diff toolboxes/FullBNT-1.0.7/bnt/examples/dynamic/HHMM/Old/mk_hhmm3_args.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/FullBNT-1.0.7/bnt/examples/dynamic/HHMM/Old/mk_hhmm3_args.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,165 @@
+function bnet = mk_hhmm3(varargin)
+% MK_HHMM3 Make a 3 level Hierarchical HMM
+% bnet = mk_hhmm3(...)
+%
+% 3-layer hierarchical HMM where level 1 only connects to level 2, not 3 or obs.
+% This enforces sub-models (which differ only in their Q1 index) to be shared.
+% Also, we enforce the fact that each model always starts in its initial state
+% and only finishes in its final state. However, the prob. of finishing (as opposed to
+% self-transitioning to the final state) can be learned.
+% The fact that we always finish from the same state means we do not need to condition
+% F(i) on Q(i-1), since finishing prob is indep of calling context.
+%
+% The DBN is the same as Fig 10 in my tech report.
+%
+%   Q1 ---------->  Q1
+%   |              / |
+%   |             /  |
+%   |  F2 -------    |
+%   |  ^         \   |
+%   | /|          \  |
+%   v  |           v v
+%   Q2-| -------->   Q2
+%  /|  |             ^
+% / |  |            /|
+% | |  F3 ---------/ |
+% | |  ^           \ |
+% | v /              v
+% | Q3 ----------->  Q3
+% |  |    
+% \  | 
+%  v v    
+%   O
+%
+% Q1 (slice 1) is clamped to be uniform.
+% Q2 (slice 1) is clamped to always start in state 1.
+% Q3 (slice 1) is clamped to always start in state 1.
+% F3 by default will only finish if Q3 is in its last state (F3 is a tabular_CPD)
+% F2 by default gets the default hhmmF_CPD params.
+% Q1:Q3 (slice 2) by default gets the default hhmmQ_CPD params.
+% O by default gets the default tabular/Gaussian params.
+%
+% Optional arguments in name/value format [default]
+%
+% Qsizes      - sizes at each level [ none ]
+% Osize       - size of O node [ none ]
+% discrete_obs - 1 means O is tabular_CPD, 0 means O is gaussian_CPD [0]
+% Oargs       - cell array of args to pass to the O CPD  [ {} ]
+% Q1args      - args to be passed to constructor for Q1 (slice 2) [ {} ]
+% Q2args      - args to be passed to constructor for Q2 (slice 2) [ {} ]
+% Q3args      - args to be passed to constructor for Q3 (slice 2) [ {} ]
+% F2args       - args to be passed to constructor for F2 [ {} ]
+% F3args       - args to be passed to constructor for F3 [ {'CPT', finish in last Q3 state} ]
+%
+
+ss = 6; D = 3;
+Q1 = 1; Q2 = 2; Q3 = 3; F3 = 4; F2 = 5; obs = 6;
+Qnodes = [Q1 Q2 Q3]; Fnodes = [F2 F3];
+names = {'Q1', 'Q2', 'Q3', 'F3', 'F2', 'obs'};
+
+intra = zeros(ss);
+intra(Q1, Q2) = 1;
+intra(Q2, [F2 Q3 obs]) = 1;
+intra(Q3, [F3 obs]) = 1;
+intra(F3, F2) = 1;
+
+inter = zeros(ss);
+inter(Q1,Q1) = 1;
+inter(Q2,Q2) = 1;
+inter(Q3,Q3) = 1;
+inter(F2,[Q1 Q2]) = 1;
+inter(F3,[Q2 Q3]) = 1;
+
+
+% get sizes of nodes
+args = varargin;
+nargs = length(args);
+Qsizes = [];
+Osize = 0;
+for i=1:2:nargs
+  switch args{i},
+   case 'Qsizes', Qsizes = args{i+1}; 
+   case 'Osize', Osize = args{i+1}; 
+  end
+end
+if isempty(Qsizes), error('must specify Qsizes'); end
+if Osize==0, error('must specify Osize'); end
+  
+% set default params
+discrete_obs = 0;
+Oargs = {};
+Q1args = {};
+Q2args = {};
+Q3args = {};
+F2args = {};
+
+% P(Q3, F3)
+CPT = zeros(Qsizes(3), 2);
+% Each model can only terminate in its final state.
+% 0 params will remain 0 during EM, thus enforcing this constraint.
+CPT(:, 1) = 1.0; % all states turn F off ...
+p = 0.5;
+CPT(Qsizes(3), 2) = p; % except the last one
+CPT(Qsizes(3), 1) = 1-p;
+F3args = {'CPT', CPT};
+
+for i=1:2:nargs
+  switch args{i},
+   case 'discrete_obs', discrete_obs = args{i+1}; 
+   case 'Oargs',        Oargs = args{i+1};
+   case 'Q1args',       Q1args = args{i+1};
+   case 'Q2args',       Q2args = args{i+1};
+   case 'Q3args',       Q3args = args{i+1};
+   case 'F2args',       F2args = args{i+1};
+   case 'F3args',       F3args = args{i+1};
+  end
+end
+
+ns = zeros(1,ss);
+ns(Qnodes) = Qsizes;
+ns(obs) = Osize;
+ns(Fnodes) = 2;
+
+dnodes = [Qnodes Fnodes];
+if discrete_obs
+  dnodes = [dnodes obs];
+end
+onodes = [obs];
+
+bnet = mk_dbn(intra, inter, ns, 'observed', onodes, 'discrete', dnodes, 'names', names);
+eclass = bnet.equiv_class;
+
+% SLICE 1
+
+% We clamp untied nodes in the first slice, since their params can't be estimated
+% from just one sequence
+
+% uniform prior on initial model
+CPT = normalise(ones(1,ns(Q1)));
+bnet.CPD{eclass(Q1,1)} = tabular_CPD(bnet, Q1, 'CPT', CPT, 'adjustable', 0);
+
+% each model always starts in state 1
+CPT = zeros(ns(Q1), ns(Q2));
+CPT(:, 1) = 1.0;
+bnet.CPD{eclass(Q2,1)} = tabular_CPD(bnet, Q2, 'CPT', CPT, 'adjustable', 0);
+
+% each model always starts in state 1
+CPT = zeros(ns(Q2), ns(Q3));
+CPT(:, 1) = 1.0;
+bnet.CPD{eclass(Q3,1)} = tabular_CPD(bnet, Q3, 'CPT', CPT, 'adjustable', 0);
+
+bnet.CPD{eclass(F2,1)}  = hhmmF_CPD(bnet, F2, Qnodes, 2, D, F2args{:});
+
+bnet.CPD{eclass(F3,1)}  = tabular_CPD(bnet, F3, F3args{:});
+
+if discrete_obs
+  bnet.CPD{eclass(obs,1)} = tabular_CPD(bnet, obs, Oargs{:});
+else
+  bnet.CPD{eclass(obs,1)} = gaussian_CPD(bnet, obs, Oargs{:});
+end
+
+% SLICE 2
+
+bnet.CPD{eclass(Q1,2)} = hhmmQ_CPD(bnet, Q1+ss, Qnodes, 1, D, Q1args{:});
+bnet.CPD{eclass(Q2,2)} = hhmmQ_CPD(bnet, Q2+ss, Qnodes, 2, D, Q2args{:});
+bnet.CPD{eclass(Q3,2)} = hhmmQ_CPD(bnet, Q3+ss, Qnodes, 3, D, Q3args{:});