R_netSNE: Compute similarities, Bht-SNE and Net-SNE.
In schwikowskilab/rNetSNE: Run Net-SNE on R
Description
Usage
Arguments
Examples
Description
A function that enables to run Computes_similarities, RunBhtSNE and RunNetSNE in a single time, or to chose between them. It also facilitates the managemnt of the output and input files created by those function.
Input: Depends on the paramter: 'to.run'.
Output: Depends on the paramter: 'to.run'.
Requirment: C++ implementation of Net-SNE installed and functional.
Usage
1
R_netSNE(to.run = c("Compute.sim", "BhtSNE", "NetSNE.basic", "NetSNE.train", "NetSNE.project"), path.netSNE.dir, out.dims = 2L, max.iter = 1000L, perp = 70L, theta.BhtSNE = 0.5, theta.NetSNE = 0.5, mom.init = 0.5, mom.final = 0.8, mom.switch.iter = 250L, early.exag.iter = 250L, learn.rate.bhtSNE = 200, learn.rate.netSNE = 0.02, NN.layers = 2L, NN.units = 50L, NN.function = "relu", sgd = TRUE, batch.frac.bhtSNE = NULL, batch.frac.netSNE = 0.1, random.init = TRUE, local.sample = 20L, min.sample.Z = 0.1, l2.reg.param = 0, step.method = "adam", save.iters.cache = NULL, permute.after.iters = NULL, seed = -1, verbose = TRUE, path.output.dir = path.output.dir, train.data = NULL, test.data = NULL, ref.embedding = c("BhtSNE", "NetSNE.basic"), path.to.bin.train.file = NULL, path.to.bin.test.file = NULL, force.rm.old.outdir = TRUE, name.bhtSNE.output.dir = "Bhtsne_out", name.netSNE.output.dir = "Netsne_out")
Arguments
to.run
Character; Vector to choose the functions to use (default: c("Compute.sim", "BhtSNE", "NetSNE.basic", "NetSNE.train", "NetSNE.project") for running everything)
path.netSNE.dir
Character; The path to the directory containing the executables created after Net-SNE installation (usually : path/to/netsne-master/bin). Must end with the name of directory with exectuables (here: '/bin')
out.dims
Integer; Specifies the output dimensionality (default: 2)
max.iter
Integer; Specifies the number of iterations (default: 1e3)
perp
Integer; Stands for 'Perplexity', an integer between 0 and 100 (see t-SNE documentation, default: 70)
theta.BhtSNE
Double; Bounded by 0 and 1, controls the accuracy-efficiency tradeoff in SPTree for Bht-SNE gradient computation; 0 means exact (default: 0.5)
theta.NetSNE
Double; Bounded by 0 and 1, controls the accuracy-efficiency tradeoff in SPTree for Net-SNE gradient computation; 0 means exact (default: 0.5)
mom.init
Double; Bounded by 0 and 1, defines the momentum used before n=mom.switch.iter iterations (default: 0.5)
mom.final
Double; Bounded by 0 and 1, defines the momentum used after n=mom.switch.iter iterations (default: 0.8)
mom.switch.iter
Integer; Number of iterations before switching the value of momentum (default: 250)
early.exag.iter
Integer; Number of iterations of early exaggeration (default: 250)
learn.rate.bhtSNE
Double; Learning rate used for Bht-SNE gradient steps (default: 200.0)
learn.rate.netSNE
Double; Learning rate used for Net-SNE gradient steps (default: 0.02)
NN.layers
Integer: Number of layers in Net-SNE's Neural Network (default: 2)
NN.units
Integer: Number of units for each layer in Net-SNE's Neural Network (default: 50)
NN.function
Character: Specifies the activation function of Net-SNE's Neural Network. Possible values: 'sigmoid' or 'relu' (default: relu)
sgd
Logical; Set to TRUE to use SGD acceleration during Net-SNE computation. If set to FALSE (effective for small datasets), equivalent to t-SNE with an additional backpropagation step to train a neural network (default: TRUE)
batch.frac.bhtSNE
Integer: Number of points to update at each iteration of Bht-SNE (default: NULL, i.e. all of them)
batch.frac.netSNE
Integer: Fraction of data to sample for Net-SNE's mini-batch (default: 0.1, i.e. 10%)
random.init
Logical; Set to TRUE to allow random initialization for Bht-SNE (default: TRUE)
local.sample
Integer: Number of local samples for each data point in Net-SNE's mini-batch (default: 20)
min.sample.Z
Double; Minimum fraction of data to use for approximating the normalization factor Z in Net-SNE's gradient (default: 0.1, i.e. 10%)
l2.reg.param
Numerical; L2 regularization parameter for introducing sparcity in Net-SNE's Neural Network and avoid train data overfitting (default: 0, i.e. no sparcity)
step.method
Character; Specifies Net-SNE's gradient step schedule. Possible values: 'adam', 'mom' (momentum), 'mom_gain' (momentum with gains) or 'fixed' (default: adam)
save.iters.cache
Integer; Number of iterations after which an intermediary embedding is repeatidly recorded. The final embedding (Y_final.txt) is always saved (default: NULL, i.e. no intermediary embedding is recorded, only the definitive one after max.iter)
permute.after.iters
Integer; Number of iterations after which the ordering of data points is repeatidly permuted for Net-SNE's fast mini-batching (default: NULL, i.e. permute.after.iters = max.iter)
seed
Integer; Equivalent to set.seed (default: -1, i.e. use current time as seed)
verbose
Logical; Should the outputs be printed to the console? (default: TRUE)
path.output.dir
Character; The path to save to output directories of Bht-SNE (name.bhtSNE.output.dir) and Net-SNE (name.netSNE.output.dir).
