From 8070dc963753142bb86c4ed698d91fd623ed28e7 Mon Sep 17 00:00:00 2001 From: ziejd2 Date: Thu, 28 Sep 2017 15:04:40 -0500 Subject: 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 --- .../dynamic/@hmm_inf_engine/private/CVS/Entries | 3 ++ .../dynamic/@hmm_inf_engine/private/CVS/Repository | 1 + .../dynamic/@hmm_inf_engine/private/CVS/Root | 1 + .../private/mk_hmm_obs_lik_matrix.m | 30 +++++++++++++ .../@hmm_inf_engine/private/mk_hmm_obs_lik_vec.m | 52 ++++++++++++++++++++++ 5 files changed, 87 insertions(+) create mode 100644 sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Entries create mode 100644 sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Repository create mode 100644 sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Root create mode 100644 sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_matrix.m create mode 100644 sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_vec.m (limited to 'sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private') diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Entries b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Entries new file mode 100644 index 00000000..a35185ea --- /dev/null +++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Entries @@ -0,0 +1,3 @@ +/mk_hmm_obs_lik_matrix.m/1.1.1.1/Sun May 4 21:42:26 2003// +/mk_hmm_obs_lik_vec.m/1.1.1.1/Thu Jan 23 18:50:10 2003// +D diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Repository b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Repository new file mode 100644 index 00000000..20dfc6fd --- /dev/null +++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Repository @@ -0,0 +1 @@ +FullBNT/BNT/inference/dynamic/@hmm_inf_engine/private diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Root b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Root new file mode 100644 index 00000000..f3bd14a6 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/CVS/Root @@ -0,0 +1 @@ +:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_matrix.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_matrix.m new file mode 100644 index 00000000..441f3c0a --- /dev/null +++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_matrix.m @@ -0,0 +1,30 @@ +function obslik = mk_hmm_obs_lik_matrix(engine, evidence) + +T = size(evidence,2); +Q = length(engine.startprob); +obslik = ones(Q, T); +bnet = bnet_from_engine(engine); +% P(o1,o2| Q1,Q2) = P(o1|Q1,Q2) * P(o2|Q1,Q2) +onodes = bnet.observed; +for i=1:length(onodes) + data = cell2num(evidence(onodes(i),:)); + if bnet.auto_regressive(onodes(i)) + params = engine.obsprob{i}; + mu = params.big_mu; + Sigma = params.big_Sigma, + W = params.big_W; + mu0 = params.big_mu0; + Sigma0 = params.big_Sigma0; + %obslik_i = mk_arhmm_obs_lik(data, mu, Sigma, W, mu0, Sigma0 + obslik_i = clg_prob(data(:,1:T-1), data(:,2:T), mu, Sigma, W); + obslik_i = [mixgauss_prob(data(:,1), mu0, Sigma0) obslik_i]; + elseif myismember(onodes(i), bnet.dnodes) + %obslik_i = eval_pdf_cond_multinomial(data, engine.obsprob{i}.big_CPT); + obslik_i = multinomial_prob(data, engine.obsprob{i}.big_CPT); + else + %obslik_i = eval_pdf_cond_gauss(data, engine.obsprob{i}.big_mu, engine.obsprob{i}.big_Sigma); + obslik_i = mixgauss_prob(data, engine.obsprob{i}.big_mu, engine.obsprob{i}.big_Sigma); + end + obslik = obslik .* obslik_i; +end + diff --git a/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_vec.m b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_vec.m new file mode 100644 index 00000000..16d30aec --- /dev/null +++ b/sourcecodes/bnt-master/BNT/inference/dynamic/@hmm_inf_engine/private/mk_hmm_obs_lik_vec.m @@ -0,0 +1,52 @@ +function obslik = mk_hmm_obs_lik_vec(engine, evidence) + +% P(o1,o2| h) = P(o1|h) * P(o2|h) where h = Q1,Q2,... + +bnet = bnet_from_engine(engine); +ss = length(bnet.intra); +onodes = bnet.observed; +hnodes = mysetdiff(1:ss, onodes); +ns = bnet.node_sizes(:); +ns(onodes) = 1; + +Q = length(engine.startprob); +obslik = ones(Q, 1); + +for i=1:length(onodes) + o = onodes(i); + %data = cell2num(evidence(o,1)); + data = evidence{o,1}; + if myismember(o, bnet.dnodes) + obslik_i = eval_pdf_cond_multinomial(data, engine.obsprob{i}.CPT); + else + if bnet.auto_regressive(o) + error('can''t handle AR nodes') + end + %% calling mk_ghmm_obs_lik, which calls gaussian_prob, is slow, so we inline it + %% and use the pre-computed inverse matrix + %obslik_i = mk_ghmm_obs_lik(data, engine.obsprob{i}.mu, engine.obsprob{i}.Sigma); + x = data(:); + m = engine.obsprob{i}.mu; + Qi = size(m, 2); + obslik_i = size(Qi, 1); + invC = engine.obsprob{i}.inv_Sigma; + denom = engine.obsprob{i}.denom; + for j=1:Qi + numer = exp(-0.5 * (x-m(:,j))' * invC(:,:,j) * (x-m(:,j))); + obslik_i(j) = numer / denom(j); + end + end + % convert P(o|ps) into P(o|h) by multiplying onto a (h,o) potential of all 1s + ps = bnet.parents{o}; + dom = [ps o]; + obspot_i = dpot(dom, ns(dom), obslik_i); + dom = [hnodes o]; + obspot = dpot(dom, ns(dom)); + obspot = multiply_by_pot(obspot, obspot_i); + % compute p(oi|h) * p(oj|h) + S = struct(obspot); + obslik = obslik .* S.T(:); +end + + + -- cgit 1.4.1