kerntools (version 1.2.0)

svm_imp: SVM feature importance

Description

Recovering the features importances from a SVM model.

Usage

svm_imp(
  X,
  svindx,
  coeff,
  result = "absolute",
  cos.norm = FALSE,
  center = FALSE,
  scale = FALSE
)

Value

The importance of each feature (a vector).

Arguments

X

Matrix or data.frame that contains real numbers ("integer", "float" or "double"). X is NOT the kernel matrix, but the original dataset used to compute the kernel matrix.

svindx

Indices of the support vectors.

coeff

target * alpha.

result

A string. If "absolute", the absolute values of the importances are returned. If "squared", the squared values are returned. Any other input will result in the original (positive and/or negative) importance values (see Details). (Defaults: "absolute").

cos.norm

Boolean. Was the data cosine normalized prior to training the model? (Defaults: FALSE).

center

Boolean. Was the data centered prior to training the model? (Defaults: FALSE).

scale

Boolean. Was the data scaled prior to training the model? (Defaults: FALSE).

Details

This function may be not valid for all kernels. Do not use it with the RBF, Laplacian, Bray-Curtis, Jaccard/Ruzicka, or Kendall's tau kernels unless you know exactly what you are doing.

Usually the sign of the importances is irrelevant, thus justifying working with the absolute or squared values; see for instance Guyon et al. (2002). Some classification tasks are an exception to this, when it can be demonstrated that the feature space is strictly nonnegative. In that case, a positive importance implies that a feature contributes to the "positive" class, and the same with a negative importance and the "negative" class.

References

Guyon, I., Weston, J., Barnhill, S., and Vapnik, V. (2002) Gene selection for cancer classification using support vector machines. Machine learning, 46, 389-422. Link

Examples

data1 <- iris[1:100,]
sv_index <- c( 24, 42, 58, 99)
coefficients <- c(-0.2670988, -0.3582848,  0.2129282,  0.4124554)
# This SV and coefficients were obtained from a model generated with kernlab:
# model <- kernlab::ksvm(Species ~ .,data=data1, kernel="vanilladot",scaled = TRUE)
# sv_index <- unlist(kernlab::alphaindex(model))
# coefficients <- kernlab::unlist(coef(model))
# Now we compute the importances:
svm_imp(X=data1[,-5],svindx=sv_index,coeff=coefficients,center=TRUE,scale=TRUE)