--- a
+++ b/bin/knn.r
@@ -0,0 +1,112 @@
+setwd(".")
+options(stringsAsFactors = FALSE)
+# library("clusterSim")
+library("PRROC")
+library("e1071")
+
+source("./confusion_matrix_rates.r")
+threshold <- 0.5
+
+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 trainingset
+maxK <- 100 #NEW
+
+mcc_array <- character(length(maxK))
+
+# NEW PART:
+
+cat("\n[Optimization of the hyper-parameter k start]\n")
+# optimizaion loop
+for(thisK in 1:maxK)
+{
+  # 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("\n[Training the kNN model (with k=",thisK,") on training set & applying the kNN model to validation set]\n", sep="")
+  
+  cancer_data_validation_pred <- knn(train = cancer_data_train, test = cancer_data_validation, cl = cancer_data_train_labels, k=thisK)
+  cancer_data_validation_pred_binary <- as.numeric (cancer_data_validation_pred)-1
+   
+  mcc_outcome <- mcc(cancer_data_validation_labels, cancer_data_validation_pred_binary)
+  cat("When k=",thisK,", the MCC value is ",mcc_outcome, "\t (worst possible: -1; best possible: +1)\n", sep="")
+  
+  mcc_array[thisK] <- mcc_outcome
+  
+}
+
+# select the k corresponding to the highest MCC and call it k_best
+bestMCC <- max(mcc_array)
+bestK <- match(bestMCC, mcc_array)
+cat("\nThe best k value is ", bestK,", corresponding to MCC=", mcc_array[bestK],"\n", sep="")
+
+cat("[Optimization end]\n\n")
+
+cat("\n @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ @ \n")
+
+# apply k-NN with k_best to the test set
+
+cat("[Training the kNN model (with the OPTIMIZED hyper-parameter k=",bestK,") on training set & applying the kNN 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)
+
+cancer_data_test_pred <- as.numeric(cancer_data_test_pred)-1
+
+
+confusion_matrix_rates(cancer_data_test_labels, cancer_data_test_pred, "@@@ Test set @@@")
+