train.data
Marix;
test.data
ref.embedding
path.to.bin.train.file
path.to.bin.test.file
force.rm.old.outdir
name.bhtSNE.output.dir
name.netSNE.output.dir
Examples
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##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (to.run = c("Compute.sim", "BhtSNE", "NetSNE.basic",
"NetSNE.train", "NetSNE.project"), path.netSNE.dir, out.dims = 2L,
max.iter = 1000L, perp = 70L, theta.BhtSNE = 0.5, theta.NetSNE = 0.5,
mom.init = 0.5, mom.final = 0.8, mom.switch.iter = 250L,
early.exag.iter = 250L, learn.rate.bhtSNE = 200, learn.rate.netSNE = 0.02,
NN.layers = 2L, NN.units = 50L, NN.function = "relu", sgd = TRUE,
batch.frac.bhtSNE = NULL, batch.frac.netSNE = 0.1, random.init = TRUE,
local.sample = 20L, min.sample.Z = 0.1, l2.reg.param = 0,
step.method = "adam", save.iters.cache = NULL, permute.after.iters = NULL,
seed = -1, verbose = TRUE, path.output.dir = path.output.dir,
train.data = NULL, test.data = NULL, ref.embedding = c("BhtSNE",
"NetSNE.basic"), path.to.bin.train.file = NULL, path.to.bin.test.file = NULL,
force.rm.old.outdir = TRUE, name.bhtSNE.output.dir = "Bhtsne_out",
name.netSNE.output.dir = "Netsne_out")
{
wd = getwd()
setwd("~/")
to.run = unique(tolower(to.run))
to.rm = c()
if (length(to.run) == 0) {
stop("You didn't specify anything in param: 'to.run'. Please do so !\nPossible values:\n\t- 'Compute.sim': to compute a knn-graph used by Bht-SNE and NetSNE\n\t- 'Bht-SNE': to get a usual t-SNE embedding of a dataset\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.basic': to perform a t-SNE-like embedding using Net-SNE\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.train': train Net-SNE on a training/sampled dataset to latter project new data on the embedding\n---> Requirments : to.run = c('Compute.sim', 'BhtSNE' &/| 'NetSNE.basic')\n\t- 'NetSNE.project': project a new dataset on a prior embedding\n---> Requirments: to.run = c('Compute.sim, 'BhtSNE' &/| 'NetSNE.basic', 'NetSNE.train')",
call. = FALSE)
}
for (i in 1:length(to.run)) {
if (!to.run[i] %in% c("compute.sim", "bhtsne", "netsne.basic",
"netsne.train", "netsne.project")) {
to.rm[(length(to.rm) + 1)] = to.run[i]
}
}
if (length(to.rm) > 0) {
stop(paste(paste(to.rm, collapse = " and "), ": Unknown task(s) for param: to.run.\nPossible values:\n\t- 'Compute.sim': to compute a knn-graph used by Bht-SNE and NetSNE\n\t- 'Bht-SNE': to get a usual t-SNE embedding of a dataset\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.basic': to perform a t-SNE-like embedding using Net-SNE\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.train': train Net-SNE on a training/sampled dataset to latter project new data on the embedding\n---> Requirments : to.run = c('Compute.sim', 'BhtSNE' &/| 'NetSNE.basic')\n\t- 'NetSNE.project': project a new dataset on a prior embedding\n---> Requirments: to.run = c('Compute.sim, 'BhtSNE' &/| 'NetSNE.basic', 'NetSNE.train')"),
call. = FALSE)
}
else {
rm(to.rm)
}
if ("netsne.train" %in% to.run) {
if (length(ref.embedding) != 1) {
stop("When training Net-SNE on a reference embedding (param: 'ref.embedding'), you can only use one of those options: 'BhtSNE' or 'NetSNE.basic' (corresponds to a t-SNE-like embedding). Therefore, c('",
paste(ref.embedding, collapse = "', '"), "') is not an acceptable value.",
call. = FALSE)
}
else {
ref.embedding = unique(tolower(ref.embedding))
if (length(which(c("bhtsne", "netsne.basic", "netsne") %in%
ref.embedding)) < 1) {
stop(ref.embedding, " is not a correct option for 'ref.embedding'.\nPossible values:\n\n\t- 'BhtSNE'\n ---> Requirment: to.run = 'BhtSNE'\n\n\t- 'NetSNE.basic'\n ---> Requirment: to.run = 'NetSNE.basic'",
call. = FALSE)
}
}
}
path.output.dir = strsplit(path.output.dir, "/")[[1]]
if (0 %in% nchar(path.output.dir)) {
path.output.dir = path.output.dir[-which(path.output.dir ==
"")]
}
if (!dir.exists(paste(path.output.dir, collapse = "/"))) {
dir.create(paste(path.output.dir, collapse = "/"), recursive = FALSE)
}
path.netSNE.dir = strsplit(path.netSNE.dir, "/")[[1]]
if (0 %in% nchar(path.netSNE.dir)) {
path.netSNE.dir = path.netSNE.dir[-which(path.netSNE.dir ==
"")]
}
if (path.netSNE.dir[length(path.netSNE.dir)] != "bin") {
path.netSNE.dir[length(path.netSNE.dir) + 1] = "bin"
}
path.netSNE.dir = paste(path.netSNE.dir, collapse = "/")
if (!file.exists(path.netSNE.dir)) {
if (!file.exists(paste("/", path.netSNE.dir, sep = ""))) {
stop(paste("The specified path to the 'bin' directory containing the executable files (",
path.netSNE.dir, ") does not exist", sep = ""),
call. = FALSE)
}
else {
path.netSNE.dir = paste("/", path.netSNE.dir, sep = "")
}
}
if (length(which(c("netsne.basic", "netsne.train", "netsne.project") %in%
to.run)) > 0) {
name.netSNE.output.dir = strsplit(name.netSNE.output.dir,
"/")[[1]]
if (0 %in% nchar(name.netSNE.output.dir)) {
name.netSNE.output.dir = name.netSNE.output.dir[-which(name.netSNE.output.dir ==
"")]
}
name.netSNE.output.dir = name.netSNE.output.dir[length(name.netSNE.output.dir)]
}
if (length(which(c("compute.sim", "bhtsne", "netsne.basic",
"netsne.train") %in% to.run)) > 0) {
if (is.null(train.data) & is.null(path.to.bin.train.file)) {
stop("Neither the train data ('train.data') nor the path to train data binary file ('path.to.bin.train.file') were specified, please re-lunch the function with one of them as input.\n---> Required for running ",
paste(to.run[which(to.run %in% c("compute.sim",
"netsne.basic", "netsne.train"))], collapse = " and "),
call. = FALSE)
}
else if (!is.null(path.to.bin.train.file)) {
path.to.bin.train.file = strsplit(path.to.bin.train.file,
"/")[[1]]
if (0 %in% nchar(path.to.bin.train.file)) {
path.to.bin.train.file = path.to.bin.train.file[-which(path.to.bin.train.file ==
"")]
}
name.train = path.to.bin.train.file[length(path.to.bin.train.file)]
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
name.sim = strsplit(name.train, "\.")[[1]]
extention = name.sim[length(name.sim)]
name.sim = name.sim[-length(name.sim)]
name.sim = paste(name.sim, collapse = ".")
name.sim = paste(name.sim, "_", perp, "_P.",
extention, sep = "")
}
if (!dir.exists(paste(path.to.bin.train.file[1:(length(path.to.bin.train.file) -
1)], collapse = "/"))) {
dir.create(paste(path.to.bin.train.file[1:(length(path.to.bin.train.file) -
1)], collapse = "/"), recursive = TRUE)
}
path.to.bin.train.file = paste(path.to.bin.train.file,
collapse = "/")
if (!is.null(train.data)) {
if (file.exists(path.to.bin.train.file)) {
status = suppressWarnings(file.remove(path.to.bin.train.file))
if (!status) {
stop("Impossible to remove the file '", name.train,
"' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
". Please do it yourself or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.train,
"' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
sep = "")
}
}
cat("\nWriting '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
"\n", sep = "")
Write_binary_file(train.data, path.to.bin.train.file)
}
else if (!file.exists(path.to.bin.train.file)) {
stop("The file '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
" doesn't exist and you didn't provide a matrix corresponding to the training data. Please provide the data train matrix or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nUsing the file '", name.train, "' in ",
substr(path.to.bin.train.file, 1, nchar(path.to.bin.train.file) -
nchar(name.train)), ".\n", sep = "")
}
}
else {
name.train = gsub(pattern = "\[.*", replacement = "",
deparse(substitute(train.data)))
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
name.sim = paste(name.train, "_", perp, "_P.dat",
sep = "")
}
name.train = paste(name.train, "dat", sep = ".")
