add: eeg_sim,

add: Higher Order PCA (hopca)
This commit is contained in:
Daniel Kapla 2022-05-24 21:07:40 +02:00
parent b94b48091e
commit 62f1656d96
10 changed files with 260 additions and 19 deletions

202
simulations/eeg_sim.R Normal file
View File

@ -0,0 +1,202 @@
library(tensorPredictors)
suppressPackageStartupMessages({
library(ggplot2)
})
################################################################################
### Loading EEG Data ###
################################################################################
# Load as 3D predictors `X` and flat response `y`
c(X, y) %<-% local({
# Load from file
ds <- readRDS("eeg_data.rds")
# Dimension values
n <- nrow(ds) # sample size (nr. of people)
p <- 64L # nr. of predictors (count of sensorce)
t <- 256L # nr. of time points (measurements)
# Extract dimension names
nNames <- ds$PersonID
tNames <- as.character(seq(t))
pNames <- unlist(strsplit(colnames(ds)[2 + t * seq(p)], "_"))[c(TRUE, FALSE)]
# Split into predictors (with proper dims and names) and response
X <- array(as.matrix(ds[, -(1:2)]),
dim = c(person = n, time = t, sensor = p),
dimnames = list(person = nNames, time = tNames, sensor = pNames)
)
y <- ds$Case_Control
list(X, y)
})
################################################################################
### LOO-CV for Multiple Methods ###
################################################################################
# compatibility wrapper for function implemented with the "old" API
toNewAPI <- function(func) {
function(...) {
res <- func(...)
list(alphas = list(res$beta, res$alpha))
}
}
# Number of (2D)^2 PCA components per axis
npcs <- list(c(3, 4), c(15, 15), c(20, 30), dim(X)[-1])
# setup methods for simulation (with unified API)
methods <- list(
kpir.base = list(
fun = toNewAPI(kpir.base),
is.applicable = function(npc) prod(npc) < 100
),
kpir.new.vlp = list(
fun = toNewAPI(function(X, Fy) kpir.new(X, Fy, init.method = "vlp")),
is.applicable = function(npc) prod(npc) < 100
),
kpir.new.ls = list(
fun = toNewAPI(function(X, Fy) kpir.new(X, Fy, init.method = "ls")),
is.applicable = function(npc) prod(npc) < 100
),
kpir.ls = list(
fun = kpir.ls,
is.applicable = function(npc) TRUE
),
kpir.momentum.vlp = list(
fun = toNewAPI(function(X, Fy) kpir.momentum(X, Fy, init.method = "vlp")),
is.applicable = function(npc) prod(npc) < 100
),
kpir.momentum.ls = list(
fun = toNewAPI(function(X, Fy) kpir.momentum(X, Fy, init.method = "ls")),
is.applicable = function(npc) prod(npc) < 100
),
kpir.approx.vlp = list(
fun = toNewAPI(function(X, Fy) kpir.approx(X, Fy, init.method = "vlp")),
is.applicable = function(npc) prod(npc) < 100
),
kpir.approx.ls = list(
fun = toNewAPI(function(X, Fy) kpir.approx(X, Fy, init.method = "ls")),
is.applicable = function(npc) TRUE
)
)
# define AUC for reporting while simulation is running
auc <- function(y_true, y_pred) pROC::roc(y_true, y_pred, quiet = TRUE)$auc[1]
# init complete simulation as empty
sim <- NULL
for (npc in npcs) {
# check if any PC count is smaller than the axis
if (any(npc < dim(X)[-1])) {
# Reduce dimensions using (2D)^2 PCA, which is a special case of the Higher
# Order Principal Component Analysis
pcs <- hopca(X, npc = npc, sample.axis = 1)
# Reduce dimensions
X.pc <- mlm(X, Map(t, pcs), modes = 2:3)
} else {
# No reduction
X.pc <- X
}
for (name in names(methods)) {
# check if method can be applied to current reduction dimensions
if (!methods[[name]]$is.applicable(npc)) {
next
}
