nonlinear_SNE: Stochastic Neighbor Embedding
In Rdimtools: Dimension Reduction and Estimation Methods

do.sne

R Documentation

Stochastic Neighbor Embedding

Description

Stochastic Neighbor Embedding (SNE) is a probabilistic approach to mimick distributional description in high-dimensional - possible, nonlinear - subspace on low-dimensional target space. do.sne fully adopts algorithm details in an original paper by Hinton and Roweis (2002).

Usage

do.sne(
  X,
  ndim = 2,
  perplexity = 30,
  eta = 0.05,
  maxiter = 2000,
  jitter = 0.3,
  jitterdecay = 0.99,
  momentum = 0.5,
  pca = TRUE,
  pcascale = FALSE,
  symmetric = FALSE
)

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.
`perplexity`	desired level of perplexity; ranging [5,50].
`eta`	learning parameter.
`maxiter`	maximum number of iterations.
`jitter`	level of white noise added at the beginning.
`jitterdecay`	decay parameter in `(0,1)`. The closer to 0, the faster artificial noise decays.
`momentum`	level of acceleration in learning.
`pca`	whether to use PCA as preliminary step; `TRUE` for using it, `FALSE` otherwise.
`pcascale`	a logical; `FALSE` for using Covariance, `TRUE` for using Correlation matrix. See also `do.pca` for more details.
`symmetric`	a logical; `FALSE` to solve it naively, and `TRUE` to adopt symmetrization scheme.

Value

a named Rdimtools S3 object containing

Y: an (n\times ndim) matrix whose rows are embedded observations.
vars: a vector containing betas used in perplexity matching.
algorithm: name of the algorithm.

Author(s)

Kisung You

References

\insertRef

hinton_stochastic_2003Rdimtools

Examples


## load iris data
data(iris)
set.seed(100)
subid = sample(1:150,50)
X     = as.matrix(iris[subid,1:4])
label = as.factor(iris[subid,5])

## try different perplexity values
out1 <- do.sne(X, perplexity=5)
out2 <- do.sne(X, perplexity=25)
out3 <- do.sne(X, perplexity=50)

## Visualize two comparisons
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(out1$Y, pch=19, col=label, main="perplexity=5")
plot(out2$Y, pch=19, col=label, main="perplexity=25")
plot(out3$Y, pch=19, col=label, main="perplexity=50")
par(opar)

Rdimtools documentation built on Nov. 5, 2025, 5:28 p.m.