if (file.exists(paste(paste(path.output.dir, collapse = "/"),
name.train, sep = "/"))) {
path.to.bin.train.file = paste(paste(path.output.dir,
collapse = "/"), name.train, sep = "/")
rm.file = TRUE
}
else {
path.to.bin.train.file = paste(paste(path.output.dir[1:(length(path.output.dir) -
1)], collapse = "/"), name.train, sep = "/")
if (file.exists(path.to.bin.train.file)) {
rm.file = TRUE
}
else {
rm.file = FALSE
}
}
if (rm.file) {
status = suppressWarnings(file.remove(path.to.bin.train.file))
if (!status) {
stop("Impossible to remove the file '", name.train,
"' in ", substr(path.to.bin.train.file, 1,
nchar(path.to.bin.train.file) - nchar(name.train)),
". Please do it yourself or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.train, "' in ",
substr(path.to.bin.train.file, 1, nchar(path.to.bin.train.file) -
nchar(name.train)), "\n", sep = "")
}
}
cat("\nWriting '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
"\n", sep = "")
Write_binary_file(train.data, path.to.bin.train.file)
}
}
if ("netsne.project" %in% to.run) {
if (is.null(test.data) & is.null(path.to.bin.test.file)) {
stop("Neither the test data ('test.data') nor the path to test data binary file ('path.to.bin.test.file') were specified, please re-lunch the function with one of them as input.\n---> Required for running to.run = c('netsne.project')",
call. = FALSE)
}
else if (!is.null(path.to.bin.test.file)) {
path.to.bin.test.file = strsplit(path.to.bin.test.file,
"/")[[1]]
if (0 %in% nchar(path.to.bin.test.file)) {
path.to.bin.test.file = path.to.bin.test.file[-which(path.to.bin.test.file ==
"")]
}
name.test = path.to.bin.test.file[length(path.to.bin.test.file)]
if (!dir.exists(paste(path.to.bin.test.file[1:(length(path.to.bin.test.file) -
1)], collapse = "/"))) {
dir.create(paste(path.to.bin.test.file[1:(length(path.to.bin.test.file) -
1)], collapse = "/"), recursive = TRUE)
}
path.to.bin.test.file = paste(path.to.bin.test.file,
collapse = "/")
if (!is.null(test.data)) {
if (file.exists(path.to.bin.test.file)) {
status = suppressWarnings(file.remove(path.to.bin.test.file))
if (!status) {
stop("Impossible to remove the file '", name.test,
"' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
". Please do it yourself or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), sep = "")
}
}
cat("\nWriting '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
"\n", sep = "")
Write_binary_file(test.data, path.to.bin.test.file)
}
else if (!file.exists(path.to.bin.test.file)) {
stop("The file '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
" doesn't exist and you didn't provide a matrix corresponding to the testing data. Please provide the data test matrix or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nUsing the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), ".\n", sep = "")
}
}
else {
name.test = gsub(pattern = "\[.*", replacement = "",
deparse(substitute(test.data)))
name.test = paste(name.test, "dat", sep = ".")
if (file.exists(paste(paste(path.output.dir, collapse = "/"),
name.test, sep = "/"))) {
path.to.bin.test.file = paste(paste(path.output.dir,
collapse = "/"), name.test, sep = "/")
rm.file = TRUE
}
else {
path.to.bin.test.file = paste(paste(path.output.dir[1:(length(path.output.dir) -
1)], collapse = "/"), name.test, sep = "/")
if (file.exists(path.to.bin.test.file)) {
rm.file = TRUE
}
else {
rm.file = FALSE
}
}
if (rm.file) {
status = suppressWarnings(file.remove(path.to.bin.test.file))
if (!status) {
stop("Impossible to remove the file '", name.test,
"' in ", substr(path.to.bin.test.file, 1,
nchar(path.to.bin.test.file) - nchar(name.test)),
". Please do it yourself or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), "\n", sep = "")
}
}
cat("\nWriting '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
"\n", sep = "")
Write_binary_file(test.data, path.to.bin.test.file)
}
}
path.output.dir = paste(path.output.dir, collapse = "/")
if (length(which(c("bhtsne", "netsne.train") %in% to.run)) >
0) {
name.bhtSNE.output.dir = strsplit(name.bhtSNE.output.dir,
"/")[[1]]
if (0 %in% nchar(name.bhtSNE.output.dir)) {
name.bhtSNE.output.dir = name.bhtSNE.output.dir[-which(name.bhtSNE.output.dir ==
"")]
}
name.bhtSNE.output.dir = name.bhtSNE.output.dir[length(name.bhtSNE.output.dir)]
path.BhtSNE.output.dir = paste(path.output.dir, name.bhtSNE.output.dir,
sep = "/")
}
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
path.to.bin.P = paste(path.output.dir, name.sim, sep = "/")
}
if ("compute.sim" %in% to.run) {
if (file.exists(path.to.bin.P)) {
if (force.rm.old.outdir) {
status = suppressWarnings(file.remove(path.to.bin.P))
if (!status) {
stop("Impossible to remove the file '", name.sim,
"' in ", path.output.dir, ". Please do it yourself or remove 'compute.sim' from param: to.run if the file is correct.",
call. = FALSE)
}
else {
compute.sim = TRUE
}
}
else {
WALL = TRUE
while (WALL) {
cat("The binary file '", name.sim, "' specifying the similarities seems to already exist (PATH: ",
path.to.bin.P, ").\nPlease choose:\n\t- [1]: Remove the file and compute similarities,\n\t- [2]: Keep the file and skip the computing of similarities,\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
status = suppressWarnings(file.remove(path.to.bin.P))
if (!status) {
stop("Impossible to remove the file '",
name.sim, "' in ", path.output.dir,
". Please do it yourself or remove 'compute.sim' from param: to.run if the file is correct.",
call. = FALSE)
}
}
else if (answer == "2") {
compute.sim = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
compute.sim = TRUE
}
if (compute.sim) {
Compute_similarities(perp = perp, verbose = verbose,
path.netSNE.dir = path.netSNE.dir, path.to.bin.file = path.to.bin.train.file,
path.output.file = path.to.bin.P)
}
}
else {
compute.sim = FALSE
}
if (!compute.sim && length(which(c("bhtsne", "netsne.basic") %in%
to.run)) > 0 && !file.exists(path.to.bin.P)) {
stop("The file ", name.sim, " in ", path.output.dir,
" is unreachable.", call. = FALSE)
}
if ("bhtsne" %in% to.run) {
if (dir.exists(path.BhtSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.BhtSNE.output.dir, recursive = TRUE)
run.bhtsne = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.bhtSNE.output.dir,
"' for saving the outputs of Bht-SNE seems to already exist (PATH: ",
path.BhtSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Bht-SNE,\n\t- [2]: Keep the directory and skip the computing of Bht-SNE,\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.BhtSNE.output.dir, recursive = TRUE)
run.bhtsne = TRUE
}
else if (answer == "2") {
run.bhtsne = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.bhtsne = TRUE
}
if (run.bhtsne) {
