R: Laplacian Eigenmaps

LaplacianEigenmaps-class {dimRed} | R Documentation

## Laplacian Eigenmaps

### Description

An S4 Class implementing Laplacian Eigenmaps

### Details

Laplacian Eigenmaps use a kernel and were originally developed to separate non-convex clusters under the name spectral clustering.

### Slots

`fun`

  A function that does the embedding and returns a dimRedResult object.

`stdpars`

  The standard parameters for the function.

### General usage

Dimensionality reduction methods are S4 Classes that either be used directly, in which case they have to be initialized and a full list with parameters has to be handed to the `@fun()` slot, or the method name be passed to the embed function and parameters can be given to the `...`, in which case missing parameters will be replaced by the ones in the `@stdpars`.

### Parameters

`LaplacianEigenmaps` can take the following parameters:

ndim

  the number of output dimensions.

sparse

  A character vector specifying hot to make the graph sparse, `"knn"` means that a K-nearest neighbor graph is constructed, `"eps"` an epsilon neighborhood graph is constructed, else a dense distance matrix is used.

knn

  The number of nearest neighbors to use for the knn graph.

eps

  The distance for the epsilon neighborhood graph.

t

  Parameter for the transformation of the distance matrix by w=exp(-d^2/t), larger values give less weight to differences in distance, `t == Inf` treats all distances != 0 equally.

norm

  logical, should the normed laplacian be used?

### Implementation

Wraps around `spec.emb`.

### References

Belkin, M., Niyogi, P., 2003. Laplacian Eigenmaps for Dimensionality Reduction and Data Representation. Neural Computation 15, 1373.

### Examples

    dat <- loadDataSet("3D S Curve")
    leim <- LaplacianEigenmaps()
    emb <- leim@fun(dat, leim@stdpars)

    plot(emb@data@data)

[Package dimRed version 0.1.0 Index]