updated niche/functional

fastlib/u/niche/functional/test_genes_postica.m

@@ -1,24 +1,56 @@
+clear;
+load gene_results;
+
 % discriminant analysis using pc features %
 % pc_scores is d x N
 
 g1_indices = find(phases == g1_phase);
 nong1_indices = find(phases ~=g1_phase & phases ~= unknown_phase);
 
-ic_scores = ic_scores(1:5,:);
+used_scores = pc_scores;
 
-svm_data = [ic_scores(:,g1_indices) ic_scores(:,nong1_indices)]';
+used_scores = used_scores(1:5,:);
+
+svm_data = [used_scores(:,g1_indices) used_scores(:,nong1_indices)]';
 svm_labels = [1 * ones(length(g1_indices),1);
 	      -1 * ones(length(nong1_indices),1)];
 
+% write data so that we can efficiently call svmltrain many times
+svmlwrite('funknet', svm_data, svm_labels);
 
-latestSVM = svml('latestSVM','Kernel',2,'KernelParam',.01,'C',.2, ...
-		 'ExecPath','/home/niche/matlab/toolboxes/svml');
+% set initial svm options %
+svm_options = ...
+    svmlopt('Kernel', 2, 'KernelParam', .01, 'C', .2, 'ComputeLOO', 1, ...
+	    'ExecPath','/home/niche/matlab/toolboxes/svml');
+C = 1e-3;
+
+C_epoch = 1;
+
+while C < 100
+
+  % set option for C (the regularization parameter)
+  svm_options = ...
+      svmlopt(svm_options, 'C', C);
+  
+  latestSVM = svml('latestSVM', svm_options);
 
-for i=1:size(svm_data, 1)
   latestSVM = ...
-      svmltrain(latestSVM, [svm_data([1:(i-1) (i+1):end], :)], ...
-		svm_labels([1:(i-1) (i+1):end]));
-  ypred(i) = svmlfwd(latestSVM, svm_data(i,:), svm_labels(i));
+      svmltrain(latestSVM, 'funknet');
+  
+  load loocv_error.txt
+  
+  C_array(C_epoch) = C;
+  loocv_errors(C_epoch) = loocv_error;
+  
+  C = C * 1.01; % geometrically increase C
+  C_epoch = C_epoch + 1;
 end
 
-sum((2 * (ypred > 0) - 1) == svm_labels') / length(svm_labels) 
+% for i=1:size(svm_data, 1)
+%   latestSVM = ...
+%       svmltrain(latestSVM, [svm_data([1:(i-1) (i+1):end], :)], ...
+% 		svm_labels([1:(i-1) (i+1):end]));
+%   ypred(i) = svmlfwd(latestSVM, svm_data(i,:), svm_labels(i));
+% end
+
+% sum((2 * (ypred > 0) - 1) == svm_labels') / length(svm_labels)