t)] = fwd(engine.tbn_engine, f{t-1}, ev(:,t), t);
+end
+LL = sum(ll);
+b{T} = backT(engine.tbn_engine, f{T}, T);
+for t=T-1:-1:1
+  b{t} = back(engine.tbn_engine, b{t+1}, f{t}, t);
+end
+engine.b = b;
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/find_mpe.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/find_mpe.m
new file mode 100644
index 00000000..5415f120
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/find_mpe.m
@@ -0,0 +1,33 @@
+function mpe = find_mpe(engine, ev)
+% FIND_MPE Find the most probable explanation (Viterbi)
+% mpe = enter_evidence(engine, evidence, ...)
+%
+% evidence{i,t} = [] if if X(i,t) is hidden, and otherwise contains its observed value (scalar or column vector)
+%
+
+mpe = cell(size(ev));
+engine.tbn_engine = set_fields(engine.tbn_engine, 'maximize', 1);
+
+T = size(ev, 2);
+f = cell(1,T);
+b = cell(1,T); % b{t}.clpot{c}
+ll = zeros(1,T);
+[f{1}, ll(1)] = fwd1(engine.tbn_engine, ev(:,1), 1);
+for t=2:T
+  [f{t}, ll(t)] = fwd(engine.tbn_engine, f{t-1}, ev(:,t), t);
+end
+
+if T==1
+  [b{1}, mpe(:,1)] = backT_mpe(engine.tbn_engine, f{1}, ev(:,1), 1);
+else
+  [b{T}, mpe(:,T)] = backT_mpe(engine.tbn_engine, f{T}, ev(:,T-1:T), T);
+  for t=T-1:-1:2
+    [b{t}, mpe(:,t)] = back_mpe(engine.tbn_engine, b{t+1}, f{t}, ev(:,t-1:t), t);
+  end
+  t = 1;
+  [b{t}, mpe(:,t)] = back1_mpe(engine.tbn_engine, b{t+1}, f{t}, ev(:,1), t);
+end
+engine.b = b;
+  
+
+
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_family.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_family.m
new file mode 100644
index 00000000..b7b0d7ec
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_family.m
@@ -0,0 +1,6 @@
+function marginal = marginal_family(engine, i, t, add_ev)
+% MARGINAL_FAMILY Compute the joint distribution on a set of family (smoother_engine)
+% function marginal = marginal_family(engine, i, t, add_ev)
+
+if nargin < 4, add_ev = 0; end
+marginal = marginal_family(engine.tbn_engine, engine.b{t}, i, t, add_ev);
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_nodes.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_nodes.m
new file mode 100644
index 00000000..e8574c53
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/marginal_nodes.m
@@ -0,0 +1,7 @@
+function marginal = marginal_nodes(engine, nodes, t, add_ev)
+% MARGINAL_NODES Compute the joint distribution on a set of nodes (smoother_engine)
+% function marginal = marginal_nodes(engine, nodes, t, add_ev)
+
+if nargin < 4, add_ev = 0; end
+
+marginal = marginal_nodes(engine.tbn_engine, engine.b{t}, nodes, t, add_ev);
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/smoother_engine.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/smoother_engine.m
new file mode 100644
index 00000000..adf7ede8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/smoother_engine.m
@@ -0,0 +1,12 @@
+function engine = smoother_engine(tbn_engine)
+% SMOOTHER_ENGINE Create an engine which does offline (fixed-interval) smoothing in O(T) space/time
+% function engine = smoother_engine(tbn_engine)
+%
+% tbn_engine is any 2TBN inference engine which supports the following methods:
+% fwd, fwd1, back, backT, back, marginal_nodes and marginal_family.
+
+engine.tbn_engine = tbn_engine;
+engine.b = []; % space to store smoothed messages
+engine = class(engine, 'smoother_engine');
+%engine = class(engine, 'smoother_engine', inf_engine(bnet_from_engine(tbn_engine)));
+
diff --git a/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/update_engine.m b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/update_engine.m
new file mode 100644
index 00000000..ffe0661e
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/inference/online/@smoother_engine/update_engine.m
@@ -0,0 +1,5 @@
+function engine = update_engine(engine, newCPDs)
+% UPDATE_ENGINE Update the engine to take into account the new parameters (smoother_engine).
+% engine = update_engine(engine, newCPDs)
+
+engine.tbn_engine = update_engine(engine.tbn_engine, newCPDs);