R: Kernel Maximum Mean Discrepancy.

kmmd {kernlab} | R Documentation

## Kernel Maximum Mean Discrepancy.

### Description

The Kernel Maximum Mean Discrepancy `kmmd` performs a non-parametric distribution test.

### Usage

    ## S4 method for signature 'matrix'
    kmmd(x, y, kernel="rbfdot",kpar="automatic", alpha = 0.05,
         asymptotic = FALSE, replace = TRUE, ntimes = 150, frac = 1, ...)

    ## S4 method for signature 'kernelMatrix'
    kmmd(x, y, Kxy, alpha = 0.05,
         asymptotic = FALSE, replace = TRUE, ntimes = 100, frac = 1, ...)

    ## S4 method for signature 'list'
    kmmd(x, y, kernel="stringdot",
         kpar = list(type = "spectrum", length = 4), alpha = 0.05,
         asymptotic = FALSE, replace = TRUE, ntimes = 150, frac = 1, ...)

### Arguments

`x` | data values, in a `matrix`, `list`, or `kernelMatrix`
`y` | data values, in a `matrix`, `list`, or `kernelMatrix`
`Kxy` | `kernlMatrix` between x and y values (only for the kernelMatrix interface)
`kernel` | the kernel function used in training and predicting. This parameter can be set to any function, of class kernel, which computes a dot product between two vector arguments. `kernlab` provides the most popular kernel functions which can be used by setting the kernel parameter to the following strings: `rbfdot` Radial Basis kernel function "Gaussian" `polydot` Polynomial kernel function `vanilladot` Linear kernel function `tanhdot` Hyperbolic tangent kernel function `laplacedot` Laplacian kernel function `besseldot` Bessel kernel function `anovadot` ANOVA RBF kernel function `splinedot` Spline kernel `stringdot` String kernel The kernel parameter can also be set to a user defined function of class kernel by passing the function name as an argument.
`kpar` | the list of hyper-parameters (kernel parameters). This is a list which contains the parameters to be used with the kernel function. Valid parameters for existing kernels are : `sigma` inverse kernel width for the Radial Basis kernel function "rbfdot" and the Laplacian kernel "laplacedot". `degree, scale, offset` for the Polynomial kernel "polydot" `scale, offset` for the Hyperbolic tangent kernel function "tanhdot" `sigma, order, degree` for the Bessel kernel "besseldot". `sigma, degree` for the ANOVA kernel "anovadot". `lenght, lambda, normalized` for the "stringdot" kernel where length is the length of the strings considered, lambda the decay factor and normalized a logical parameter determining if the kernel evaluations should be normalized. Hyper-parameters for user defined kernels can be passed through the `kpar` parameter as well. In the case of a Radial Basis kernel function (Gaussian) kpar can also be set to the string "automatic" which uses the heuristics in 'sigest' to calculate a good 'sigma' value for the Gaussian RBF or Laplace kernel, from the data. (default = "automatic").
`alpha` | the confidence level of the test (default: 0.05)
`asymptotic` | calculate the bounds asymptotically (suitable for smaller datasets) (default: FALSE)
`replace` | use replace when sampling for computing the asymptotic bounds (default : TRUE)
`ntimes` | number of times repeating the sampling procedure (default : 150)
`frac` | fraction of points to sample (frac : 1)
`...` | additional parameters.

### Details

`kmmd` calculates the kernel maximum mean discrepancy for samples from two distributions and conducts a test as to whether the samples are from different distributions with level `alpha`.

### Value

An S4 object of class `kmmd` containing the results of whether the H0 hypothesis is rejected or not. H0 being that the samples x and y come from the same distribution. The object contains the following slots :

``H0`` | is H0 rejected (logical)
``AsympH0`` | is H0 rejected according to the asymptotic bound (logical)
``kernelf`` | the kernel function used.
``mmdstats`` | the test statistics (vector of two)
``Radbound`` | the Rademacher bound
``Asymbound`` | the asymptotic bound

see `kmmd-class` for more details.

### Author(s)

Alexandros Karatzoglou
alexandros.karatzoglou@ci.tuwien.ac.at

### References

Gretton, A., K. Borgwardt, M. Rasch, B. Schoelkopf and A. Smola
A Kernel Method for the Two-Sample-Problem
Neural Information Processing Systems 2006, Vancouver
http://papers.nips.cc/paper/3110-a-kernel-method-for-the-two-sample-problem.pdf

### See Also

`ksvm`

### Examples

    # create data
    x <- matrix(runif(300),100)
    y <- matrix(runif(300)+1,100)

    mmdo <- kmmd(x, y)

    mmdo

[Package kernlab version 0.9-25 Index]