Register Seriation Based on 1D t-SNE

Description

Use t-distributed stochastic neighbor embedding (t-SNE) to create a seriation order.

Usage

register_tsne()

Details

Registers the method "tsne" for seriate. This method applies 1D t-SNE to data represented by a distance matrix and extracts the order from the 1D embedding. To speed up the process, an initial embedding is created using multi-dimensional scaling (MDS) which is improved by t-SNE.

The control parameter mds controls if MDS is used to create an initial embedding. See Rtsne to learn about the other available control parameters.

Note: Package Rtsne needs to be installed.

References

van der Maaten, L.J.P. & Hinton, G.E., 2008. Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research, 9, pp.2579-2605.

See Also

seriate, Rtsne in Rtsne.

Examples

## Not run: 
register_tsne()
get_seriation_method("dist", "tsne")

d <- dist(random.robinson(50, pre=TRUE, noise=.1))

o <- seriate(d, method = "tsne")
pimage(d, o)

## End(Not run)