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--- a +++ b/gleason_classifier.m @@ -0,0 +1,739 @@ +function gleason_classifer +addpath /Volumes/Hydra/Analyses/SD_Recurrence/roi_tile_output/ + +%% Load and partition data +load feature_tbl.mat +load feature_tbl2.mat +%% +% train/test = unbalanced data +% train2 = balanaced +% train_hln/test_hln = train2 split into high, low, normal (semi-balanced lol) +% train_ng/test_ng = train2 split into normal vs all other grades + +training = []; % training subject labels +testing = []; % testing subject labels + +% Z-score first +train = []; +for i = 1:numel(training) + trainingIdx = find(tbl.Subject == training(i)); + train = cat(1,train,tbl(trainingIdx,[1,2,7:end])); +end +train2 = train; +for i = 1:40 + train2{:,i+2} = zscore(train{:,i+2}); +end + + +test = []; +for i = 1:numel(testing) + testingIdx = find(tbl.Subject == testing(i)); + test = cat(1,test,tbl(testingIdx,[1,2,7:end])); +end +test2 = test; +for i = 1:24 + ave = mean(train{:,i+2}); + stdev = std(train{:,i+2},'omitnan'); + + for j = 1:height(test2) + test2{j,i+2} = (test2{j,i+2} - ave)/stdev; + end +end + + +% Z-score first +trainingIdx = find(tbl.Category == "Training"); +train = tbl(trainingIdx,[2,7:end-2]); +train2 = train; +for i = 1:40 + train2{:,i+1} = zscore(train{:,i+1}); +end + +testingIdx = find(tbl.Category == "Testing"); +test = tbl(testingIdx,[2,7:end-2]); + +test2 = test; +for i = 1:24 + ave = mean(train{:,i+1}); + stdev = std(train{:,i+1},'omitnan'); + + for j = 1:height(test2) + test2{j,i+1} = (test2{j,i+1} - ave)/stdev; + end +end + +% Z-score whole mounts used for demonstrations +load feature_tbl_2235.mat +load feature_tbl_2181.mat +load feature_tbl_1163.mat + +for i = 1:24 + ave = mean(train{:,i+2}); + stdev = std(train{:,i+2},'omitnan'); + + for j = 1:height(feature_tbl_2235) + feature_tbl_2235{j,i+7} = (feature_tbl_2235{j,i+7} - ave)/stdev; + end +end + +for i = 1:24 + ave = mean(train{:,i+2}); + stdev = std(train{:,i+2},'omitnan'); + + for j = 1:height(feature_tbl_2181) + feature_tbl_2181{j,i+7} = (feature_tbl_2181{j,i+7} - ave)/stdev; + end +end + +for i = 1:24 + ave = mean(train{:,i+2}); + stdev = std(train{:,i+2},'omitnan'); + + for j = 1:height(feature_tbl_1163) + feature_tbl_1163{j,i+5} = (feature_tbl_1163{j,i+5} - ave)/stdev; + end +end + +%% H/L/N +train_hln = train2; +loc = find(train_hln.Anot_Class == 'Atrophy' | train_hln.Anot_Class == 'HGPIN' ... + | train_hln.Anot_Class == 'Seminal_Vesicles' | train_hln.Anot_Class == 'Tissue'); +train_hln.Anot_Class(loc) = 'Normal'; + +loc = find(train_hln.Anot_Class == 'G3'); +train_hln.Anot_Class(loc) = 'Low'; + +loc = find(train_hln.Anot_Class == 'G4FG' | train_hln.Anot_Class == 'G4CG' | train_hln.Anot_Class == 'G5'); +train_hln.Anot_Class(loc) = 'High'; +% +test_hln = test2; +loc = find(test_hln.Anot_Class == 'Atrophy' | test_hln.Anot_Class == 'HGPIN' ... + | test_hln.Anot_Class == 'Seminal_Vesicles' | test_hln.Anot_Class == 'Tissue'); +test_hln.Anot_Class(loc) = 'Normal'; + +loc = find(test_hln.Anot_Class == 'G3'); +test_hln.Anot_Class(loc) = 'Low'; + +loc = find(test_hln.Anot_Class == 'G4FG' | test_hln.Anot_Class == 'G4CG' | test_hln.Anot_Class == 'G5'); +test_hln.Anot_Class(loc) = 'High'; +% +loc = find(feature_tbl_2235.Anot_Class == 'Atrophy' | feature_tbl_2235.Anot_Class == 'HGPIN' ... + | feature_tbl_2235.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2235.Anot_Class == 'Tissue'); +feature_tbl_2235.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_2235.Anot_Class == 'G3'); +feature_tbl_2235.Anot_Class(loc) = 'Low'; + +loc = find(feature_tbl_2235.Anot_Class == 'G4FG' | feature_tbl_2235.Anot_Class == 'G4CG' | feature_tbl_2235.Anot_Class == 'G5'); +feature_tbl_2235.Anot_Class(loc) = 'High'; +% +loc = find(feature_tbl_2181.Anot_Class == 'Atrophy' | feature_tbl_2181.Anot_Class == 'HGPIN' ... + | feature_tbl_2181.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2181.Anot_Class == 'Tissue'); +feature_tbl_2181.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_2181.Anot_Class == 'G3'); +feature_tbl_2181.Anot_Class(loc) = 'Low'; + +loc = find(feature_tbl_2181.Anot_Class == 'G4FG' | feature_tbl_2181.Anot_Class == 'G4CG' | feature_tbl_2181.Anot_Class == 'G5'); +feature_tbl_2181.Anot_Class(loc) = 'High'; +% +loc = find(feature_tbl_1163.Anot_Class == 'Atrophy' | feature_tbl_1163.Anot_Class == 'HGPIN' ... + | feature_tbl_1163.Anot_Class == 'Seminal_Vesicles' | feature_tbl_1163.Anot_Class == 'Tissue'); +feature_tbl_1163.