# extract method to be applied
method <- methods[[name]]$fun
# report name of current simulation method
cat(sprintf("npc: (t = %d, p = %d), method: %s\n", npc[1], npc[2], name))
# Leave-One-Out Cross-Validation
loo.cv <- data.frame(
y_true = y, y_pred = NA, # CV responses
elapsed = NA, sys.self = NA, user.self = NA # execution time
)
for (i in seq_len(nrow(X.pc))) {
# report progress
cat(sprintf("\r%3d/%d", i, nrow(X.pc)))
# Split into training/test data
X.train <- X.pc[-i, , ]
y.train <- scale(y[-i], scale = FALSE)
X.test <- X.pc[i, , , drop = FALSE]
y.test <- scale(y[i], center = attr(y.train, "scaled:center"), scale = FALSE)
# fit reduction (with method one of the methods to be "validated")
time <- system.time(sdr <- method(X.train, c(y.train)))
# reduce training data and fit a GLM
x.train <- mlm(X.train, Map(t, sdr$alphas), modes = 2:3)
fit <- glm(y ~ x, family = binomial(link = "logit"),
data = data.frame(y = y[-i], x = matrix(x.train, nrow(x.train))))
# predict from reduced test data
x.test <- mlm(X.test, Map(t, sdr$alphas), modes = 2:3)
y.pred <- predict(fit, data.frame(x = matrix(x.test, 1)), type = "response")
loo.cv[i, "y_pred"] <- y.pred
loo.cv[i, "elapsed"] <- time["elapsed"]
loo.cv[i, "sys.self"] <- time["sys.self"]
loo.cv[i, "user.self"] <- time["user.self"]
}
# accumulate LOO-CV results to previous results
loo.cv$method <- factor(name)
loo.cv$npc <- factor(sprintf("(%d, %d)", npc[1], npc[2]))
sim <- rbind(sim, loo.cv)
# Report partial sim done and one of the interesting measures
cat(sprintf(" (Done) AUC: %f\n", with(loo.cv, auc(y_true, y_pred))))
# dump simulation (after each fold) to file
saveRDS(sim, "eeg_sim.rds")
}
}
################################################################################
### Simulation Stats ###
################################################################################
# sim <- readRDS("eeg_sim.rds")
metrics <- list(
# acc: Accuracy. P(Yhat = Y). Estimated as: (TP+TN)/(P+N).
"Acc" = function(y_true, y_pred) mean(round(y_pred) == y_true),
# err: Error rate. P(Yhat != Y). Estimated as: (FP+FN)/(P+N).
"Err" = function(y_true, y_pred) mean(round(y_pred) != y_true),
# fpr: False positive rate. P(Yhat = + | Y = -). aliases: Fallout.
"FPR" = function(y_true, y_pred) mean((round(y_pred) == 1)[y_true == 0]),
# tpr: True positive rate. P(Yhat = + | Y = +). aliases: Sensitivity, Recall.
"TPR" = function(y_true, y_pred) mean((round(y_pred) == 1)[y_true == 1]),
# fnr: False negative rate. P(Yhat = - | Y = +). aliases: Miss.
"FNR" = function(y_true, y_pred) mean((round(y_pred) == 0)[y_true == 1]),
# tnr: True negative rate. P(Yhat = - | Y = -).
"TNR" = function(y_true, y_pred) mean((round(y_pred) == 0)[y_true == 0]),
# auc: Area Under the Curve
"AUC" = function(y_true, y_pred) pROC::roc(y_true, y_pred, quiet = TRUE)$auc[1],
# auc.sd: Estimated standard error of the AUC estimate
"sd(AUC)" = function(y_true, y_pred)
sqrt(pROC::var(pROC::roc(y_true, y_pred, quiet = TRUE)))
)
# Applies metrics on a group
do.stats <- function(group) {
stat <- Map(do.call, metrics, list(as.list(group[c("y_true", "y_pred")])))
data.frame(method = group$method[1], npc = group$npc[1], stat, check.names = FALSE)
}
# Call stats for each grouping
stats <- do.call(rbind, Map(do.stats, split(sim, ~ method + npc, sep = " ")))
rownames(stats) <- NULL
print(stats, digits = 2)
# and execution time stats
times <- aggregate(cbind(elapsed, sys.self, user.self) ~ method + npc, sim, median)
print(times, digits = 2)