RunBhtSNE(out.dims = out.dims, max.iter = max.iter,
theta = theta.BhtSNE, mom.init = mom.init, mom.final = mom.final,
mom.switch.iter = mom.switch.iter, early.exag.iter = early.exag.iter,
learn.rate = learn.rate.bhtSNE, batch.frac = batch.frac.bhtSNE,
seed = seed, verbose = verbose, random.init = random.init,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.file = path.to.bin.train.file, path.to.simil.file = path.to.bin.P,
path.output.dir = path.BhtSNE.output.dir)
}
}
else {
run.bhtsne = FALSE
}
if ("netsne.basic" %in% to.run) {
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"basic", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.basic = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (t-SNE-like use) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.basic (t-SNE-like),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (t-SNE-like),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.basic = TRUE
}
else if (answer == "2") {
run.netsne.basic = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.basic = TRUE
}
if (run.netsne.basic) {
RunNetSNE(utilis = "t-SNE", out.dims = out.dims,
max.iter = max.iter, theta = theta.NetSNE, step.method = step.method,
NN.layers = NN.layers, NN.units = NN.units, NN.function = NN.function,
l2.reg.param = l2.reg.param, mom.init = mom.init,
mom.final = mom.final, mom.switch.iter = mom.switch.iter,
early.exag.iter = early.exag.iter, learn.rate = learn.rate.netSNE,
local.sample = local.sample, batch.frac = batch.frac.netSNE,
min.sample.Z = min.sample.Z, sgd = sgd, seed = seed,
verbose = verbose, permute.after.iters = permute.after.iters,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train.file = path.to.bin.train.file,
path.to.bin.test.file = NULL, path.to.simil.file = path.to.bin.P,
path.output.dir = path.NetSNE.output.dir, path.ref.embedding = NULL,
path.to.model.dir = NULL, model.prefix = "WHATEVER")
}
}
else {
run.netsne.basic = FALSE
}
if ("netsne.train" %in% to.run) {
if (ref.embedding == "bhtsne") {
path.ref.embedding = paste(path.output.dir, name.bhtSNE.output.dir,
"Y_final.txt", sep = "/")
}
else {
path.ref.embedding = paste(path.output.dir, paste(name.netSNE.output.dir,
"basic", sep = "_"), "Y_final.txt", sep = "/")
}
if (!file.exists(path.ref.embedding)) {
stop("There is no embedding for Net-SNE to learn in ",
path.ref.embedding, ". Please change the value of param: 'ref.embedding' or include the relevant option in 'to.run'.",
call. = FALSE)
}
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"model", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.train = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (model creation after learning embedding) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.train (learn embedding),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (learn embedding),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.train = TRUE
}
else if (answer == "2") {
run.netsne.train = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.train = TRUE
}
if (run.netsne.train) {
RunNetSNE(utilis = "Learn", out.dims = out.dims,
max.iter = max.iter, theta = theta.NetSNE, step.method = step.method,
NN.layers = NN.layers, NN.units = NN.units, NN.function = NN.function,
l2.reg.param = l2.reg.param, mom.init = mom.init,
mom.final = mom.final, mom.switch.iter = mom.switch.iter,
early.exag.iter = early.exag.iter, learn.rate = learn.rate.netSNE,
local.sample = local.sample, batch.frac = batch.frac.netSNE,
min.sample.Z = min.sample.Z, sgd = sgd, seed = seed,
verbose = verbose, permute.after.iters = permute.after.iters,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train.file = path.to.bin.train.file,
path.to.bin.test.file = NULL, path.to.simil.file = NULL,
path.output.dir = path.NetSNE.output.dir, path.ref.embedding = path.ref.embedding,
path.to.model.dir = NULL, model.prefix = "whatever")
}
}
else {
run.netsne.train = FALSE
}
if ("netsne.project" %in% to.run) {
path.to.model.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"model", sep = "_"), sep = "/")
if (!dir.exists(path.to.model.dir)) {
stop("The directory '", path.to.model.dir, "' supposed to contain the model of Net-SNE (after learning a reference embedding) does not exist.")
}
l = list.files(path.to.model.dir, pattern = "_.*[.txt]",
full.names = FALSE, include.dirs = FALSE)
l = l[which(regexpr("_L[0-9]*_[:alnum:]*", l) > 0)]
l = gsub("_L[0-9]*_.*.txt", "", l)
if (length(unique(l)) == 1) {
model.prefix = unique(l)
}
else {
stop("Impossible to find a model prefix (usually 'model_final') in ",
path.to.model.dir, ". Please check the content of the directory, and re-run the function (maybe with 'netsne.train' in to.run) ",
call. = FALSE)
}
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"projection", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.project = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (projection) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.project (to project),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (to project),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.project = TRUE
}
else if (answer == "2") {
run.netsne.project = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.project = TRUE
}
if (run.netsne.project) {
RunNetSNE(utilis = "Project", verbose = TRUE, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train = "irrelevant", path.to.bin.test = path.to.bin.test.file,
path.output.dir = path.NetSNE.output.dir, path.to.model.dir = path.to.model.dir,
model.prefix = model.prefix)
}
}
else {
run.netsne.project = FALSE
}
Result = list()
i = 1
if (run.bhtsne) {
Result[[i]] = read.table(file = paste(path.BhtSNE.output.dir,
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Bht-SNE"
i = i + 1
}
if (run.netsne.basic) {
Result[[i]] = read.table(file = paste(path.output.dir,
paste(name.netSNE.output.dir, "basic", sep = "_"),
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Net-SNE (Basic)"
i = i + 1
}
if (run.netsne.project) {
Result[[i]] = read.table(file = paste(path.output.dir,
paste(name.netSNE.output.dir, "projection", sep = "_"),
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Net-SNE (Projection)"
i = i + 1
}
setwd(wd)
return(Result)
}
schwikowskilab/rNetSNE documentation built on May 4, 2019, 6:40 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Examples
Description
A function that enables to run Computes_similarities, RunBhtSNE and RunNetSNE in a single time, or to chose between them. It also facilitates the managemnt of the output and input files created by those function.
Input: Depends on the paramter: 'to.run'.
Output: Depends on the paramter: 'to.run'.
Requirment: C++ implementation of Net-SNE installed and functional.
