Sierpinski3d. pt-SNE+FIt-SNE

library(bigMap)
# source graph plot
source('../graphs.R')
# source FIt-SNE
source('~/FitSNE/fast_tsne.R', chdir = T)

## FIt-SNE R wrapper loading.

## FIt-SNE root directory was set to /home/jgarriga/FitSNE

Load data

load('../s3d.RData')

Load pt-SNE embedding with ppx = 1948 and thread_ratio = 0.25

load('../fig2/s3d_ppx_1948.RData')
# get pt-SNE embedding with thread_ratio = 0.25
g <- g.list[[6]]
str(g$ptsne[c('threads', 'layers')])

## List of 2
##  $ threads: num 8
##  $ layers : num 2

# get initial mapping
Y.init <- g$ptsne$Y[, 1:2]

Run FIt-SNE (ppx = 10) with pt-SNE intialization (ppx = 1948)

g.10 <- g
g.10$ptsne$Y <- fftRtsne(s3d$data, perplexity = 10, initialization = Y.init, exaggeration_factor = 1.0, no_momentum_during_exag = 1, max_iter = 500)
graph.plot(g.10, s3d$edges)

Run FIt-SNE (ppx = 20) with pt-SNE intialization (ppx = 1948)

g.20 <- g
g.20$ptsne$Y <- fftRtsne(s3d$data, perplexity = 20, initialization = Y.init, exaggeration_factor = 1.0, no_momentum_during_exag = 1, max_iter = 500)
graph.plot(g.20, s3d$edges)

Run FIt-SNE (ppx = 102) with pt-SNE intialization (ppx = 1948)

g.102 <- g.list[[3]]
g.102$ptsne$Y <- fftRtsne(s3d$data, perplexity = 102, initialization = Y.init, exaggeration_factor = 1.0, no_momentum_during_exag = 1, max_iter = 500)
graph.plot(g.102, s3d$edges)

Save

g.list <- list(g.10, g.20, g.102)
save(g.list, file = './glist_combo.RData')