View File

@ -70,7 +70,7 @@ sim <- function(X, Fy, alpha.true, beta.true, max.iter = 500L) {
logger = logger("new.ls")) logger = logger("new.ls"))
# Least Squares estimate (alternating estimation) # Least Squares estimate (alternating estimation)
kpir.ls(X, Fy, sample.mode = 1L, max.iter = max.iter, logger = logger("ls")) kpir.ls(X, Fy, sample.axis = 1L, max.iter = max.iter, logger = logger("ls"))
# Gradient Descent with Nesterov Momentum # Gradient Descent with Nesterov Momentum
kpir.momentum(X, Fy, max.iter = max.iter, init.method = "vlp", kpir.momentum(X, Fy, max.iter = max.iter, init.method = "vlp",
@ -237,7 +237,7 @@ for (rep in 1:reps) {
)) ))
dim(Fy) <- c(n, k, r) dim(Fy) <- c(n, k, r)
X <- mlm(Fy, alpha.1, alpha.2, modes = 3:2) X <- mlm(Fy, alpha.1, alpha.2, modes = 3:2)
X <- X + rtensornorm(n, 0, Delta.1, Delta.2, sample.mode = 1L) X <- X + rtensornorm(n, 0, Delta.1, Delta.2, sample.axis = 1L)
hist.sim <- sim(X, Fy, alpha.1.true, alpha.2.true, max.iter = max.iter) hist.sim <- sim(X, Fy, alpha.1.true, alpha.2.true, max.iter = max.iter)
hist.sim$repetition <- rep hist.sim$repetition <- rep
@ -331,7 +331,7 @@ sim3 <- function(X, Fy, alphas.true, max.iter = 500L) {
)) ))
# Approximated MLE with Nesterov Momentum # Approximated MLE with Nesterov Momentum
kpir.ls(X, Fy, sample.mode = 1L, max.iter = max.iter, logger = logger("ls")) kpir.ls(X, Fy, sample.axis = 1L, max.iter = max.iter, logger = logger("ls"))
# Add method tags # Add method tags
hist.ls$method <- factor("ls") hist.ls$method <- factor("ls")

View File

@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand # Generated by roxygen2: do not edit by hand
export("%<-%")
export("%x_1%") export("%x_1%")
export("%x_2%") export("%x_2%")
export("%x_3%") export("%x_3%")
@ -13,6 +14,7 @@ export(approx.kronecker)
export(colKronecker) export(colKronecker)
export(dist.projection) export(dist.projection)
export(dist.subspace) export(dist.subspace)
export(hopca)
export(kpir.approx) export(kpir.approx)
export(kpir.base) export(kpir.base)
export(kpir.ls) export(kpir.ls)

View File

@ -0,0 +1,37 @@
#' Higher Order Principal Component Analysis
#'
#' @param X multi-dimensional array (at least a matrix)
#' @param npc Number of Principal Components for each axis, if not specified
#' its the maximum
#' @param sample.axis index of the sample mode, a.k.a. observation axis index
#'
#' @return list of matrices, each entry are the first PCs of the corresponding
#' axis. The `i`'th entry are the `npc[i]` first Principal Components of the
#' `i`th axis excluding the sample axis (note: this means there is an index
#' shift after the sample axis).
#'
#' @export
hopca <- function(X, npc = dim(X)[-sample.axis], sample.axis = 1L) {
# observation index numbers (all axis except the sample axis)
modes <- seq_along(dim(X))[-sample.axis]
# Mean (a.k.a. sum elements over the sample axis)
mu <- apply(X, modes, mean, simplify = TRUE)
# Center `X` by subtraction of the mean `mu` from each observation
X.centered <- sweep(X, modes, mu)
# PCA for each mode (axis)
PCs <- Map(function(i) {
La.svd(mcrossprod(X.centered, modes[i]), npc[i], 0)$u
}, seq_along(modes))
# Set names if any
if (!is.null(dimnames(X))) {
names(PCs) <- names(dimnames(X)[-sample.axis])
for (i in seq_along(modes)) {
dimnames(PCs[[i]]) <- list(dimnames(X)[-sample.axis][[i]], NULL)
}
}
PCs
}