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_1163.Anot_Class == 'G3'); +feature_tbl_1163.Anot_Class(loc) = 'Low'; + +loc = find(feature_tbl_1163.Anot_Class == 'G4FG' | feature_tbl_1163.Anot_Class == 'G4CG' | feature_tbl_1163.Anot_Class == 'G5'); +feature_tbl_1163.Anot_Class(loc) = 'High'; + +mdl_hln_nb = fitcnb(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','all'); +mdl_hln_knn = fitcknn(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','all'); +mdl_hln_tree = fitctree(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','all'); +mdl_hln_ecoc = fitcecoc(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','auto'); % +mdl_hln_ensemble = fitcensemble(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','all'); +mdl_hln_net = fitcnet(train_hln(:,2:25),train_hln.Anot_Class,'OptimizeHyperparameters','all'); + +%% N/G +train_ng = train2; +loc = find(train_ng.Anot_Class == 'Atrophy' | train_ng.Anot_Class == 'HGPIN' ... + | train_ng.Anot_Class == 'Seminal_Vesicles' | train_ng.Anot_Class == 'Tissue'); +train_ng.Anot_Class(loc) = 'Normal'; +% +test_ng = test2; +loc = find(test_ng.Anot_Class == 'Atrophy' | test_ng.Anot_Class == 'HGPIN' ... + | test_ng.Anot_Class == 'Seminal_Vesicles' | test_ng.Anot_Class == 'Tissue'); +test_ng.Anot_Class(loc) = 'Normal'; +% +loc = find(feature_tbl_2235.Anot_Class == 'Atrophy' | feature_tbl_2235.Anot_Class == 'HGPIN' ... + | feature_tbl_2235.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2235.Anot_Class == 'Tissue'); +feature_tbl_2235.Anot_Class(loc) = 'Normal'; +% +loc = find(feature_tbl_2181.Anot_Class == 'Atrophy' | feature_tbl_2181.Anot_Class == 'HGPIN' ... + | feature_tbl_2181.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2181.Anot_Class == 'Tissue'); +feature_tbl_2181.Anot_Class(loc) = 'Normal'; +% +loc = find(feature_tbl_1163.Anot_Class == 'Atrophy' | feature_tbl_1163.Anot_Class == 'HGPIN' ... + | feature_tbl_1163.Anot_Class == 'Seminal_Vesicles' | feature_tbl_1163.Anot_Class == 'Tissue'); +feature_tbl_1163.Anot_Class(loc) = 'Normal'; + +mdl_ng_nb = fitcnb(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','all'); +mdl_ng_knn = fitcknn(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','all'); +mdl_ng_tree = fitctree(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','all'); +mdl_ng_ecoc = fitcecoc(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','auto'); +mdl_ng_ensemble = fitcensemble(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','all'); +mdl_ng_net = fitcnet(train_ng(:,2:25),train_ng.Anot_Class,'OptimizeHyperparameters','all'); + + + +%% Cancer v Noncancer +train_nc = train2; +loc = find(train_nc.Anot_Class == 'Atrophy' | train_nc.Anot_Class == 'HGPIN' ... + | train_nc.Anot_Class == 'Seminal_Vesicles' | train_nc.Anot_Class == 'Tissue'); +train_nc.Anot_Class(loc) = 'Normal'; + +loc = find(train2.Anot_Class == 'G3' | train2.Anot_Class == 'G4FG' ... + | train2.Anot_Class == 'G4CG' | train2.Anot_Class == 'G5'); +train_nc.Anot_Class(loc) = 'Cancer'; +% +test_nc = test2; +loc = find(test_nc.Anot_Class == 'Atrophy' | test_nc.Anot_Class == 'HGPIN' ... + | test_nc.Anot_Class == 'Seminal_Vesicles' | test_nc.Anot_Class == 'Tissue'); +test_nc.Anot_Class(loc) = 'Normal'; + +loc = find(test2.Anot_Class == 'G3' | test2.Anot_Class == 'G4FG' ... + | test2.Anot_Class == 'G4CG' | test2.Anot_Class == 'G5'); +test_nc.Anot_Class(loc) = 'Cancer'; +% +loc = find(feature_tbl_2235.Anot_Class == 'Atrophy' | feature_tbl_2235.Anot_Class == 'HGPIN' ... + | feature_tbl_2235.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2235.Anot_Class == 'Tissue'); +feature_tbl_2235.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_2235.Anot_Class == 'G3' | feature_tbl_2235.Anot_Class == 'G4FG' ... + | feature_tbl_2235.Anot_Class == 'G4CG' | feature_tbl_2235.Anot_Class == 'G5'); +feature_tbl_2235.Anot_Class(loc) = 'Cancer'; +% +loc = find(feature_tbl_2181.Anot_Class == 'Atrophy' | feature_tbl_2181.Anot_Class == 'HGPIN' ... + | feature_tbl_2181.Anot_Class == 'Seminal_Vesicles' | feature_tbl_2181.Anot_Class == 'Tissue'); +feature_tbl_2181.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_2181.Anot_Class == 'G3' | feature_tbl_2181.Anot_Class == 'G4FG' ... + | feature_tbl_2181.Anot_Class == 'G4CG' | feature_tbl_2181.Anot_Class == 'G5'); +feature_tbl_2181.Anot_Class(loc) = 'Cancer'; +% +loc = find(feature_tbl_1163.Anot_Class == 'Atrophy' | feature_tbl_1163.Anot_Class == 'HGPIN' ... + | feature_tbl_1163.Anot_Class == 'Seminal_Vesicles' | feature_tbl_1163.Anot_Class == 'Tissue'); +feature_tbl_1163.Anot_Class(loc) = 'Normal'; + +loc = find(feature_tbl_1163.Anot_Class == 'G3' | feature_tbl_1163.Anot_Class == 'G4FG' ... + | feature_tbl_1163.Anot_Class == 'G4CG' | feature_tbl_1163.Anot_Class == 'G5'); +feature_tbl_1163.Anot_Class(loc) = 'Cancer'; + +mdl_nc_nb = fitcnb(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','all'); +mdl_nc_knn = fitcknn(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','all'); +mdl_nc_tree = fitctree(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','all'); +mdl_nc_ecoc = fitcecoc(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','auto'); +mdl_nc_ensemble = fitcensemble(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','all'); +mdl_nc_net = fitcnet(train_nc(:,2:25),train_nc.Anot_Class,'OptimizeHyperparameters','all'); + +%% All Gleason +mdl_nb = fitcnb(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','all'); +mdl_knn = fitcknn(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','all'); +mdl_tree = fitctree(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','all'); +mdl_ecoc = fitcecoc(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','auto'); +mdl_ensemble = fitcensemble(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','all'); +mdl_net = fitcnet(train2(:,2:25),train2.Anot_Class,'OptimizeHyperparameters','all'); + +%% Check Model Performance +mdl_nb_pred = predict(mdl_nb, test2(:,2:25)); +mdl_knn_pred = predict(mdl_knn, test2(:,2:25)); +mdl_tree_pred = predict(mdl_tree, test2(:,2:25)); +mdl_ecoc_pred = predict(mdl_ecoc, test2(:,2:25)); +mdl_ensemble_pred = predict(mdl_ensemble, test2(:,2:25)); +mdl_net_pred = predict(mdl_net, test2(:,2:25)); + +mdl_hln_nb_pred = predict(mdl_hln_nb, test_hln(:,2:25)); +mdl_hln_knn_pred = predict(mdl_hln_knn, test_hln(:,2:25)); +mdl_hln_tree_pred = predict(mdl_hln_tree, test_hln(:,2:25)); +mdl_hln_ecoc_pred = predict(mdl_hln_ecoc, test_hln(:,2:25)); +mdl_hln_ensemble_pred = predict(mdl_hln_ensemble, test_hln(:,2:25)); +mdl_hln_net_pred = predict(mdl_hln_net, test_hln(:,2:25)); + +mdl_nc_nb_pred = predict(mdl_nc_nb, test_nc(:,2:25)); +mdl_nc_knn_pred = predict(mdl_nc_knn, test_nc(:,2:25)); +mdl_nc_tree_pred = predict(mdl_nc_tree, test_nc(:,2:25)); +mdl_nc_ecoc_pred = predict(mdl_nc_ecoc, test_nc(:,2:25)); +mdl_nc_ensemble_pred = predict(mdl_nc_ensemble, test_nc(:,2:25)); +mdl_nc_net_pred = predict(mdl_nc_net, test_nc(:,2:25)); + +mdl_ng_nb_pred = predict(mdl_ng_nb, test_ng(:,2:25)); +mdl_ng_knn_pred = predict(mdl_ng_knn, test_ng(:,2:25)); +mdl_ng_tree_pred = predict(mdl_ng_tree, test_ng(:,2:25)); +mdl_ng_ecoc_pred = predict(mdl_ng_ecoc, test_ng(:,2:25)); +mdl_ng_ensemble_pred = predict(mdl_ng_ensemble, test_ng(:,2:25)); +mdl_ng_net_pred = predict(mdl_ng_net, test_ng(:,2:25)); +% +tbl_mdl_nb = calculate_error(test2.Anot_Class,mdl_nb_pred); +tbl_mdl_knn = calculate_error(test2.Anot_Class,mdl_knn_pred); +tbl_mdl_tree = calculate_error(test2.Anot_Class,mdl_tree_pred); +tbl_mdl_ecoc = calculate_error(test2.Anot_Class,mdl_ecoc_pred); +tbl_mdl_ensemble = calculate_error(test2.Anot_Class,mdl_ensemble_pred); +tbl_mdl_net = calculate_error(test2.Anot_Class,mdl_net_pred); + +tbl_mdl_hln_nb = calculate_error(test_hln.Anot_Class,mdl_hln_nb_pred); +tbl_mdl_hln_knn = calculate_error(test_hln.Anot_Class,mdl_hln_knn_pred); +tbl_mdl_hln_tree = calculate_error(test_hln.Anot_Class,mdl_hln_tree_pred); +tbl_mdl_hln_ecoc = calculate_error(test_hln.Anot_Class,mdl_hln_ecoc_pred); +tbl_mdl_hln_ensemble = calculate_error(test_hln.Anot_Class,mdl_hln_ensemble_pred); +tbl_mdl_hln_net = calculate_error(test_hln.Anot_Class,mdl_hln_net_pred); + +tbl_mdl_nc_nb = calculate_error(test_nc.Anot_Class,mdl_nc_nb_pred); +tbl_mdl_nc_knn = calculate_error(test_nc.Anot_Class,mdl_nc_knn_pred); +tbl_mdl_nc_tree = calculate_error(test_nc.Anot_Class,mdl_nc_tree_pred); +tbl_mdl_nc_ecoc = calculate_error(test_nc.Anot_Class,mdl_nc_ecoc_pred); +tbl_mdl_nc_ensemble = calculate_error(test_nc.Anot_Class,mdl_nc_ensemble_pred); +tbl_mdl_nc_net = calculate_error(test_nc.Anot_Class,mdl_nc_net_pred); + +tbl_mdl_ng_nb = calculate_error(test_ng.Anot_Class,mdl_nc_nb_pred); +tbl_mdl_ng_knn = calculate_error(test_ng.Anot_Class,mdl_nc_knn_pred); +tbl_mdl_ng_tree = calculate_error(test_ng.Anot_Class,mdl_nc_tree_pred); +tbl_mdl_ng_ecoc = calculate_error(test_ng.Anot_Class,mdl_nc_ecoc_pred); +tbl_mdl_ng_ensemble = calculate_error(test_ng.Anot_Class,mdl_nc_ensemble_pred); +tbl_mdl_ng_net = calculate_error(test_ng.Anot_Class,mdl_nc_net_pred); +% +prec_mdl_nb = sum(tbl_mdl_nb.TP) / (sum(tbl_mdl_nb.TP) + sum(tbl_mdl_nb.FP)); +prec_mdl_knn = sum(tbl_mdl_knn.TP) / (sum(tbl_mdl_knn.TP) + sum(tbl_mdl_knn.FP)); +prec_mdl_tree = sum(tbl_mdl_tree.TP) / (sum(tbl_mdl_tree.TP) + sum(tbl_mdl_tree.FP)); +prec_mdl_ecoc = sum(tbl_mdl_ecoc.TP) / (sum(tbl_mdl_ecoc.TP) + sum(tbl_mdl_ecoc.FP)); +prec_mdl_ensemble = sum(tbl_mdl_ensemble.TP) / (sum(tbl_mdl_ensemble.TP) + sum(tbl_mdl_ensemble.FP)); +prec_mdl_net = sum(tbl_mdl_net.TP) / (sum(tbl_mdl_net.TP) + sum(tbl_mdl_net.FP)); + +prec_mdl_hln_nb = sum(tbl_mdl_hln_nb.TP) / (sum(tbl_mdl_hln_nb.TP) + sum(tbl_mdl_hln_nb.FP)); +prec_mdl_hln_knn = sum(tbl_mdl_hln_knn.TP) / (sum(tbl_mdl_hln_knn.TP) + sum(tbl_mdl_hln_knn.FP)); +prec_mdl_hln_tree = sum(tbl_mdl_hln_tree.TP) / (sum(tbl_mdl_hln_tree.TP) + sum(tbl_mdl_hln_tree.FP)); +prec_mdl_hln_ecoc = sum(tbl_mdl_hln_ecoc.TP) / (sum(tbl_mdl_hln_ecoc.TP) + sum(tbl_mdl_hln_ecoc.FP)); +prec_mdl_hln_ensemble = sum(tbl_mdl_hln_ensemble.TP) / (sum(tbl_mdl_hln_ensemble.TP) + sum(tbl_mdl_hln_ensemble.FP)); +prec_mdl_hln_net = sum(tbl_mdl_hln_net.TP) / (sum(tbl_mdl_hln_net.TP) + sum(tbl_mdl_hln_net.FP)); + +prec_mdl_nc_nb = sum(tbl_mdl_nc_nb.TP) / (sum(tbl_mdl_nc_nb.TP) + sum(tbl_mdl_nc_nb.FP)); +prec_mdl_nc_knn = sum(tbl_mdl_nc_knn.TP) / (sum(tbl_mdl_nc_knn.TP) + sum(tbl_mdl_nc_knn.FP)); +prec_mdl_nc_tree = sum(tbl_mdl_nc_tree.TP) / (sum(tbl_mdl_nc_tree.TP) + sum(tbl_mdl_nc_tree.FP)); +prec_mdl_nc_ecoc = sum(tbl_mdl_nc_ecoc.TP) / (sum(tbl_mdl_nc_ecoc.TP) + sum(tbl_mdl_nc_ecoc.FP)); +prec_mdl_nc_ensemble = sum(tbl_mdl_nc_ensemble.TP) / (sum(tbl_mdl_nc_ensemble.TP) + sum(tbl_mdl_nc_ensemble.FP)); +prec_mdl_nc_net = sum(tbl_mdl_nc_net.TP) / (sum(tbl_mdl_nc_net.TP) + sum(tbl_mdl_nc_net.FP)); + +prec_mdl_ng_nb = sum(tbl_mdl_ng_nb.TP) / (sum(tbl_mdl_ng_nb.TP) + sum(tbl_mdl_ng_nb.FP)); +prec_mdl_ng_knn = sum(tbl_mdl_ng_knn.TP) / (sum(tbl_mdl_ng_knn.TP) + sum(tbl_mdl_ng_knn.FP)); +prec_mdl_ng_tree = sum(tbl_mdl_ng_tree.TP) / (sum(tbl_mdl_ng_tree.TP) + sum(tbl_mdl_ng_tree.FP)); +prec_mdl_ng_ecoc = sum(tbl_mdl_ng_ecoc.TP) / (sum(tbl_mdl_ng_ecoc.TP) + sum(tbl_mdl_ng_ecoc.FP)); +prec_mdl_ng_ensemble = sum(tbl_mdl_ng_ensemble.TP) / (sum(tbl_mdl_ng_ensemble.TP) + sum(tbl_mdl_ng_ensemble.FP)); +prec_mdl_ng_net = sum(tbl_mdl_ng_net.TP) / (sum(tbl_mdl_ng_net.TP) + sum(tbl_mdl_ng_net.FP)); +% +rec_mdl_nb = sum(tbl_mdl_nb.TP) / (sum(tbl_mdl_nb.TP) + sum(tbl_mdl_nb.FN)); +rec_mdl_knn = sum(tbl_mdl_knn.TP) / (sum(tbl_mdl_knn.TP) + sum(tbl_mdl_knn.FN)); +rec_mdl_tree = sum(tbl_mdl_tree.TP) / (sum(tbl_mdl_tree.TP) + sum(tbl_mdl_tree.FN)); +rec_mdl_ecoc = sum(tbl_mdl_ecoc.TP) / (sum(tbl_mdl_ecoc.TP) + sum(tbl_mdl_ecoc.FN)); +rec_mdl_ensemble = sum(tbl_mdl_ensemble.TP) / (sum(tbl_mdl_ensemble.TP) + sum(tbl_mdl_ensemble.FN)); +rec_mdl_net = sum(tbl_mdl_net.TP) / (sum(tbl_mdl_net.TP) + sum(tbl_mdl_net.FN)); + +rec_mdl_hln_nb = sum(tbl_mdl_hln_nb.TP) / (sum(tbl_mdl_hln_nb.TP) + sum(tbl_mdl_hln_nb.FN)); +rec_mdl_hln_knn = sum(tbl_mdl_hln_knn.TP) / (sum(tbl_mdl_hln_knn.TP) + sum(tbl_mdl_hln_knn.FN)); +rec_mdl_hln_tree = sum(tbl_mdl_hln_tree.TP) / (sum(tbl_mdl_hln_tree.TP) + sum(tbl_mdl_hln_tree.FN)); +rec_mdl_hln_ecoc = sum(tbl_mdl_hln_ecoc.TP) / (sum(tbl_mdl_hln_ecoc.TP) + sum(tbl_mdl_hln_ecoc.FN)); +rec_mdl_hln_ensemble = sum(tbl_mdl_hln_ensemble.TP) / (sum(tbl_mdl_hln_ensemble.TP) + sum(tbl_mdl_hln_ensemble.FN)); +rec_mdl_hln_net = sum(tbl_mdl_hln_net.TP) / (sum(tbl_mdl_hln_net.TP) + sum(tbl_mdl_hln_net.FN)); + +rec_mdl_nc_nb = sum(tbl_mdl_nc_nb.TP) / (sum(tbl_mdl_nc_nb.TP) + sum(tbl_mdl_nc_nb.FN)); +rec_mdl_nc_knn = sum(tbl_mdl_nc_knn.TP) / (sum(tbl_mdl_nc_knn.TP) + sum(tbl_mdl_nc_knn.FN)); +rec_mdl_nc_tree = sum(tbl_mdl_nc_tree.TP) / (sum(tbl_mdl_nc_tree.TP) + sum(tbl_mdl_nc_tree.FN)); +rec_mdl_nc_ecoc = sum(tbl_mdl_nc_ecoc.TP) / (sum(tbl_mdl_nc_ecoc.TP) + sum(tbl_mdl_nc_ecoc.FN)); +rec_mdl_nc_ensemble = sum(tbl_mdl_nc_ensemble.TP) / (sum(tbl_mdl_nc_ensemble.TP) + sum(tbl_mdl_nc_ensemble.FN)); +rec_mdl_nc_net = sum(tbl_mdl_nc_net.TP) / (sum(tbl_mdl_nc_net.TP) + sum(tbl_mdl_nc_net.FN)); + +rec_mdl_ng_nb = sum(tbl_mdl_ng_nb.TP) / (sum(tbl_mdl_ng_nb.TP) + sum(tbl_mdl_ng_nb.FN)); +rec_mdl_ng_knn = sum(tbl_mdl_ng_knn.TP) / (sum(tbl_mdl_ng_knn.TP) + sum(tbl_mdl_ng_knn.FN)); +rec_mdl_ng_tree = sum(tbl_mdl_ng_tree.TP) / (sum(tbl_mdl_ng_tree.TP) + sum(tbl_mdl_ng_tree.FN)); +rec_mdl_ng_ecoc = sum(tbl_mdl_ng_ecoc.TP) / (sum(tbl_mdl_ng_ecoc.TP) + sum(tbl_mdl_ng_ecoc.FN)); +rec_mdl_ng_ensemble = sum(tbl_mdl_ng_ensemble.TP) / (sum(tbl_mdl_ng_ensemble.TP) + sum(tbl_mdl_ng_ensemble.FN)); +rec_mdl_ng_net = sum(tbl_mdl_ng_net.TP) / (sum(tbl_mdl_ng_net.TP) + sum(tbl_mdl_ng_net.FN)); +% +F_mdl_nb = 2*(prec_mdl_nb * rec_mdl_nb) / (prec_mdl_nb + rec_mdl_nb); +F_mdl_knn = 2*(prec_mdl_knn * rec_mdl_knn) / (prec_mdl_knn + rec_mdl_knn); +F_mdl_tree = 2*(prec_mdl_tree * rec_mdl_tree) / (prec_mdl_tree + rec_mdl_tree); +F_mdl_ecoc = 2*(prec_mdl_ecoc * rec_mdl_ecoc) / (prec_mdl_ecoc + rec_mdl_ecoc); +F_mdl_ensemble = 2*(prec_mdl_ensemble * rec_mdl_ensemble) / (prec_mdl_ensemble + rec_mdl_ensemble); +F_mdl_net = 2*(prec_mdl_net * rec_mdl_net) / (prec_mdl_net + rec_mdl_net); + +F_mdl_hln_nb = 2*(prec_mdl_hln_nb * rec_mdl_hln_nb) / (prec_mdl_hln_nb + rec_mdl_hln_nb); +F_mdl_hln_knn = 2*(prec_mdl_hln_knn * rec_mdl_hln_knn) / (prec_mdl_hln_knn + rec_mdl_hln_knn); +F_mdl_hln_tree = 2*(prec_mdl_hln_tree * rec_mdl_hln_tree) / (prec_mdl_hln_tree + rec_mdl_hln_tree); +F_mdl_hln_ecoc = 2*(prec_mdl_hln_ecoc * rec_mdl_hln_ecoc) / (prec_mdl_hln_ecoc + rec_mdl_hln_ecoc); +F_mdl_hln_ensemble = 2*(prec_mdl_hln_ensemble * rec_mdl_hln_ensemble) / (prec_mdl_hln_ensemble + rec_mdl_hln_ensemble); +F_mdl_hln_net = 2*(prec_mdl_hln_net * rec_mdl_hln_net) / (prec_mdl_hln_net + rec_mdl_hln_net); + +F_mdl_nc_nb = 2*(prec_mdl_nc_nb * rec_mdl_nc_nb) / (prec_mdl_nc_nb + rec_mdl_nc_nb); +F_mdl_nc_knn = 2*(prec_mdl_nc_knn * rec_mdl_nc_knn) / (prec_mdl_nc_knn + rec_mdl_nc_knn); +F_mdl_nc_tree = 2*(prec_mdl_nc_tree * rec_mdl_nc_tree) / (prec_mdl_nc_tree + rec_mdl_nc_tree); +F_mdl_nc_ecoc = 2*(prec_mdl_nc_ecoc * rec_mdl_nc_ecoc) / (prec_mdl_nc_ecoc + rec_mdl_nc_ecoc); +F_mdl_nc_ensemble = 2*(prec_mdl_nc_ensemble * rec_mdl_nc_ensemble) / (prec_mdl_nc_ensemble + rec_mdl_nc_ensemble); +F_mdl_nc_net = 2*(prec_mdl_nc_net * rec_mdl_nc_net) / (prec_mdl_nc_net + rec_mdl_nc_net); + +F_mdl_ng_nb = 2*(prec_mdl_ng_nb * rec_mdl_ng_nb) / (prec_mdl_ng_nb + rec_mdl_ng_nb); +F_mdl_ng_knn = 2*(prec_mdl_ng_knn * rec_mdl_ng_knn) / (prec_mdl_ng_knn + rec_mdl_ng_knn); +F_mdl_ng_tree = 2*(prec_mdl_ng_tree * rec_mdl_ng_tree) / (prec_mdl_ng_tree + rec_mdl_ng_tree); +F_mdl_ng_ecoc = 2*(prec_mdl_ng_ecoc * rec_mdl_ng_ecoc) / (prec_mdl_ng_ecoc + rec_mdl_ng_ecoc); +F_mdl_ng_ensemble = 2*(prec_mdl_ng_ensemble * rec_mdl_ng_ensemble) / (prec_mdl_ng_ensemble + rec_mdl_ng_ensemble); +F_mdl_ng_net = 2*(prec_mdl_ng_net * rec_mdl_ng_net) / (prec_mdl_ng_net + rec_mdl_ng_net); +% +acc_mdl_nb = (sum(tbl_mdl_nb.TP )+ sum(tbl_mdl_nb.TN)) / (sum(tbl_mdl_nb.TP) + sum(tbl_mdl_nb.FP) + sum(tbl_mdl_nb.TN) + sum(tbl_mdl_nb.FN)); +acc_mdl_knn = (sum(tbl_mdl_knn.TP )+ sum(tbl_mdl_knn.TN)) / (sum(tbl_mdl_knn.TP) + sum(tbl_mdl_knn.FP) + sum(tbl_mdl_knn.TN) + sum(tbl_mdl_knn.FN)); +acc_mdl_tree = (sum(tbl_mdl_tree.TP )+ sum(tbl_mdl_tree.TN)) / (sum(tbl_mdl_tree.TP) + sum(tbl_mdl_tree.FP) + sum(tbl_mdl_tree.TN) + sum(tbl_mdl_tree.FN)); +acc_mdl_ecoc = (sum(tbl_mdl_ecoc.TP )+ sum(tbl_mdl_ecoc.TN)) / (sum(tbl_mdl_ecoc.TP) + sum(tbl_mdl_ecoc.FP) + sum(tbl_mdl_ecoc.TN) + sum(tbl_mdl_ecoc.FN)); +acc_mdl_ensemble = (sum(tbl_mdl_ensemble.TP )+ sum(tbl_mdl_ensemble.TN)) / (sum(tbl_mdl_ensemble.TP) + sum(tbl_mdl_ensemble.FP) + sum(tbl_mdl_ensemble.TN) + sum(tbl_mdl_ensemble.FN)); +acc_mdl_net = (sum(tbl_mdl_net.TP )+ sum(tbl_mdl_net.TN)) / (sum(tbl_mdl_net.TP) + sum(tbl_mdl_net.FP) + sum(tbl_mdl_net.TN) + sum(tbl_mdl_net.FN)); + +acc_mdl_hln_nb = (sum(tbl_mdl_hln_nb.TP )+ sum(tbl_mdl_hln_nb.TN)) / (sum(tbl_mdl_hln_nb.TP) + sum(tbl_mdl_hln_nb.FP) + sum(tbl_mdl_hln_nb.TN) + sum(tbl_mdl_hln_nb.FN)); +acc_mdl_hln_knn = (sum(tbl_mdl_hln_knn.TP )+ sum(tbl_mdl_hln_knn.TN)) / (sum(tbl_mdl_hln_knn.TP) + sum(tbl_mdl_hln_knn.FP) + sum(tbl_mdl_hln_knn.TN) + sum(tbl_mdl_hln_knn.FN)); +acc_mdl_hln_tree = (sum(tbl_mdl_hln_tree.TP )+ sum(tbl_mdl_hln_tree.TN)) / (sum(tbl_mdl_hln_tree.TP) + sum(tbl_mdl_hln_tree.FP) + sum(tbl_mdl_hln_tree.TN) + sum(tbl_mdl_hln_tree.FN)); +acc_mdl_hln_ecoc = (sum(tbl_mdl_hln_ecoc.TP )+ sum(tbl_mdl_hln_ecoc.TN)) / (sum(tbl_mdl_hln_ecoc.TP) + sum(tbl_mdl_hln_ecoc.FP) + sum(tbl_mdl_hln_ecoc.TN) + sum(tbl_mdl_hln_ecoc.FN)); +acc_mdl_hln_ensemble = (sum(tbl_mdl_hln_ensemble.TP )+ sum(tbl_mdl_hln_ensemble.TN)) / (sum(tbl_mdl_hln_ensemble.TP) + sum(tbl_mdl_hln_ensemble.FP) + sum(tbl_mdl_hln_ensemble.TN) + sum(tbl_mdl_hln_ensemble.FN)); +acc_mdl_hln_net = (sum(tbl_mdl_hln_net.TP )+ sum(tbl_mdl_hln_net.TN)) / (sum(tbl_mdl_hln_net.TP) + sum(tbl_mdl_hln_net.FP) + sum(tbl_mdl_hln_net.TN) + sum(tbl_mdl_hln_net.FN)); + +acc_mdl_nc_nb = (sum(tbl_mdl_nc_nb.TP )+ sum(tbl_mdl_nc_nb.TN)) / (sum(tbl_mdl_nc_nb.TP) + sum(tbl_mdl_nc_nb.FP) + sum(tbl_mdl_nc_nb.TN) + sum(tbl_mdl_nc_nb.FN)); +acc_mdl_nc_knn = (sum(tbl_mdl_nc_knn.TP )+ sum(tbl_mdl_nc_knn.TN)) / (sum(tbl_mdl_nc_knn.TP) + sum(tbl_mdl_nc_knn.FP) + sum(tbl_mdl_nc_knn.TN) + sum(tbl_mdl_nc_knn.FN)); +acc_mdl_nc_tree = (sum(tbl_mdl_nc_tree.TP )+ sum(tbl_mdl_nc_tree.TN)) / (sum(tbl_mdl_nc_tree.TP) + sum(tbl_mdl_nc_tree.FP) + sum(tbl_mdl_nc_tree.TN) + sum(tbl_mdl_nc_tree.FN)); +acc_mdl_nc_ecoc = (sum(tbl_mdl_nc_ecoc.TP )+ sum(tbl_mdl_nc_ecoc.TN)) / (sum(tbl_mdl_nc_ecoc.TP) + sum(tbl_mdl_nc_ecoc.FP) + sum(tbl_mdl_nc_ecoc.TN) + sum(tbl_mdl_nc_ecoc.FN)); +acc_mdl_nc_ensemble = (sum(tbl_mdl_nc_ensemble.TP )+ sum(tbl_mdl_nc_ensemble.TN)) / (sum(tbl_mdl_nc_ensemble.TP) + sum(tbl_mdl_nc_ensemble.FP) + sum(tbl_mdl_nc_ensemble.TN) + sum(tbl_mdl_nc_ensemble.FN)); +acc_mdl_nc_net = (sum(tbl_mdl_nc_net.TP )+ sum(tbl_mdl_nc_net.TN)) / (sum(tbl_mdl_nc_net.TP) + sum(tbl_mdl_nc_net.FP) + sum(tbl_mdl_nc_net.TN) + sum(tbl_mdl_nc_net.FN)); + +acc_mdl_ng_nb = (sum(tbl_mdl_ng_nb.TP )+ sum(tbl_mdl_ng_nb.TN)) / (sum(tbl_mdl_ng_nb.TP) + sum(tbl_mdl_ng_nb.FP) + sum(tbl_mdl_ng_nb.TN) + sum(tbl_mdl_ng_nb.FN)); +acc_mdl_ng_knn = (sum(tbl_mdl_ng_knn.TP )+ sum(tbl_mdl_ng_knn.TN)) / (sum(tbl_mdl_ng_knn.TP) + sum(tbl_mdl_ng_knn.FP) + sum(tbl_mdl_ng_knn.TN) + sum(tbl_mdl_ng_knn.FN)); +acc_mdl_ng_tree = (sum(tbl_mdl_ng_tree.TP )+ sum(tbl_mdl_ng_tree.TN)) / (sum(tbl_mdl_ng_tree.TP) + sum(tbl_mdl_ng_tree.FP) + sum(tbl_mdl_ng_tree.TN) + sum(tbl_mdl_ng_tree.FN)); +acc_mdl_ng_ecoc = (sum(tbl_mdl_ng_ecoc.TP )+ sum(tbl_mdl_ng_ecoc.TN)) / (sum(tbl_mdl_ng_ecoc.TP) + sum(tbl_mdl_ng_ecoc.FP) + sum(tbl_mdl_ng_ecoc.TN) + sum(tbl_mdl_ng_ecoc.FN)); +acc_mdl_ng_ensemble = (sum(tbl_mdl_ng_ensemble.TP )+ sum(tbl_mdl_ng_ensemble.TN)) / (sum(tbl_mdl_ng_ensemble.TP) + sum(tbl_mdl_ng_ensemble.FP) + sum(tbl_mdl_ng_ensemble.TN) + sum(tbl_mdl_ng_ensemble.FN)); +acc_mdl_ng_net = (sum(tbl_mdl_ng_net.TP )+ sum(tbl_mdl_ng_net.TN)) / (sum(tbl_mdl_ng_net.TP) + sum(tbl_mdl_ng_net.FP) + sum(tbl_mdl_ng_net.TN) + sum(tbl_mdl_ng_net.FN)); +% +spec_mdl_nb = sum(tbl_mdl_nb.TN) / (sum(tbl_mdl_nb.TN) + sum(tbl_mdl_nb.FP)); +spec_mdl_knn = sum(tbl_mdl_knn.TN) / (sum(tbl_mdl_knn.TN) + sum(tbl_mdl_knn.FP)); +spec_mdl_tree = sum(tbl_mdl_tree.TN) / (sum(tbl_mdl_tree.TN) + sum(tbl_mdl_tree.FP)); +spec_mdl_ecoc = sum(tbl_mdl_ecoc.TN) / (sum(tbl_mdl_ecoc.TN) + sum(tbl_mdl_ecoc.FP)); +spec_mdl_ensemble = sum(tbl_mdl_ensemble.TN) / (sum(tbl_mdl_ensemble.TN) + sum(tbl_mdl_ensemble.FP)); +spec_mdl_net = sum(tbl_mdl_net.TN) / (sum(tbl_mdl_net.TN) + sum(tbl_mdl_net.FP)); + +spec_mdl_hln_nb = sum(tbl_mdl_hln_nb.TN) / (sum(tbl_mdl_hln_nb.TN) + sum(tbl_mdl_hln_nb.FP)); +spec_mdl_hln_knn = sum(tbl_mdl_hln_knn.TN) / (sum(tbl_mdl_hln_knn.TN) + sum(tbl_mdl_hln_knn.FP)); +spec_mdl_hln_tree = sum(tbl_mdl_hln_tree.TN) / (sum(tbl_mdl_hln_tree.TN) + sum(tbl_mdl_hln_tree.FP)); +spec_mdl_hln_ecoc = sum(tbl_mdl_hln_ecoc.TN) / (sum(tbl_mdl_hln_ecoc.TN) + sum(tbl_mdl_hln_ecoc.FP)); +spec_mdl_hln_ensemble = sum(tbl_mdl_hln_ensemble.TN) / (sum(tbl_mdl_hln_ensemble.TN) + sum(tbl_mdl_hln_ensemble.FP)); +spec_mdl_hln_net = sum(tbl_mdl_hln_net.TN) / (sum(tbl_mdl_hln_net.TN) + sum(tbl_mdl_hln_net.FP)); + +spec_mdl_nc_nb = sum(tbl_mdl_nc_nb.TN) / (sum(tbl_mdl_nc_nb.TN) + sum(tbl_mdl_nc_nb.FP)); +spec_mdl_nc_knn = sum(tbl_mdl_nc_knn.TN) / (sum(tbl_mdl_nc_knn.TN) + sum(tbl_mdl_nc_knn.FP)); +spec_mdl_nc_tree = sum(tbl_mdl_nc_tree.TN) / (sum(tbl_mdl_nc_tree.TN) + sum(tbl_mdl_nc_tree.FP)); +spec_mdl_nc_ecoc = sum(tbl_mdl_nc_ecoc.TN) / (sum(tbl_mdl_nc_ecoc.TN) + sum(tbl_mdl_nc_ecoc.FP)); +spec_mdl_nc_ensemble = sum(tbl_mdl_nc_ensemble.TN) / (sum(tbl_mdl_nc_ensemble.TN) + sum(tbl_mdl_nc_ensemble.FP)); +spec_mdl_nc_net = sum(tbl_mdl_nc_net.TN) / (sum(tbl_mdl_nc_net.TN) + sum(tbl_mdl_nc_net.FP)); + +spec_mdl_ng_nb = sum(tbl_mdl_ng_nb.TN) / (sum(tbl_mdl_ng_nb.TN) + sum(tbl_mdl_ng_nb.FP)); +spec_mdl_ng_knn = sum(tbl_mdl_ng_knn.TN) / (sum(tbl_mdl_ng_knn.TN) + sum(tbl_mdl_ng_knn.FP)); +spec_mdl_ng_tree = sum(tbl_mdl_ng_tree.TN) / (sum(tbl_mdl_ng_tree.TN) + sum(tbl_mdl_ng_tree.FP)); +spec_mdl_ng_ecoc = sum(tbl_mdl_ng_ecoc.TN) / (sum(tbl_mdl_ng_ecoc.TN) + sum(tbl_mdl_ng_ecoc.FP)); +spec_mdl_ng_ensemble = sum(tbl_mdl_ng_ensemble.TN) / (sum(tbl_mdl_ng_ensemble.TN) + sum(tbl_mdl_ng_ensemble.FP)); +spec_mdl_ng_net = sum(tbl_mdl_ng_net.TN) / (sum(tbl_mdl_ng_net.TN) + sum(tbl_mdl_ng_net.FP)); + +%% Make Final Tables +tbl_mdl = [tbl_mdl_nb;tbl_mdl_knn;tbl_mdl_tree;tbl_mdl_ecoc;tbl_mdl_ensemble;tbl_mdl_net;... + tbl_mdl_hln_nb;tbl_mdl_hln_knn;tbl_mdl_hln_tree;tbl_mdl_hln_ecoc;tbl_mdl_hln_ensemble;tbl_mdl_hln_net;... + tbl_mdl_nc_nb;tbl_mdl_nc_knn;tbl_mdl_nc_tree;tbl_mdl_nc_ecoc;tbl_mdl_nc_ensemble;tbl_mdl_nc_net;... + tbl_mdl_ng_nb;tbl_mdl_ng_knn;tbl_mdl_ng_tree;tbl_mdl_ng_ecoc;tbl_mdl_ng_ensemble;tbl_mdl_ng_net]; + +overall_tbl = [prec_mdl_nb, rec_mdl_nb, spec_mdl_nb, F_mdl_nb, acc_mdl_nb;... + prec_mdl_knn, rec_mdl_knn, spec_mdl_knn, F_mdl_knn, acc_mdl_knn;... + prec_mdl_tree, rec_mdl_tree, spec_mdl_tree, F_mdl_tree, acc_mdl_tree;... + prec_mdl_ecoc, rec_mdl_ecoc, spec_mdl_ecoc, F_mdl_ecoc, acc_mdl_ecoc;... + prec_mdl_ensemble, rec_mdl_ensemble, spec_mdl_ensemble, F_mdl_ensemble, acc_mdl_ensemble;... + prec_mdl_net, rec_mdl_net, spec_mdl_net, F_mdl_net, acc_mdl_net;... + + prec_mdl_hln_nb, rec_mdl_hln_nb, spec_mdl_hln_nb, F_mdl_hln_nb, acc_mdl_hln_nb;... + prec_mdl_hln_knn, rec_mdl_hln_knn, spec_mdl_hln_knn, F_mdl_hln_knn, acc_mdl_hln_knn;... + prec_mdl_hln_tree, rec_mdl_hln_tree, spec_mdl_hln_tree, F_mdl_hln_tree, acc_mdl_hln_tree;... + prec_mdl_hln_ecoc, rec_mdl_hln_ecoc, spec_mdl_hln_ecoc, F_mdl_hln_ecoc, acc_mdl_hln_ecoc;... + prec_mdl_hln_ensemble, rec_mdl_hln_ensemble, spec_mdl_hln_ensemble, F_mdl_hln_ensemble, acc_mdl_hln_ensemble;... + prec_mdl_hln_net, rec_mdl_hln_net, spec_mdl_hln_net, F_mdl_hln_net, acc_mdl_hln_net;... + + prec_mdl_nc_nb, rec_mdl_nc_nb, spec_mdl_nc_nb, F_mdl_nc_nb, acc_mdl_nc_nb;... + prec_mdl_nc_knn, rec_mdl_nc_knn, spec_mdl_nc_knn, F_mdl_nc_knn, acc_mdl_nc_knn;... + prec_mdl_nc_tree, rec_mdl_nc_tree, spec_mdl_nc_tree, F_mdl_nc_tree, acc_mdl_nc_tree;... + prec_mdl_nc_ecoc, rec_mdl_nc_ecoc, spec_mdl_nc_ecoc, F_mdl_nc_ecoc, acc_mdl_nc_ecoc;... + prec_mdl_nc_ensemble, rec_mdl_nc_ensemble, spec_mdl_nc_ensemble, F_mdl_nc_ensemble, acc_mdl_nc_ensemble;... + prec_mdl_nc_net, rec_mdl_nc_net, spec_mdl_nc_net, F_mdl_nc_net, acc_mdl_nc_net;... + + prec_mdl_ng_nb, rec_mdl_ng_nb, spec_mdl_ng_nb, F_mdl_ng_nb, acc_mdl_ng_nb;... + prec_mdl_ng_knn, rec_mdl_ng_knn, spec_mdl_ng_knn, F_mdl_ng_knn, acc_mdl_ng_knn;... + prec_mdl_ng_tree, rec_mdl_ng_tree, spec_mdl_ng_tree, F_mdl_ng_tree, acc_mdl_ng_tree;... + prec_mdl_ng_ecoc, rec_mdl_ng_ecoc, spec_mdl_ng_ecoc, F_mdl_ng_ecoc, acc_mdl_ng_ecoc;... + prec_mdl_ng_ensemble, rec_mdl_ng_ensemble, spec_mdl_ng_ensemble, F_mdl_ng_ensemble, acc_mdl_ng_ensemble;... + prec_mdl_ng_net, rec_mdl_ng_net, spec_mdl_ng_net, F_mdl_ng_net, acc_mdl_ng_net]; + +% +figure(); confusionchart(char(test2.Anot_Class), char(mdl_nb_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test2.Anot_Class), char(mdl_knn_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test2.Anot_Class), char(mdl_tree_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test2.Anot_Class), char(mdl_ecoc_