Usage
1 | R_netSNE(to.run = c("Compute.sim", "BhtSNE", "NetSNE.basic", "NetSNE.train", "NetSNE.project"), path.netSNE.dir, out.dims = 2L, max.iter = 1000L, perp = 70L, theta.BhtSNE = 0.5, theta.NetSNE = 0.5, mom.init = 0.5, mom.final = 0.8, mom.switch.iter = 250L, early.exag.iter = 250L, learn.rate.bhtSNE = 200, learn.rate.netSNE = 0.02, NN.layers = 2L, NN.units = 50L, NN.function = "relu", sgd = TRUE, batch.frac.bhtSNE = NULL, batch.frac.netSNE = 0.1, random.init = TRUE, local.sample = 20L, min.sample.Z = 0.1, l2.reg.param = 0, step.method = "adam", save.iters.cache = NULL, permute.after.iters = NULL, seed = -1, verbose = TRUE, path.output.dir = path.output.dir, train.data = NULL, test.data = NULL, ref.embedding = c("BhtSNE", "NetSNE.basic"), path.to.bin.train.file = NULL, path.to.bin.test.file = NULL, force.rm.old.outdir = TRUE, name.bhtSNE.output.dir = "Bhtsne_out", name.netSNE.output.dir = "Netsne_out")
|
Arguments
to.run |
Character; Vector to choose the functions to use (default: c("Compute.sim", "BhtSNE", "NetSNE.basic", "NetSNE.train", "NetSNE.project") for running everything) |
path.netSNE.dir |
Character; The path to the directory containing the executables created after Net-SNE installation (usually : path/to/netsne-master/bin). Must end with the name of directory with exectuables (here: '/bin') |
out.dims |
Integer; Specifies the output dimensionality (default: 2) |
max.iter |
Integer; Specifies the number of iterations (default: 1e3) |
perp |
Integer; Stands for 'Perplexity', an integer between 0 and 100 (see t-SNE documentation, default: 70) |
theta.BhtSNE |
Double; Bounded by 0 and 1, controls the accuracy-efficiency tradeoff in SPTree for Bht-SNE gradient computation; 0 means exact (default: 0.5) |
theta.NetSNE |
Double; Bounded by 0 and 1, controls the accuracy-efficiency tradeoff in SPTree for Net-SNE gradient computation; 0 means exact (default: 0.5) |
mom.init |
Double; Bounded by 0 and 1, defines the momentum used before n=mom.switch.iter iterations (default: 0.5) |
mom.final |
Double; Bounded by 0 and 1, defines the momentum used after n=mom.switch.iter iterations (default: 0.8) |
mom.switch.iter |
Integer; Number of iterations before switching the value of momentum (default: 250) |
early.exag.iter |
Integer; Number of iterations of early exaggeration (default: 250) |
learn.rate.bhtSNE |
Double; Learning rate used for Bht-SNE gradient steps (default: 200.0) |
learn.rate.netSNE |
Double; Learning rate used for Net-SNE gradient steps (default: 0.02) |
NN.layers |
Integer: Number of layers in Net-SNE's Neural Network (default: 2) |
NN.units |
Integer: Number of units for each layer in Net-SNE's Neural Network (default: 50) |
NN.function |
Character: Specifies the activation function of Net-SNE's Neural Network. Possible values: 'sigmoid' or 'relu' (default: relu) |
sgd |
Logical; Set to TRUE to use SGD acceleration during Net-SNE computation. If set to FALSE (effective for small datasets), equivalent to t-SNE with an additional backpropagation step to train a neural network (default: TRUE) |
batch.frac.bhtSNE |
Integer: Number of points to update at each iteration of Bht-SNE (default: NULL, i.e. all of them) |
batch.frac.netSNE |
Integer: Fraction of data to sample for Net-SNE's mini-batch (default: 0.1, i.e. 10%) |
random.init |
Logical; Set to TRUE to allow random initialization for Bht-SNE (default: TRUE) |
local.sample |
Integer: Number of local samples for each data point in Net-SNE's mini-batch (default: 20) |
min.sample.Z |
Double; Minimum fraction of data to use for approximating the normalization factor Z in Net-SNE's gradient (default: 0.1, i.e. 10%) |
l2.reg.param |
Numerical; L2 regularization parameter for introducing sparcity in Net-SNE's Neural Network and avoid train data overfitting (default: 0, i.e. no sparcity) |
step.method |
Character; Specifies Net-SNE's gradient step schedule. Possible values: 'adam', 'mom' (momentum), 'mom_gain' (momentum with gains) or 'fixed' (default: adam) |
save.iters.cache |
Integer; Number of iterations after which an intermediary embedding is repeatidly recorded. The final embedding (Y_final.txt) is always saved (default: NULL, i.e. no intermediary embedding is recorded, only the definitive one after max.iter) |
permute.after.iters |
Integer; Number of iterations after which the ordering of data points is repeatidly permuted for Net-SNE's fast mini-batching (default: NULL, i.e. permute.after.iters = max.iter) |
seed |
Integer; Equivalent to set.seed (default: -1, i.e. use current time as seed) |
verbose |
Logical; Should the outputs be printed to the console? (default: TRUE) |
path.output.dir |
Character; The path to save to output directories of Bht-SNE (name.bhtSNE.output.dir) and Net-SNE (name.netSNE.output.dir). |
train.data |
Marix; |
test.data |
|
ref.embedding |
|
path.to.bin.train.file |
|
path.to.bin.test.file |
|
force.rm.old.outdir |
|
name.bhtSNE.output.dir |
|
name.netSNE.output.dir |
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (to.run = c("Compute.sim", "BhtSNE", "NetSNE.basic",
"NetSNE.train", "NetSNE.project"), path.netSNE.dir, out.dims = 2L,
max.iter = 1000L, perp = 70L, theta.BhtSNE = 0.5, theta.NetSNE = 0.5,
mom.init = 0.5, mom.final = 0.8, mom.switch.iter = 250L,
early.exag.iter = 250L, learn.rate.bhtSNE = 200, learn.rate.netSNE = 0.02,
NN.layers = 2L, NN.units = 50L, NN.function = "relu", sgd = TRUE,
batch.frac.bhtSNE = NULL, batch.frac.netSNE = 0.1, random.init = TRUE,
local.sample = 20L, min.sample.Z = 0.1, l2.reg.param = 0,
step.method = "adam", save.iters.cache = NULL, permute.after.iters = NULL,
seed = -1, verbose = TRUE, path.output.dir = path.output.dir,
train.data = NULL, test.data = NULL, ref.embedding = c("BhtSNE",
"NetSNE.basic"), path.to.bin.train.file = NULL, path.to.bin.test.file = NULL,
force.rm.old.outdir = TRUE, name.bhtSNE.output.dir = "Bhtsne_out",
name.netSNE.output.dir = "Netsne_out")
{
wd = getwd()
setwd("~/")
to.run = unique(tolower(to.run))
to.rm = c()
if (length(to.run) == 0) {