View File

@ -57,7 +57,7 @@ kpir.approx <- function(X, Fy, shape = c(dim(X)[-1], dim(Fy[-1])),
dim(Fy) <- c(n, k, r) dim(Fy) <- c(n, k, r)
dim(X) <- c(n, p, q) dim(X) <- c(n, p, q)
ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.mode = 1L, eps = eps) ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.axis = 1L, eps = eps)
c(beta0, alpha0) %<-% ls$alphas c(beta0, alpha0) %<-% ls$alphas
} else { # Van Loan and Pitsianis } else { # Van Loan and Pitsianis
# Vectorize # Vectorize

View File

@ -1,9 +1,9 @@
#' Per mode (axis) alternating least squares estimate #' Per mode (axis) alternating least squares estimate
#' #'
#' @param sample.mode index of the sample mode, a.k.a. observation axis index #' @param sample.axis index of the sample mode, a.k.a. observation axis index
#' #'
#' @export #' @export
kpir.ls <- function(X, Fy, max.iter = 20L, sample.mode = 1L, kpir.ls <- function(X, Fy, max.iter = 20L, sample.axis = 1L,
eps = .Machine$double.eps, logger = NULL eps = .Machine$double.eps, logger = NULL
) { ) {
# Check if X and Fy have same number of observations # Check if X and Fy have same number of observations
@ -11,20 +11,20 @@ kpir.ls <- function(X, Fy, max.iter = 20L, sample.mode = 1L,
# scalar response case (add new axis of size 1) # scalar response case (add new axis of size 1)
dim(Fy) <- local({ dim(Fy) <- local({
dims <- rep(1, length(dim(X))) dims <- rep(1, length(dim(X)))
dims[sample.mode] <- length(Fy) dims[sample.axis] <- length(Fy)
dims dims
}) })
} else { } else {
stopifnot(dim(X)[sample.mode] == dim(Fy)[sample.mode]) stopifnot(dim(X)[sample.axis] == dim(Fy)[sample.axis])
} }
# Check dimensions # Check dimensions
stopifnot(length(dim(X)) == length(dim(Fy))) stopifnot(length(dim(X)) == length(dim(Fy)))
stopifnot(dim(X)[sample.mode] == dim(Fy)[sample.mode]) stopifnot(dim(X)[sample.axis] == dim(Fy)[sample.axis])
# and model constraints # and model constraints
stopifnot(all(dim(Fy) <= dim(X))) stopifnot(all(dim(Fy) <= dim(X)))
# mode index sequence (exclude sample mode, a.k.a. observation axis) # mode index sequence (exclude sample mode, a.k.a. observation axis)
modes <- seq_along(dim(X))[-sample.mode] modes <- seq_along(dim(X))[-sample.axis]
### Step 1: initial per mode estimates ### Step 1: initial per mode estimates
@ -68,7 +68,7 @@ kpir.ls <- function(X, Fy, max.iter = 20L, sample.mode = 1L,
R <- X - mlm(Fy, alphas, modes = modes) R <- X - mlm(Fy, alphas, modes = modes)
# Moment estimates for `Delta_i`s # Moment estimates for `Delta_i`s
Deltas <- Map(mcrossprod, list(R), mode = modes) Deltas <- Map(mcrossprod, list(R), mode = modes)
Deltas <- Map(`*`, 1 / dim(X)[sample.mode], Deltas) Deltas <- Map(`*`, 1 / dim(X)[sample.axis], Deltas)
list( list(
alphas = structure(alphas, names = as.character(modes)), alphas = structure(alphas, names = as.character(modes)),