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test2.Anot_Class), char(mdl_ensemble_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test2.Anot_Class), char(mdl_net_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); + +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_nb_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_knn_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_tree_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_ecoc_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_ensemble_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_hln.Anot_Class), char(mdl_hln_net_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); + +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_nb_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_knn_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_tree_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_ecoc_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_ensemble_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_nc.Anot_Class), char(mdl_nc_net_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); + +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_nb_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_knn_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_tree_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_ecoc_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_ensemble_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); +figure(); confusionchart(char(test_ng.Anot_Class), char(mdl_ng_net_pred), 'RowSummary','row-normalized','ColumnSummary','column-normalized'); + +%% Demonstration models +figure +confusionchart(feature_tbl_2235.Anot_Class,predict(mdl_auto_nc_unbal,feature_tbl_2235(:,(8:end))),'RowSummary','row-normalized','ColumnSummary','column-normalized') +title('confusion matrix 2235') +figure +confusionchart(feature_tbl_2181.Anot_Class,predict(mdl_auto_nc_unbal,feature_tbl_2181(:,(8:end))),'RowSummary','row-normalized','ColumnSummary','column-normalized') +title('confusion matrix 2181') + + +mdl_2181 = 1 - loss(mdl_auto_nc_unbal,feature_tbl_2181(:,[2,8:end]),'Anot_Class'); +mdl_2181_lbs = predict(mdl_auto_nc_unbal,feature_tbl_2181(:,[8:end])); + +mdl_2235 = 1 - loss(mdl_auto_nc_unbal,feature_tbl_2235(:,[4,8:end]),'Anot_Class'); +mdl_2235_lbs = predict(mdl_auto_nc_unbal,feature_tbl_2235(:,[8:end])); + +mdl_1163 = 1 - loss(mdl_auto_nc_unbal,feature_tbl_1163(:,[2,6:end]),'Anot_Class'); +mdl_1163_lbs = predict(mdl_auto_nc_unbal,feature_tbl_1163(:,[6:end])); + +%%%%%% +mdl_2181 = 1 - loss(mdl_auto_unbal_ng,feature_tbl_2181(:,[2,8:end]),'Anot_Class'); +mdl_2181_lbs = predict(new_mdl,table2array(feature_tbl_2181(:,8:end))); + +mdl_2235 = 1 - loss(mdl_auto_unbal_ng,feature_tbl_2235(:,4,8:end),'Anot_Class'); +mdl_2235_lbs = predict(new_mdl,table2array(feature_tbl_2235(:,8:end))); + +mdl_1163 = 1 - loss(mdl_auto_unbal_ng,feature_tbl_1163(:,2,6:end),'Anot_Class'); +mdl_1163_lbs = predict(new_mdl,table2array(feature_tbl_1163(:,6:end))); + +figure +confusionchart(train_ng.Anot_Class,predict(mdl_auto_unbal_ng,table2array(train_ng(:,2:25))),'RowSummary','row-normalized','ColumnSummary','column-normalized') +title('confusion matrix test') + + +%% Create Whole Mounts +% anot_names = {'Atrophy','Seminal_Vesicles','HGPIN','Tissue','G3','G4CG','G4FG','G5','Background'}; +% map = [0 0 0 % atrophy +% 0 0 255 +% 255 120 0 +% 220 140 200 %% +% 50 255 0 +% 255 20 255 +% 255 250 20 +% 0 255 255 +% 220 222 221]; +% +anot_names = {'Normal','G3','G4CG','G4FG','G5','Background'}; +map = [220 140 200 + 50 255 0 + 255 20 255 + 255 250 20 + 0 255 255 + 220 222 221]; + +% anot_names = {'Normal','Cancer','Background'}; +% map = [220 140 200 +% 50 255 0 +% 255 20 255 +% 255 250 20 +% 0 255 255 +% 255 255 255]; +% % 220 222 221]; + +anot_names = {'Normal','Low','High','Background'}; +map = [220 140 200 + 255 0 0 + 0 0 255 + 220 222 221]; +map = uint8(map); + +feature_tbl_2181 = [feature_tbl_2181 table(mdl_2181_lbs)]; +feature_tbl_2181.Properties.VariableNames{32} = 'prediction'; +feature_tbl_2181.prediction = categorical(feature_tbl_2181.prediction); + +for i = 1:numel(anot_names) + loc = find(feature_tbl_2181.prediction == anot_names{i}); + feature_tbl_2181(loc,33) = {i}; +end +feature_tbl_2181.Properties.VariableNames{33} = 'pred_indx'; + +wm2181 = zeros(34,41); +for h = 1:height(feature_tbl_2181) + tile = feature_tbl_2181.Tile_Name{h}; + name = strsplit(tile,{'_','.'}); + i = str2num(name{4}(2:end)); + j = str2num(name{5}(2:end)); + wm2181(j,i) = feature_tbl_2181.pred_indx(h); +end +wm2181(find(wm2181==0)) = numel(anot_names); + +figure(); +imagesc(wm2181); colormap(map); title('classifier'); + + +feature_tbl_2235 = [feature_tbl_2235 table(mdl_2235_lbs)]; +feature_tbl_2235.Tile_Name = cellstr(feature_tbl_2235.Tile_Name); +feature_tbl_2235.Properties.VariableNames{32} = 'prediction'; +feature_tbl_2235.prediction = categorical(feature_tbl_2235.prediction); +for i = 1:numel(anot_names) + loc = find(feature_tbl_2235.prediction == anot_names{i}); + feature_tbl_2235(loc,33) = {i}; +end +feature_tbl_2235.Properties.VariableNames{33} = 'pred_indx'; + + +wm2235 = zeros(24,31); +for h = 1:height(feature_tbl_2235) + tile = feature_tbl_2235.Tile_Name{h}; + name = strsplit(tile,{'_','.'