nonlinear_LISOMAP: Landmark Isometric Feature Mapping

In Rdimtools: Dimension Reduction and Estimation Methods

Landmark Isometric Feature Mapping

Description

Landmark Isomap is a variant of Isomap in that it first finds a low-dimensional embedding using a small portion of given dataset and graft the others in a manner to preserve as much pairwise distance from all the other data points to landmark points as possible.

Usage

do.lisomap(
  X,
  ndim = 2,
  ltype = c("random", "MaxMin"),
  npoints = max(nrow(X)/5, ndim + 1),
  preprocess = c("center", "scale", "cscale", "decorrelate", "whiten"),
  type = c("proportion", 0.1),
  symmetric = c("union", "intersect", "asymmetric"),
  weight = TRUE
)

Arguments

X	an (n\times p) matrix or data frame whose rows are observations and columns represent independent variables.
ndim	an integer-valued target dimension.
ltype	on how to select landmark points, either "random" or "MaxMin".
npoints	the number of landmark points to be drawn.
preprocess	an option for preprocessing the data. Default is "center". See also aux.preprocess for more details.
type	a vector of neighborhood graph construction. Following types are supported; c("knn",k), c("enn",radius), and c("proportion",ratio). Default is c("proportion",0.1), connecting about 1/10 of nearest data points among all data points. See also aux.graphnbd for more details.
symmetric	one of "intersect", "union" or "asymmetric" is supported. Default is "union". See also aux.graphnbd for more details.
weight	TRUE to perform Landmark Isomap on weighted graph, or FALSE otherwise.

Value

a named list containing

Y

an (n\times ndim) matrix whose rows are embedded observations.

trfinfo

a list containing information for out-of-sample prediction.

Author(s)

Kisung You

References

\insertRef

silva_global_2003Rdimtools

See Also

do.isomap

Examples

## use iris data
data(iris)
X   <- as.matrix(iris[,1:4])
lab <- as.factor(iris[,5])

## use different number of data points as landmarks
output1 <- do.lisomap(X, npoints=10, type=c("proportion",0.25))
output2 <- do.lisomap(X, npoints=25, type=c("proportion",0.25))
output3 <- do.lisomap(X, npoints=50, type=c("proportion",0.25))

## visualize three different projections
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(output1$Y, pch=19, col=lab, main="10 landmarks")
plot(output2$Y, pch=19, col=lab, main="25 landmarks")
plot(output3$Y, pch=19, col=lab, main="50 landmarks")
par(opar)

Rdimtools documentation built on Dec. 28, 2022, 1:44 a.m.