View File

@ -54,7 +54,7 @@ kpir.momentum <- function(X, Fy, shape = c(dim(X)[-1], dim(Fy[-1])),
if (init.method == "ls") { if (init.method == "ls") {
dim(X) <- c(n, p, q) dim(X) <- c(n, p, q)
dim(Fy) <- c(n, k, r) dim(Fy) <- c(n, k, r)
ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.mode = 1L, eps = eps) ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.axis = 1L, eps = eps)
c(beta0, alpha0) %<-% ls$alphas c(beta0, alpha0) %<-% ls$alphas
dim(X) <- c(n, p * q) dim(X) <- c(n, p * q)
dim(Fy) <- c(n, k * r) dim(Fy) <- c(n, k * r)

View File

@ -51,7 +51,7 @@ kpir.new <- function(X, Fy, shape = c(dim(X)[-1], dim(Fy[-1])),
if (init.method == "ls") { if (init.method == "ls") {
dim(X) <- c(n, p, q) dim(X) <- c(n, p, q)
dim(Fy) <- c(n, k, r) dim(Fy) <- c(n, k, r)
ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.mode = 1L, eps = eps) ls <- kpir.ls(X, Fy, max.iter = max.init.iter, sample.axis = 1L, eps = eps)
c(beta, alpha) %<-% ls$alphas c(beta, alpha) %<-% ls$alphas
dim(X) <- c(n, p * q) dim(X) <- c(n, p * q)
dim(Fy) <- c(n, k * r) dim(Fy) <- c(n, k * r)

View File

@ -23,7 +23,7 @@
#' # extracting the first three valus from the vector of length 10. #' # extracting the first three valus from the vector of length 10.
#' } #' }
#' #'
#' @keywords internal #' @export
"%<-%" <- function(lhs, rhs) { "%<-%" <- function(lhs, rhs) {
var.names <- make.names(as.list(substitute(lhs))[-1]) var.names <- make.names(as.list(substitute(lhs))[-1])
values <- as.list(rhs) values <- as.list(rhs)
@ -31,5 +31,5 @@
for (i in seq_along(var.names)) { for (i in seq_along(var.names)) {
assign(var.names[i], values[[i]], envir = env) assign(var.names[i], values[[i]], envir = env)
} }
lhs invisible(lhs)
} }

View File

@ -7,7 +7,7 @@
#' X <- rtensornorm(n, 0, Sigma.1, Sigma.2) #' X <- rtensornorm(n, 0, Sigma.1, Sigma.2)
#' #'
#' @export #' @export
rtensornorm <- function(n, mean, ..., sample.mode) { rtensornorm <- function(n, mean, ..., sample.axis) {
# get covariance matrices # get covariance matrices
cov <- list(...) cov <- list(...)
@ -38,10 +38,10 @@ rtensornorm <- function(n, mean, ..., sample.mode) {
# permute axis for indeing observations on sample mode (permute first axis # permute axis for indeing observations on sample mode (permute first axis
# with sample mode axis) # with sample mode axis)
if (!missing(sample.mode)) { if (!missing(sample.axis)) {
axis <- seq_len(length(dims) - 1) axis <- seq_len(length(dims) - 1)
start <- seq_len(sample.mode - 1) start <- seq_len(sample.axis - 1)
end <- seq_len(length(dims) - sample.mode) + sample.mode - 1 end <- seq_len(length(dims) - sample.axis) + sample.axis - 1
X <- aperm(X, c(axis[start], length(dims), axis[end])) X <- aperm(X, c(axis[start], length(dims), axis[end]))
} }