}); + i = str2num(name{4}(2:end)); + j = str2num(name{5}(2:end)); + wm2235(j,i) = feature_tbl_2235.pred_indx(h); +end + +wm2235(find(wm2235==0)) = numel(anot_names); + +figure(); +imagesc(wm2235); colormap(map); title('classifier'); + + +feature_tbl_1163 = [feature_tbl_1163 table(mdl_1163_lbs)]; +feature_tbl_1163.Tile_Name = cellstr(feature_tbl_1163.Tile_Name); +feature_tbl_1163.Properties.VariableNames{30} = 'prediction'; +feature_tbl_1163.prediction = categorical(feature_tbl_1163.prediction); +for i = 1:numel(anot_names) + loc = find(feature_tbl_1163.prediction == anot_names{i}); + feature_tbl_1163(loc,31) = {i}; +end +feature_tbl_1163.Properties.VariableNames{31} = 'pred_indx'; + + +wm1163 = zeros(39,33); +for h = 1:height(feature_tbl_1163) + tile = feature_tbl_1163.Tile_Name{h}; + name = strsplit(tile,{'_','.'}); + i = str2num(name{4}(2:end)); + j = str2num(name{5}(2:end)); + wm1163(j,i) = feature_tbl_1163.pred_indx(h); +end + +wm1163(find(wm1163==0)) = numel(anot_names); + +figure(); +imagesc(wm1163); colormap(map); title('classifier'); + + +anot_2181 = imread('/Volumes/Hera/Prostate_Data/2181/Hist/9/Olympus/large_recon_8_ANOT.tif'); +anot_2181 = anot_2181(:,:,1:3); +whole_image2181 = imread('/Volumes/Hera/Prostate_Data/2181/Hist/9/Olympus/large_recon_8_nowhite.tiff'); + +[Seminal_Vesicles,Atrophy,HGPIN,G3,G4FG,G4CG,G5,tissue_mask] = color_thresh_masks(anot_2181,whole_image2181,0,0); + +% Normal vs Cancer +ken2181 = (Atrophy+HGPIN+Seminal_Vesicles+tissue_mask) + 2*G3 + 3*G4CG + 4*G4FG + 5*G5; +ken2181(find(ken2181==0)) = numel(anot_names); +% figure(); imagesc(ken2181); colormap(map); + +atari_2181 = imresize(ken2181,size(wm2181),'nearest'); +% figure(); imagesc(atari_2181); colormap(map) + +wm2181(find(atari_2181 == numel(anot_names))) = numel(anot_names); +atari_2181(find(wm2181 == numel(anot_names))) = numel(anot_names); +figure(); +subplot(121); imagesc(wm2181); colormap(map); title('classifier'); axis image +subplot(122); imagesc(atari_2181); colormap(map); title('ken'); axis image + +for i = 1:numel(anot_names) + comp_table2(i,1) = {anot_names{i}}; + comp_table2(i,2) = {numel(find(atari_2181 == i))}; % Ken volume + comp_table2(i,3) = {numel(find(wm2181 == i))}; % Classifier volume + comp_table2(i,4) = {dice((atari_2181==i),(wm2181==i))}; +end + +figure +b = bar(categorical(anot_names),cell2mat(comp_table2(:,2:3))); +xtips1 = b(1).XEndPoints; +ytips1 = b(1).YEndPoints; +labels1 = string(b(1).YData); +text(xtips1,ytips1,labels1,'HorizontalAlignment','center',... + 'VerticalAlignment','bottom') +xtips2 = b(2).XEndPoints; +ytips2 = b(2).YEndPoints; +labels2 = string(b(2).YData); +text(xtips2,ytips2,labels2,'HorizontalAlignment','center',... + 'VerticalAlignment','bottom') +title('2181 Volume'); + + + +anot_1163 = imread('/Volumes/Hera/Prostate_Data/1163/Hist/7/Olympus/large_recon_8_ANOT.tif'); +anot_1163= anot_1163(:,:,1:3); +whole_image1163 = imread('/Volumes/Hera/Prostate_Data/1163/Hist/7/Olympus/large_recon_8_nowhite.tiff'); + +[Seminal_Vesicles,Atrophy,HGPIN,G3,G4FG,G4CG,G5,tissue_mask] = color_thresh_masks(anot_1163,whole_image1163,0,0); + +% % % All Annotation Classes +% ken2181 = Atrophy + 2*Seminal_Vesicles + 3*HGPIN + 4*tissue_mask + 5*G3 + 6*G4CG + 7*G4FG + 8*G5; +% ken2181(find(ken2181==0)) = numel(anot_names); +% figure(); imagesc(ken2181); colormap(map) + +% Normal vs Cancer +ken1163 = (Atrophy+HGPIN+Seminal_Vesicles+tissue_mask) + 2*G3 + 3*G4CG + 4*G4FG + 5*G5; +ken1163(find(ken1163==0)) = numel(anot_names); +% figure(); imagesc(ken2181); colormap(map); + +atari_1163 = imresize(ken1163,size(wm1163),'nearest'); +% figure(); imagesc(atari_2181); colormap(map) + +wm1163(find(atari_1163 == numel(anot_names))) = numel(anot_names); +atari_1163(find(wm1163 == numel(anot_names))) = numel(anot_names); +figure(); +subplot(121); imagesc(wm1163); colormap(map); title('classifier'); axis image +subplot(122); imagesc(atari_1163); colormap(map); title('ken'); axis image + +for i = 1:numel(anot_names) + comp_table2(i,1) = {anot_names{i}}; + comp_table2(i,2) = {numel(find(atari_2181 == i))}; % Ken volume + comp_table2(i,3) = {numel(find(wm2181 == i))}; % Classifier volume + comp_table2(i,4) = {dice((atari_2181==i),(wm2181==i))}; +end + +figure +b = bar(categorical(anot_names),cell2mat(comp_table2(:,2:3))); +xtips1 = b(1).XEndPoints; +ytips1 = b(1).YEndPoints; +labels1 = string(b(1).YData); +text(xtips1,ytips1,labels1,'HorizontalAlignment','center',... + 'VerticalAlignment','bottom') +xtips2 = b(2).XEndPoints; +ytips2 = b(2).YEndPoints; +labels2 = string(b(2).YData); +text(xtips2,ytips2,labels2,'HorizontalAlignment','center',... + 'VerticalAlignment','bottom') +title('2181 Volume');