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, 54 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/SLP/examples/test_gs2.m b/sourcecodes/bnt-master/SLP/examples/test_gs2.m
new file mode 100644
index 00000000..0188977e
--- /dev/null
+++ b/sourcecodes/bnt-master/SLP/examples/test_gs2.m
@@ -0,0 +1,54 @@
+% test Greedy Search with cache
+clear all;
+
+fprintf('\n=== Structure Learning with Greedy Search algorithm and cache implementation\n');
+
+n=8;
+names={ 'A' , 'S' , 'T' , 'L' , 'B' , 'O' , 'X' , 'D' };
+carre=ones(1,n);
+node_type={'tabular','tabular','tabular','tabular','tabular','tabular','tabular','tabular'};
+
+m=6000;
+bnet=mk_asia2_bnet;
+data = cell(n,m);
+for l = 1:m, data(:,l) = sample_bnet(bnet); end
+data=cell2mat(data);
+fprintf('Complete data have been created.\n\n');
+
+seeddag = mk_rnd_dag(n);
+
+fprintf('\t- Greedy Search (with cache)\n');
+tmp=cputime;
+L=300;
+cache=score_init_cache(n,L);
+[dag1, best_score, cache] =learn_struct_gs2(data,bnet.node_sizes,seeddag,'cache',cache,'scoring_fn','bayesian');
+%cache
+tmp=cputime-tmp;
+fprintf('\t- Execution time : %3.2f seconds\n',tmp);
+
+fprintf('\t- Greedy Search (without cache)\n');
+tmp=cputime;
+dag2=learn_struct_gs2(data,bnet.node_sizes,seeddag,'scoring_fn','bayesian');
+tmp=cputime-tmp;
+fprintf('\t- Execution time : %3.2f seconds\n',tmp);
+
+fprintf('\t- Greedy Search (with cache and MWST initialisation)\n');
+tmp=cputime;
+Tdag=learn_struct_mwst(data, ones(n,1), bnet.node_sizes, node_type,'mutual_info',ceil(n*rand));
+dag3=learn_struct_gs2(data,bnet.node_sizes,full(Tdag),'cache',cache,'scoring_fn','bayesian');
+tmp=cputime-tmp;
+fprintf('\t- Execution time : %3.2f seconds\n',tmp);
+
+
+figure;[xx yy] = make_layout(bnet.dag);
+yy=(yy-0.2)*.8/.6+.1;
+xx=(xx-0.2833)*.8/.517+.1;
+subplot(1,4,1), [xx yy]=draw_graph(bnet.dag,names,carre,xx,yy); %,carre);
+title('ASIA original graph');
+subplot(1,4,2), draw_graph(dag1,names,carre,xx,yy); %,carre);
+title('GS (cache)');
+subplot(1,4,3), [xx yy]=draw_graph(dag2,names,carre,xx,yy); %,carre);
+title('GS (without cache)');
+subplot(1,4,4), [xx yy]=draw_graph(dag3,names,carre,xx,yy); %,carre);
+title('GS (with cache and MWST init)');
+drawnow;