svm: Support Vector Machines

Description

svm is used to train a support vector machine. It can be used to carry out general regression and classification (of nu and epsilon-type), as well as density-estimation. A formula interface is provided.

Usage

## S3 method for class 'formula':
svm(formula, data = NULL, ..., subset, na.action =
na.omit, scale = TRUE)
## S3 method for class 'default':
svm(x, y = NULL, scale = TRUE, type = NULL, kernel =
"radial", degree = 3, gamma = if (is.vector(x)) 1 else 1 / ncol(x),
coef0 = 0, cost = 1, nu = 0.5,
class.weights = NULL, cachesize = 40, tolerance = 0.001, epsilon = 0.1,
shrinking = TRUE, cross = 0, probability = FALSE, fitted = TRUE, 
..., subset, na.action = na.omit)

Arguments

formula

a symbolic description of the model to be fit.

data

an optional data frame containing the variables in the model. By default the variables are taken from the environment which svm is called from.

a data matrix, a vector, or a sparse matrix (object of class Matrix provided by the Matrix package, or of class matrix.csr

a response vector with one label for each row/component of x. Can be either a factor (for classification tasks) or a numeric vector (for regression).

scale

A logical vector indicating the variables to be scaled. If scale is of length 1, the value is recycled as many times as needed. Per default, data are scaled internally (both x and y variables) to zero

type

svm can be used as a classification machine, as a regression machine, or for novelty detection. Depending of whether y is a factor or not, the default setting for type is C-classification or

kernel

the kernel used in training and predicting. You might consider changing some of the following parameters, depending on the kernel type. [object Object],[object Object],[object Object],[object Object]

degree

parameter needed for kernel of type polynomial (default: 3)

gamma

parameter needed for all kernels except linear (default: 1/(data dimension))

coef0

parameter needed for kernels of type polynomial and sigmoid (default: 0)

cost

cost of constraints violation (default: 1)---it is the C-constant of the regularization term in the Lagrange formulation.

parameter needed for nu-classification, nu-regression, and one-classification

class.weights

a named vector of weights for the different classes, used for asymmetric class sizes. Not all factor levels have to be supplied (default weight: 1). All components have to be named.

cachesize

cache memory in MB (default 40)

tolerance

tolerance of termination criterion (default: 0.001)

epsilon

epsilon in the insensitive-loss function (default: 0.1)

shrinking

option whether to use the shrinking-heuristics (default: TRUE)

cross

if a integer value k>0 is specified, a k-fold cross validation on the training data is performed to assess the quality of the model: the accuracy rate for classification and the Mean Squared Error for regression

fitted

logical indicating whether the fitted values should be computed and included in the model or not (default: TRUE)

probability

logical indicating whether the model should allow for probability predictions.

...

additional parameters for the low level fitting function svm.default

subset

An index vector specifying the cases to be used in the training sample. (NOTE: If given, this argument must be named.)

na.action

A function to specify the action to be taken if NAs are found. The default action is na.omit, which leads to rejection of cases with missing values on any required variable. An alternative is na.fail<

Value

An object of class "svm" containing the fitted model, including:
SVThe resulting support vectors (possibly scaled).
indexThe index of the resulting support vectors in the data matrix. Note that this index refers to the preprocessed data (after the possible effect of na.omit and subset)
coefsThe corresponding coefficients times the training labels.
rhoThe negative intercept.
sigmaIn case of a probabilistic regression model, the scale parameter of the hypothesized (zero-mean) laplace distribution estimated by maximum likelihood.
probA, probBnumeric vectors of length k(k-1)/2, k number of classes, containing the parameters of the logistic distributions fitted to the decision values of the binary classifiers (1 / (1 + exp(a x + b))).

Details

For multiclass-classification with k levels, k>2, libsvm uses the one-against-one-approach, in which k(k-1)/2 binary classifiers are trained; the appropriate class is found by a voting scheme. libsvm internally uses a sparse data representation, which is also high-level supported by the package SparseM. If the predictor variables include factors, the formula interface must be used to get a correct model matrix.

plot.svm allows a simple graphical visualization of classification models.

The probability model for classification fits a logistic distribution using maximum likelihood to the decision values of all binary classifiers, and computes the a-posteriori class probabilities for the multi-class problem using quadratic optimization. The probabilistic regression model assumes (zero-mean) laplace-distributed errors for the predictions, and estimates the scale parameter using maximum likelihood.

References

Chang, Chih-Chung and Lin, Chih-Jen: LIBSVM: a library for Support Vector Machines http://www.csie.ntu.edu.tw/~cjlin/libsvm
Exact formulations of models, algorithms, etc. can be found in the document: Chang, Chih-Chung and Lin, Chih-Jen: LIBSVM: a library for Support Vector Machines http://www.csie.ntu.edu.tw/~cjlin/papers/libsvm.ps.gz
More implementation details and speed benchmarks can be found on: Rong-En Fan and Pai-Hsune Chen and Chih-Jen Lin: Working Set Selection Using the Second Order Information for Training SVM http://www.csie.ntu.edu.tw/~cjlin/papers/quadworkset.pdf

Examples

Run this code

data(iris)
attach(iris)

## classification mode
# default with factor response:
model <- svm(Species ~ ., data = iris)

# alternatively the traditional interface:
x <- subset(iris, select = -Species)
y <- Species
model <- svm(x, y) 

print(model)
summary(model)

# test with train data
pred <- predict(model, x)
# (same as:)
pred <- fitted(model)

# Check accuracy:
table(pred, y)

# compute decision values and probabilities:
pred <- predict(model, x, decision.values = TRUE)
attr(pred, "decision.values")[1:4,]

# visualize (classes by color, SV by crosses):
plot(cmdscale(dist(iris[,-5])),
     col = as.integer(iris[,5]),
     pch = c("o","+")[1:150 %in% model$index + 1])

## try regression mode on two dimensions

# create data
x <- seq(0.1, 5, by = 0.05)
y <- log(x) + rnorm(x, sd = 0.2)

# estimate model and predict input values
m   <- svm(x, y)
new <- predict(m, x)

# visualize
plot(x, y)
points(x, log(x), col = 2)
points(x, new, col = 4)

## density-estimation

# create 2-dim. normal with rho=0:
X <- data.frame(a = rnorm(1000), b = rnorm(1000))
attach(X)

# traditional way:
m <- svm(X, gamma = 0.1)

# formula interface:
m <- svm(~., data = X, gamma = 0.1)
# or:
m <- svm(~ a + b, gamma = 0.1)

# test:
newdata <- data.frame(a = c(0, 4), b = c(0, 4))
predict (m, newdata)

# visualize:
plot(X, col = 1:1000 %in% m$index + 1, xlim = c(-5,5), ylim=c(-5,5))
points(newdata, pch = "+", col = 2, cex = 5)

# weights: (example not particularly sensible)
i2 <- iris
levels(i2$Species)[3] <- "versicolor"
summary(i2$Species)
wts <- 100 / table(i2$Species)
wts
m <- svm(Species ~ ., data = i2, class.weights = wts)

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