stop("You didn't specify anything in param: 'to.run'. Please do so !\nPossible values:\n\t- 'Compute.sim': to compute a knn-graph used by Bht-SNE and NetSNE\n\t- 'Bht-SNE': to get a usual t-SNE embedding of a dataset\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.basic': to perform a t-SNE-like embedding using Net-SNE\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.train': train Net-SNE on a training/sampled dataset to latter project new data on the embedding\n---> Requirments : to.run = c('Compute.sim', 'BhtSNE' &/| 'NetSNE.basic')\n\t- 'NetSNE.project': project a new dataset on a prior embedding\n---> Requirments: to.run = c('Compute.sim, 'BhtSNE' &/| 'NetSNE.basic', 'NetSNE.train')",
call. = FALSE)
}
for (i in 1:length(to.run)) {
if (!to.run[i] %in% c("compute.sim", "bhtsne", "netsne.basic",
"netsne.train", "netsne.project")) {
to.rm[(length(to.rm) + 1)] = to.run[i]
}
}
if (length(to.rm) > 0) {
stop(paste(paste(to.rm, collapse = " and "), ": Unknown task(s) for param: to.run.\nPossible values:\n\t- 'Compute.sim': to compute a knn-graph used by Bht-SNE and NetSNE\n\t- 'Bht-SNE': to get a usual t-SNE embedding of a dataset\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.basic': to perform a t-SNE-like embedding using Net-SNE\n---> Requirments: to.run = 'Compute.sim'\n\t- 'NetSNE.train': train Net-SNE on a training/sampled dataset to latter project new data on the embedding\n---> Requirments : to.run = c('Compute.sim', 'BhtSNE' &/| 'NetSNE.basic')\n\t- 'NetSNE.project': project a new dataset on a prior embedding\n---> Requirments: to.run = c('Compute.sim, 'BhtSNE' &/| 'NetSNE.basic', 'NetSNE.train')"),
call. = FALSE)
}
else {
rm(to.rm)
}
if ("netsne.train" %in% to.run) {
if (length(ref.embedding) != 1) {
stop("When training Net-SNE on a reference embedding (param: 'ref.embedding'), you can only use one of those options: 'BhtSNE' or 'NetSNE.basic' (corresponds to a t-SNE-like embedding). Therefore, c('",
paste(ref.embedding, collapse = "', '"), "') is not an acceptable value.",
call. = FALSE)
}
else {
ref.embedding = unique(tolower(ref.embedding))
if (length(which(c("bhtsne", "netsne.basic", "netsne") %in%
ref.embedding)) < 1) {
stop(ref.embedding, " is not a correct option for 'ref.embedding'.\nPossible values:\n\n\t- 'BhtSNE'\n ---> Requirment: to.run = 'BhtSNE'\n\n\t- 'NetSNE.basic'\n ---> Requirment: to.run = 'NetSNE.basic'",
call. = FALSE)
}
}
}
path.output.dir = strsplit(path.output.dir, "/")[[1]]
if (0 %in% nchar(path.output.dir)) {
path.output.dir = path.output.dir[-which(path.output.dir ==
"")]
}
if (!dir.exists(paste(path.output.dir, collapse = "/"))) {
dir.create(paste(path.output.dir, collapse = "/"), recursive = FALSE)
}
path.netSNE.dir = strsplit(path.netSNE.dir, "/")[[1]]
if (0 %in% nchar(path.netSNE.dir)) {
path.netSNE.dir = path.netSNE.dir[-which(path.netSNE.dir ==
"")]
}
if (path.netSNE.dir[length(path.netSNE.dir)] != "bin") {
path.netSNE.dir[length(path.netSNE.dir) + 1] = "bin"
}
path.netSNE.dir = paste(path.netSNE.dir, collapse = "/")
if (!file.exists(path.netSNE.dir)) {
if (!file.exists(paste("/", path.netSNE.dir, sep = ""))) {
stop(paste("The specified path to the 'bin' directory containing the executable files (",
path.netSNE.dir, ") does not exist", sep = ""),
call. = FALSE)
}
else {
path.netSNE.dir = paste("/", path.netSNE.dir, sep = "")
}
}
if (length(which(c("netsne.basic", "netsne.train", "netsne.project") %in%
to.run)) > 0) {
name.netSNE.output.dir = strsplit(name.netSNE.output.dir,
"/")[[1]]
if (0 %in% nchar(name.netSNE.output.dir)) {
name.netSNE.output.dir = name.netSNE.output.dir[-which(name.netSNE.output.dir ==
"")]
}
name.netSNE.output.dir = name.netSNE.output.dir[length(name.netSNE.output.dir)]
}
if (length(which(c("compute.sim", "bhtsne", "netsne.basic",
"netsne.train") %in% to.run)) > 0) {
if (is.null(train.data) & is.null(path.to.bin.train.file)) {
stop("Neither the train data ('train.data') nor the path to train data binary file ('path.to.bin.train.file') were specified, please re-lunch the function with one of them as input.\n---> Required for running ",
paste(to.run[which(to.run %in% c("compute.sim",
"netsne.basic", "netsne.train"))], collapse = " and "),
call. = FALSE)
}
else if (!is.null(path.to.bin.train.file)) {
path.to.bin.train.file = strsplit(path.to.bin.train.file,
"/")[[1]]
if (0 %in% nchar(path.to.bin.train.file)) {
path.to.bin.train.file = path.to.bin.train.file[-which(path.to.bin.train.file ==
"")]
}
name.train = path.to.bin.train.file[length(path.to.bin.train.file)]
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
name.sim = strsplit(name.train, "\.")[[1]]
extention = name.sim[length(name.sim)]
name.sim = name.sim[-length(name.sim)]
name.sim = paste(name.sim, collapse = ".")
name.sim = paste(name.sim, "_", perp, "_P.",
extention, sep = "")
}
if (!dir.exists(paste(path.to.bin.train.file[1:(length(path.to.bin.train.file) -
1)], collapse = "/"))) {
dir.create(paste(path.to.bin.train.file[1:(length(path.to.bin.train.file) -
1)], collapse = "/"), recursive = TRUE)
}
path.to.bin.train.file = paste(path.to.bin.train.file,
collapse = "/")
if (!is.null(train.data)) {
if (file.exists(path.to.bin.train.file)) {
status = suppressWarnings(file.remove(path.to.bin.train.file))
if (!status) {
stop("Impossible to remove the file '", name.train,
"' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
". Please do it yourself or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.train,
"' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
sep = "")
}
}
cat("\nWriting '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
"\n", sep = "")
Write_binary_file(train.data, path.to.bin.train.file)
}
else if (!file.exists(path.to.bin.train.file)) {
stop("The file '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
" doesn't exist and you didn't provide a matrix corresponding to the training data. Please provide the data train matrix or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nUsing the file '", name.train, "' in ",
substr(path.to.bin.train.file, 1, nchar(path.to.bin.train.file) -
nchar(name.train)), ".\n", sep = "")
}
}
else {
name.train = gsub(pattern = "\[.*", replacement = "",
deparse(substitute(train.data)))
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
name.sim = paste(name.train, "_", perp, "_P.dat",
sep = "")
}
name.train = paste(name.train, "dat", sep = ".")
