--- a
+++ b/bin/svm.r
@@ -0,0 +1,136 @@
+setwd(".")
+options(stringsAsFactors = FALSE)
+#library("clusterSim")
+library("e1071")
+library("PRROC")
+tau = 0.5
+
+source("./confusion_matrix_rates.r")
+
+dataFileName <- "../data/LungCancerDataset_AllRecords_NORM_27reduced_features.csv"
+cat("dataFileName = ", dataFileName, "\n", sep="")
+
+cancer_data_norm <- read.csv(file=dataFileName,head=TRUE,sep=",",stringsAsFactors=FALSE)
+cancer_data_norm <- cancer_data_norm[sample(nrow(cancer_data_norm)),] # shuffle the rows
+
+totalElements <- dim(cancer_data_norm)[1]
+
+subsets_size <- 4000
+
+if (subsets_size != totalElements) {
+    cat("!!! ATTENTION: We are running the method on a subset of the original dataset, \n", sep="")
+    cat("!!! containing only ", subsets_size, " elements \n", sep="")
+    cat("!!! instead of ", totalElements, " elements \n", sep="")
+}
+
+cancer_data_norm <- cancer_data_norm[1:subsets_size, ]
+
+dataset_dim_retriever(cancer_data_norm)
+imbalance_retriever(cancer_data_norm$Metastasis)
+
+target_index <- dim(cancer_data_norm)[2]
+
+training_set_perce <- 60
+cat("training_set_perce = ", training_set_perce, "% \n", sep="")
+validation_set_perce <- 20
+cat("validation_set_perce = ", validation_set_perce, "% \n", sep="")
+test_set_perce <- 100 - training_set_perce - validation_set_perce
+cat("test_set_perce = ", test_set_perce, "% \n", sep="")
+
+# the training set is the first 60% of the whole dataset
+training_set_first_index <- 1 # NEW
+training_set_last_index <- round(dim(cancer_data_norm)[1]*training_set_perce/100) # NEW
+
+# the validation set is the following 20% of the whole dataset
+validation_set_first_index <- round(dim(cancer_data_norm)[1]*training_set_perce/100)+1 # NEW
+validation_set_last_index <- round(dim(cancer_data_norm)[1]*(training_set_perce+validation_set_perce)/100) # NEW
+
+# the test set is the last 20% of the whole dataset
+test_set_first_index <- round(dim(cancer_data_norm)[1]*(training_set_perce+validation_set_perce)/100)+1 # NEW
+test_set_last_index <- dim(cancer_data_norm)[1] # NEW
+
+cat("[Creating the subsets for the values]\n")
+cancer_data_train <- cancer_data_norm[training_set_first_index:training_set_last_index, 1:(target_index-1)] # NEW
+cancer_data_validation <- cancer_data_norm[validation_set_first_index:validation_set_last_index, 1:(target_index-1)] # NEW
+cancer_data_test <- cancer_data_norm[test_set_first_index:test_set_last_index, 1:(target_index-1)] # NEW
+
+
+
+cat("[Creating the subsets for the labels \"1\"-\"0\"]\n")
+cancer_data_train_labels <- cancer_data_norm[training_set_first_index:training_set_last_index, target_index] # NEW
+cancer_data_validation_labels <- cancer_data_norm[validation_set_first_index:validation_set_last_index, target_index] # NEW
+cancer_data_test_labels <- cancer_data_norm[test_set_first_index:test_set_last_index, target_index]   # NEW
+
+library(class)
+library(gmodels)
+
+# The k value must be lower than the size of the training set
+maxK <- 10 #NEW
+
+mcc_array <- character(length(maxK))
+
+# NEW PART:
+
+c_array = c(0.001, 0.01, 0.1, 1, 10)
+mccCounter = 1
+
+cat("\n[Optimization of the hyper-parameter C start]\n")
+# optimizaion loop
+for(thisC in c_array)
+{
+  # apply k-NN with the current K value
+  # train on the training set, evaluate in the validation set by computing the MCC
+  # save the MCC corresponding to the current K value
+  
+  cat("[Training the SVM model (with C=",thisC,") on training set & applying the SVM model to validation set]\n", sep="")
+  
+  svm_model <- svm(cancer_data_train_labels ~ ., cost=thisC, data=cancer_data_train, method = "C-classification", kernel = "linear")
+    
+  cancer_data_validation_PRED <- predict(svm_model, cancer_data_validation)
+  
+  cancer_data_validation_pred_binary <- as.numeric (cancer_data_validation_PRED)  
+  cancer_data_validation_pred_binary[cancer_data_validation_pred_binary>=tau]<-1
+  cancer_data_validation_pred_binary[cancer_data_validation_pred_binary<tau]<-0
+  
+#   # cancer_data_validation_pred_binary
+#    fg_test <- cancer_data_validation_PRED[cancer_data_validation_labels==1]
+#    bg_test <- cancer_data_validation_PRED[cancer_data_validation_labels==0]
+# 
+#    pr_curve_val <- pr.curve(scores.class0 = fg_test, scores.class1 = bg_test, curve = F)
+#    # plot(pr_curve_test)
+#    # print(pr_curve_val)
+# 
+#    roc_curve_val  <- roc.curve(scores.class0 = fg_test, scores.class1 = bg_test, curve = F)
+#    # plot(pr_curve_test)
+  # print(roc_curve_val)
+  
+  mcc_outcome <- mcc(cancer_data_validation_labels, cancer_data_validation_pred_binary)
+  
+  cat("When C=",thisC,", the MCC value is ",mcc_outcome, "\t (worst possible: -1; best possible: +1)\n", sep="")
+  
+  mcc_array[mccCounter] <- mcc_outcome
+  mccCounter = mccCounter + 1
+}
+
+# select the k corresponding to the highest MCC and call it k_best
+bestMCC <- max(mcc_array)
+bestCindex <- match(bestMCC, mcc_array)
+cat("\nThe best C value is ", c_array[bestCindex],", corresponding to MCC=", mcc_array[bestCindex],"\n", sep="")
+
+cat("[Optimization end]\n\n")
+
+cat("\n @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ \n")
+
+# apply k-NN with k_best to the test set
+
+cat("\n[Training the SVM model (with the OPTIMIZED hyper-parameter C=",c_array[bestCindex],") on training set & applying the SVM to the test set]\n", sep="")
+#cancer_data_test_pred <- knn(train = cancer_data_train, test = cancer_data_test, cl = cancer_data_train_labels, k=bestK)
+
+svm_model_new <- svm(cancer_data_train_labels ~ ., cost=c_array[bestCindex], data=cancer_data_train, method = "C-classification", kernel = "linear")
+cancer_data_test_pred <- predict(svm_model_new, cancer_data_test)
+  
+
+confusion_matrix_rates(cancer_data_test_labels, cancer_data_test_pred, "@@@ Test set @@@")
+
+
+