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Support Vector Machine With Multiple Classes

This document discusses support vector machines (SVMs) with multiple classes. It first generates simulated data with 3 classes and fits an SVM model with a radial kernel to classify the data. Parameter tuning is then performed to find the best gamma and cost values. Next, gene expression data from a book is used to classify samples into 4 classes with a linear kernel SVM. Parameter tuning is again implemented to select the optimal cost. Performance is assessed on test data, showing the model can accurately classify samples into the 4 known classes.

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6K views5 pages

Support Vector Machine With Multiple Classes

This document discusses support vector machines (SVMs) with multiple classes. It first generates simulated data with 3 classes and fits an SVM model with a radial kernel to classify the data. Parameter tuning is then performed to find the best gamma and cost values. Next, gene expression data from a book is used to classify samples into 4 classes with a linear kernel SVM. Parameter tuning is again implemented to select the optimal cost. Performance is assessed on test data, showing the model can accurately classify samples into the 4 known classes.

Uploaded by

api-285777244
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Support Vector Machine with Multiple Classes

YIK LUN, KEI


allen29@ucla.edu
This paper is a lab from the book called An Introduction to Statistical Learning
with Applications in R. All R codes and comments below are belonged to the
book and authors.

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x[,2]

library(e1071)
set.seed(1)
x=matrix(rnorm(200*2),ncol=2);y=c(rep(1,150),rep(2,50))
x[1:100,]=x[1:100,]+2;x[101:150,]= x[101:150,]-2
x=rbind(x,matrix(rnorm(50*2),ncol =2));y=c(y,rep(0 ,50))
x[y==0,2]= x[y==0,2]+2
dat=data.frame(x=x, y=as.factor(y))
plot(x,col =(y+1))

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x[,1]

SVM
svmfit=svm(y~., data=dat , kernel ="radial", cost =10, gamma =1)
plot(svmfit , dat)

SVM classification plot

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tune
set.seed (1)
tune.out=tune(svm , y~., data=dat, kernel ="radial",
ranges =list(cost=c(0.1 ,1 ,10 ,100 ,1000),
gamma=c(0.5,1,2,3,4) ))
tune.out$best.model
##
## Call:
## best.tune(method = svm, train.x = y ~ ., data = dat, ranges = list(cost = c(0.1,
##
1, 10, 100, 1000), gamma = c(0.5, 1, 2, 3, 4)), kernel = "radial")
##
##
## Parameters:
##
SVM-Type: C-classification
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## SVM-Kernel: radial
##
cost: 1
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gamma: 0.5
##
## Number of Support Vectors:

125

svmfit=svm(y~., data=dat , kernel ="radial", cost =10, gamma =2)


plot(svmfit , dat)

SVM classification plot

x.2

Gene Expression Data


library(ISLR)
dat=data.frame(x=Khan$xtrain , y=as.factor(Khan$ytrain))
out=svm(y~., data=dat , kernel ="linear",cost =10)
summary(out)

##
## Call:
## svm(formula = y ~ ., data = dat, kernel = "linear", cost = 10)
##
##
## Parameters:
3

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##
SVM-Type: C-classification
## SVM-Kernel: linear
##
cost: 10
##
gamma: 0.0004332756
##
## Number of Support Vectors: 58
##
## ( 20 20 11 7 )
##
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## Number of Classes: 4
##
## Levels:
## 1 2 3 4
dat.te=data.frame(x=Khan$xtest , y=as.factor (Khan$ytest ))
pred.te=predict (out , newdata =dat.te)
table(pred.te,dat.te$y)
##
## pred.te 1 2 3 4
##
1 3 0 0 0
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2 0 6 2 0
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3 0 0 4 0
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4 0 0 0 5
tune.out=tune(svm , y~., data=dat, kernel ="linear",
ranges =list(cost=c(0.1 ,1 ,10)))
tune.out$best.model
##
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Call:
best.tune(method = svm, train.x = y ~ ., data = dat, ranges = list(cost = c(0.1,
1, 10)), kernel = "linear")

Parameters:
SVM-Type:
SVM-Kernel:
cost:
gamma:

C-classification
linear
0.1
0.0004332756

Number of Support Vectors:

58

out=svm(y~., data=dat , kernel ="linear",cost =0.1)


dat.te=data.frame(x=Khan$xtest , y=as.factor (Khan$ytest))
pred.te=predict (out , newdata =dat.te)
table(pred.te,dat.te$y)
##
## pred.te 1 2 3 4
##
1 3 0 0 0
4

##
##
##

2 0 6 2 0
3 0 0 4 0
4 0 0 0 5

Reference:
James, Gareth, et al. An introduction to statistical learning. New
York: springer, 2013.

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