if (file.exists(paste(paste(path.output.dir, collapse = "/"),
name.train, sep = "/"))) {
path.to.bin.train.file = paste(paste(path.output.dir,
collapse = "/"), name.train, sep = "/")
rm.file = TRUE
}
else {
path.to.bin.train.file = paste(paste(path.output.dir[1:(length(path.output.dir) -
1)], collapse = "/"), name.train, sep = "/")
if (file.exists(path.to.bin.train.file)) {
rm.file = TRUE
}
else {
rm.file = FALSE
}
}
if (rm.file) {
status = suppressWarnings(file.remove(path.to.bin.train.file))
if (!status) {
stop("Impossible to remove the file '", name.train,
"' in ", substr(path.to.bin.train.file, 1,
nchar(path.to.bin.train.file) - nchar(name.train)),
". Please do it yourself or change the path for param: 'path.to.bin.train.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.train, "' in ",
substr(path.to.bin.train.file, 1, nchar(path.to.bin.train.file) -
nchar(name.train)), "\n", sep = "")
}
}
cat("\nWriting '", name.train, "' in ", substr(path.to.bin.train.file,
1, nchar(path.to.bin.train.file) - nchar(name.train)),
"\n", sep = "")
Write_binary_file(train.data, path.to.bin.train.file)
}
}
if ("netsne.project" %in% to.run) {
if (is.null(test.data) & is.null(path.to.bin.test.file)) {
stop("Neither the test data ('test.data') nor the path to test data binary file ('path.to.bin.test.file') were specified, please re-lunch the function with one of them as input.\n---> Required for running to.run = c('netsne.project')",
call. = FALSE)
}
else if (!is.null(path.to.bin.test.file)) {
path.to.bin.test.file = strsplit(path.to.bin.test.file,
"/")[[1]]
if (0 %in% nchar(path.to.bin.test.file)) {
path.to.bin.test.file = path.to.bin.test.file[-which(path.to.bin.test.file ==
"")]
}
name.test = path.to.bin.test.file[length(path.to.bin.test.file)]
if (!dir.exists(paste(path.to.bin.test.file[1:(length(path.to.bin.test.file) -
1)], collapse = "/"))) {
dir.create(paste(path.to.bin.test.file[1:(length(path.to.bin.test.file) -
1)], collapse = "/"), recursive = TRUE)
}
path.to.bin.test.file = paste(path.to.bin.test.file,
collapse = "/")
if (!is.null(test.data)) {
if (file.exists(path.to.bin.test.file)) {
status = suppressWarnings(file.remove(path.to.bin.test.file))
if (!status) {
stop("Impossible to remove the file '", name.test,
"' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
". Please do it yourself or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), sep = "")
}
}
cat("\nWriting '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
"\n", sep = "")
Write_binary_file(test.data, path.to.bin.test.file)
}
else if (!file.exists(path.to.bin.test.file)) {
stop("The file '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
" doesn't exist and you didn't provide a matrix corresponding to the testing data. Please provide the data test matrix or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nUsing the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), ".\n", sep = "")
}
}
else {
name.test = gsub(pattern = "\[.*", replacement = "",
deparse(substitute(test.data)))
name.test = paste(name.test, "dat", sep = ".")
if (file.exists(paste(paste(path.output.dir, collapse = "/"),
name.test, sep = "/"))) {
path.to.bin.test.file = paste(paste(path.output.dir,
collapse = "/"), name.test, sep = "/")
rm.file = TRUE
}
else {
path.to.bin.test.file = paste(paste(path.output.dir[1:(length(path.output.dir) -
1)], collapse = "/"), name.test, sep = "/")
if (file.exists(path.to.bin.test.file)) {
rm.file = TRUE
}
else {
rm.file = FALSE
}
}
if (rm.file) {
status = suppressWarnings(file.remove(path.to.bin.test.file))
if (!status) {
stop("Impossible to remove the file '", name.test,
"' in ", substr(path.to.bin.test.file, 1,
nchar(path.to.bin.test.file) - nchar(name.test)),
". Please do it yourself or change the path for param: 'path.to.bin.test.file'.",
call. = FALSE)
}
else {
cat("\nRemoving the file '", name.test, "' in ",
substr(path.to.bin.test.file, 1, nchar(path.to.bin.test.file) -
nchar(name.test)), "\n", sep = "")
}
}
cat("\nWriting '", name.test, "' in ", substr(path.to.bin.test.file,
1, nchar(path.to.bin.test.file) - nchar(name.test)),
"\n", sep = "")
Write_binary_file(test.data, path.to.bin.test.file)
}
}
path.output.dir = paste(path.output.dir, collapse = "/")
if (length(which(c("bhtsne", "netsne.train") %in% to.run)) >
0) {
name.bhtSNE.output.dir = strsplit(name.bhtSNE.output.dir,
"/")[[1]]
if (0 %in% nchar(name.bhtSNE.output.dir)) {
name.bhtSNE.output.dir = name.bhtSNE.output.dir[-which(name.bhtSNE.output.dir ==
"")]
}
name.bhtSNE.output.dir = name.bhtSNE.output.dir[length(name.bhtSNE.output.dir)]
path.BhtSNE.output.dir = paste(path.output.dir, name.bhtSNE.output.dir,
sep = "/")
}
if (length(which(c("compute.sim", "bhtsne", "netsne.basic") %in%
to.run)) > 0) {
path.to.bin.P = paste(path.output.dir, name.sim, sep = "/")
}
if ("compute.sim" %in% to.run) {
if (file.exists(path.to.bin.P)) {
if (force.rm.old.outdir) {
status = suppressWarnings(file.remove(path.to.bin.P))
if (!status) {
stop("Impossible to remove the file '", name.sim,
"' in ", path.output.dir, ". Please do it yourself or remove 'compute.sim' from param: to.run if the file is correct.",
call. = FALSE)
}
else {
compute.sim = TRUE
}
}
else {
WALL = TRUE
while (WALL) {
cat("The binary file '", name.sim, "' specifying the similarities seems to already exist (PATH: ",
path.to.bin.P, ").\nPlease choose:\n\t- [1]: Remove the file and compute similarities,\n\t- [2]: Keep the file and skip the computing of similarities,\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
status = suppressWarnings(file.remove(path.to.bin.P))
if (!status) {
stop("Impossible to remove the file '",
name.sim, "' in ", path.output.dir,
". Please do it yourself or remove 'compute.sim' from param: to.run if the file is correct.",
call. = FALSE)
}
}
else if (answer == "2") {
compute.sim = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
compute.sim = TRUE
}
if (compute.sim) {
Compute_similarities(perp = perp, verbose = verbose,
path.netSNE.dir = path.netSNE.dir, path.to.bin.file = path.to.bin.train.file,
path.output.file = path.to.bin.P)
}
}
else {
compute.sim = FALSE
}
if (!compute.sim && length(which(c("bhtsne", "netsne.basic") %in%
to.run)) > 0 && !file.exists(path.to.bin.P)) {
stop("The file ", name.sim, " in ", path.output.dir,
" is unreachable.", call. = FALSE)
}
if ("bhtsne" %in% to.run) {
if (dir.exists(path.BhtSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.BhtSNE.output.dir, recursive = TRUE)
run.bhtsne = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.bhtSNE.output.dir,
"' for saving the outputs of Bht-SNE seems to already exist (PATH: ",
path.BhtSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Bht-SNE,\n\t- [2]: Keep the directory and skip the computing of Bht-SNE,\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.BhtSNE.output.dir, recursive = TRUE)
run.bhtsne = TRUE
}
else if (answer == "2") {
