Naïve Bayes

Classification learning by Probability

 Syntax
dat4<-train
View(dat4) #plot ROC
library(ROCR)
Severityf<-as.factor(dat4$Severity)
library(pROC)
dat5<-dat4[-6]
roc_nb <- roc(test$Severity, as.numeric(Prediction_Nbayes[,2]))
View(dat5)
plot(roc_nb, print.thres="best", print.thres.best.method="closest.topleft",col="blue")
dat6<-cbind(dat5,Severityf) score<- Prediction_Nbayes
View(dat6)
Confus_Matrik_NBayes <- predict(nb_dat,test)
library(naivebayes) ConMat2 <-table(test$Severity, Confus_Matrik_NBayes)

nb_dat<- print(ConMat2)
naive_bayes(Severityf~BI_RADS+Age+Shape+Margin+Density,dat
a = dat6)
akurasi2 <- (sum(diag(ConMat2)))/sum(ConMat2)
nb_dat
presisi2 <- ConMat2[1,1]/(ConMat2[1,1]+ConMat2[2,1])
recall2 <- ConMat2[1,1]/(ConMat2[1,1]+ConMat2[1,2])
library(e1071) F12 <- (2*presisi2*recall2)/(presisi2+recall2)
Nbayes <- naiveBayes(Severityf~., data=dat6) tpr2<-recall2
Prediction_Nbayes <- predict(Nbayes, test,type="raw“) tnr2<-ConMat2[2,2]/(ConMat2[2,2]+ConMat2[2,1])
Syntax (2)
Prediction <- predict(nb_dat, test)
library(ModelMetrics)
auc_c50 <- auc(test$Severity, Prediction)
#packages ModelMetrics

cat("
AKURASI =",akurasi2,
"
PRESISI =",presisi2,
"
RECALL =",recall2,
"
F1 =",F12,
"
TPR =", tpr2,
"
TNR =", tnr2,
"
AUC =", auc_c50)
Naïve Bayes

Kekuatan kanker payudara

akan berpotensi ganas
apabila :
BI RADS : 4 - 5
Age : ≥ 40 tahun
Shape : lobular dan irregular
Margin : ill-defined dan
speculated
Density : iso dan low
Validation Test
Naïve Bayes

 Akurasi : 0,8625
 Presisi : 0,87037
 Recall : 0,85975
 F1 : 0,86503
 TPR : 0,85975
 TNR : 0,86538
 AUC : 0,8529

ROC Curve
Neural Network
Classification by connecting input to output by involving hidden layer and weights
 Syntax
# Encode as a one hot vector multilabel data
#Encode target variable
target_en <- class.ind(as.factor(comp$Severity))
age_en <- class.ind(as.factor(comp$Age))
BI_RADS_en <- class.ind(as.factor(comp$BI_RADS))
shape_en <- class.ind(as.factor(comp$Shape))
margin_en <- class.ind(as.factor(comp$Margin))
density_en <- class.ind(as.factor(comp$Density))
comp2<-
cbind(age_en,BI_RADS_en,shape_en,margin_en,d
ensity_en,target_en)
comp2<- as.data.frame(comp2)
View(comp2)
# Set labels name
colnames(comp2) <-
c("age1","age2","age3","BI_RADS2","BI_RADS3","BI_RAD
S4","BI_RADS5","shape1","shape2","shape3","shape4","
margin1","margin2","margin3","margin4","margin5","de
nsity1","density2","density3","density4","severity0","severi
ty1")
n <- names(comp2)
n
f <- as.formula(paste("severity0 + severity1 ~",
paste(n[!n %in% c("severity0","severity1")],collapse = "
+ ")))
nn <- neuralnet(f,data = comp2, hidden = c(4,
3),act.fct = "logistic", linear.output = FALSE,lifesign =
"minimal")
plot(nn)
tnr2<-ConMat2[2,2]/(ConMat2[2,2]+ConMat2[2,1])
 Prediction_NN <- predict(neural, test, type = "prob")
auc_NN <- auc(test$Severity, Prediction_NN[,2]) #packages

Syntax (2) ModelMetrics

auc_NN

cat("
library(caret) AKURASI =",akurasi3,
neural <- train(Severityf~., data=dat6, method="nnet", "
trace = FALSE, preProc = c("center","scale")) PRESISI =",presisi3,
plot(neural) "
RECALL =",recall3,
Confus_Matriks_NN <- predict(neural,test) "
ConMat3<-table(test$Severity, Confus_Matriks_NN) F1 =",F13,
"
print(ConMat3) TPR =", tpr3,
"
akurasi3 <- (sum(diag(ConMat3)))/sum(ConMat3) TNR =", tnr3,
presisi3 <- ConMat3[1,1]/(ConMat3[1,1]+ConMat3[2,1]) "
recall3 <- ConMat3[1,1]/(ConMat3[1,1]+ConMat3[1,2]) AUC =", auc_NN)
F13 <- (2*presisi3*recall3)/(presisi3+recall3)
tpr3<-recall3 #make ROC
tnr3<-ConMat3[2,2]/(ConMat3[2,2]+ConMat3[2,1]) plot(roc(test$Severity, Prediction_NN[,2]))
Neural Network

Input 2-level-hidden layer Output

Validation Test
Naïve Bayes

 Akurasi : 0,85625
 Presisi : 0,82417
 Recall : 0,91463
 F1 : 0,86705
 TPR : 0,91463
 TNR : 0,79487
 AUC : 0,93333

ROC Curve