run.bhtsne = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.bhtsne = TRUE
}
if (run.bhtsne) {
RunBhtSNE(out.dims = out.dims, max.iter = max.iter,
theta = theta.BhtSNE, mom.init = mom.init, mom.final = mom.final,
mom.switch.iter = mom.switch.iter, early.exag.iter = early.exag.iter,
learn.rate = learn.rate.bhtSNE, batch.frac = batch.frac.bhtSNE,
seed = seed, verbose = verbose, random.init = random.init,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.file = path.to.bin.train.file, path.to.simil.file = path.to.bin.P,
path.output.dir = path.BhtSNE.output.dir)
}
}
else {
run.bhtsne = FALSE
}
if ("netsne.basic" %in% to.run) {
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"basic", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.basic = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (t-SNE-like use) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.basic (t-SNE-like),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (t-SNE-like),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.basic = TRUE
}
else if (answer == "2") {
run.netsne.basic = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.basic = TRUE
}
if (run.netsne.basic) {
RunNetSNE(utilis = "t-SNE", out.dims = out.dims,
max.iter = max.iter, theta = theta.NetSNE, step.method = step.method,
NN.layers = NN.layers, NN.units = NN.units, NN.function = NN.function,
l2.reg.param = l2.reg.param, mom.init = mom.init,
mom.final = mom.final, mom.switch.iter = mom.switch.iter,
early.exag.iter = early.exag.iter, learn.rate = learn.rate.netSNE,
local.sample = local.sample, batch.frac = batch.frac.netSNE,
min.sample.Z = min.sample.Z, sgd = sgd, seed = seed,
verbose = verbose, permute.after.iters = permute.after.iters,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train.file = path.to.bin.train.file,
path.to.bin.test.file = NULL, path.to.simil.file = path.to.bin.P,
path.output.dir = path.NetSNE.output.dir, path.ref.embedding = NULL,
path.to.model.dir = NULL, model.prefix = "WHATEVER")
}
}
else {
run.netsne.basic = FALSE
}
if ("netsne.train" %in% to.run) {
if (ref.embedding == "bhtsne") {
path.ref.embedding = paste(path.output.dir, name.bhtSNE.output.dir,
"Y_final.txt", sep = "/")
}
else {
path.ref.embedding = paste(path.output.dir, paste(name.netSNE.output.dir,
"basic", sep = "_"), "Y_final.txt", sep = "/")
}
if (!file.exists(path.ref.embedding)) {
stop("There is no embedding for Net-SNE to learn in ",
path.ref.embedding, ". Please change the value of param: 'ref.embedding' or include the relevant option in 'to.run'.",
call. = FALSE)
}
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"model", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.train = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (model creation after learning embedding) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.train (learn embedding),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (learn embedding),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.train = TRUE
}
else if (answer == "2") {
run.netsne.train = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.train = TRUE
}
if (run.netsne.train) {
RunNetSNE(utilis = "Learn", out.dims = out.dims,
max.iter = max.iter, theta = theta.NetSNE, step.method = step.method,
NN.layers = NN.layers, NN.units = NN.units, NN.function = NN.function,
l2.reg.param = l2.reg.param, mom.init = mom.init,
mom.final = mom.final, mom.switch.iter = mom.switch.iter,
early.exag.iter = early.exag.iter, learn.rate = learn.rate.netSNE,
local.sample = local.sample, batch.frac = batch.frac.netSNE,
min.sample.Z = min.sample.Z, sgd = sgd, seed = seed,
verbose = verbose, permute.after.iters = permute.after.iters,
save.iters.cache = save.iters.cache, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train.file = path.to.bin.train.file,
path.to.bin.test.file = NULL, path.to.simil.file = NULL,
path.output.dir = path.NetSNE.output.dir, path.ref.embedding = path.ref.embedding,
path.to.model.dir = NULL, model.prefix = "whatever")
}
}
else {
run.netsne.train = FALSE
}
if ("netsne.project" %in% to.run) {
path.to.model.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"model", sep = "_"), sep = "/")
if (!dir.exists(path.to.model.dir)) {
stop("The directory '", path.to.model.dir, "' supposed to contain the model of Net-SNE (after learning a reference embedding) does not exist.")
}
l = list.files(path.to.model.dir, pattern = "_.*[.txt]",
full.names = FALSE, include.dirs = FALSE)
l = l[which(regexpr("_L[0-9]*_[:alnum:]*", l) > 0)]
l = gsub("_L[0-9]*_.*.txt", "", l)
if (length(unique(l)) == 1) {
model.prefix = unique(l)
}
else {
stop("Impossible to find a model prefix (usually 'model_final') in ",
path.to.model.dir, ". Please check the content of the directory, and re-run the function (maybe with 'netsne.train' in to.run) ",
call. = FALSE)
}
path.NetSNE.output.dir = paste(path.output.dir, paste(name.netSNE.output.dir,
"projection", sep = "_"), sep = "/")
if (dir.exists(path.NetSNE.output.dir)) {
if (force.rm.old.outdir) {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.project = TRUE
}
else {
WALL = TRUE
while (WALL) {
cat("The output directory '", name.netSNE.output.dir,
"' for saving the outputs of Net-SNE (projection) seems to already exist (PATH: ",
path.NetSNE.output.dir, ").\nPlease choose:\n\t- [1]: Remove the directory and run Net-SNE.project (to project),\n\t- [2]: Keep the directory and skip the computing of Net-SNE (to project),\n\t- [3]: Stop and do nothing.\n",
sep = "")
answer = readline(prompt = "Your choice [[1]/[2]/[3]]: ")
if (answer %in% c(1:3)) {
WALL = FALSE
if (answer == "1") {
unlink(path.NetSNE.output.dir, recursive = TRUE)
run.netsne.project = TRUE
}
else if (answer == "2") {
run.netsne.project = FALSE
}
else {
return("Stopped")
}
}
}
}
}
else {
run.netsne.project = TRUE
}
if (run.netsne.project) {
RunNetSNE(utilis = "Project", verbose = TRUE, path.netSNE.dir = path.netSNE.dir,
path.to.bin.train = "irrelevant", path.to.bin.test = path.to.bin.test.file,
path.output.dir = path.NetSNE.output.dir, path.to.model.dir = path.to.model.dir,
model.prefix = model.prefix)
}
}
else {
run.netsne.project = FALSE
}
Result = list()
i = 1
if (run.bhtsne) {
Result[[i]] = read.table(file = paste(path.BhtSNE.output.dir,
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Bht-SNE"
i = i + 1
}
if (run.netsne.basic) {
Result[[i]] = read.table(file = paste(path.output.dir,
paste(name.netSNE.output.dir, "basic", sep = "_"),
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Net-SNE (Basic)"
i = i + 1
}
if (run.netsne.project) {
Result[[i]] = read.table(file = paste(path.output.dir,
paste(name.netSNE.output.dir, "projection", sep = "_"),
"Y_final.txt", sep = "/"), header = FALSE, skip = 2,
sep = "")
names(Result)[i] = "Net-SNE (Projection)"
i = i + 1
}
setwd(wd)
return(Result)
}
|
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