tensor_predictors/eeg_analysis/eeg_analysis_poi_step1.R

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2020-06-10 14:35:27 +00:00
# Source Code. # Loaded functions.
source('../tensor_predictors/poi.R') # POI
# Load C implentation of 'FastPOI-C' subroutine.
# Required for using 'use.C = TRUE' in the POI method.
# Compiled via.
# $ cd ../tensor_predictors/
# $ R CMD SHLIB poi.c
dyn.load('../tensor_predictors/poi.so')
# dyn.load('../tensor_predictors/poi.dll') # On Windows
# In this case 'use.C = TRUE' is required cause the R implementation is not
# sufficient due to memory exhaustion (and runtime).
# Load Dataset.
# > dataset <- read.table(file = 'egg.extracted.means.txt', header = TRUE,
# > stringsAsFactors = FALSE, check.names = FALSE)
# Save as Rdata file for faster loading.
# > saveRDS(dataset, file = 'eeg_data.rds')
dataset <- readRDS('../data_analysis/eeg_data.rds')
# Positive and negative case index.
set.seed(42)
zero <- sample(which(dataset$Case_Control == 0))
one <- sample(which(dataset$Case_Control == 1))
# 10-fold test groups.
zero <- list(zero[ 1: 4], zero[ 5: 8], zero[ 9:12], zero[13:16],
zero[17:20], zero[21:25], zero[26:30],
zero[31:35], zero[36:40], zero[41:45])
one <- list(one[ 1: 8], one[ 9:16], one[17:24], one[25:32],
one[33:40], one[41:48], one[49:56],
one[57:63], one[64:70], one[71:77])
# Iterate data folds.
folds <- vector('list', 10)
for (i in seq_along(folds)) {
cat('\r%d/%d ', i, length(folds))
# Call garbage collector.
gc()
# Formulate PFC-GEP for EEG data.
index <- c(zero[[i]], one[[i]])
X <- scale(dataset[-index, -(1:2)], scale = FALSE, center = TRUE)
Fy <- scale(dataset$Case_Control[-index], scale = FALSE, center = TRUE)
B <- crossprod(X) / nrow(X) # Sigma
P_Fy <- Fy %*% solve(crossprod(Fy), t(Fy))
A <- crossprod(X, P_Fy %*% X) / nrow(X) # Sigma_fit
# Before Starting POI on (very big GEP) call the garbage collector.
gc()
poi <- POI(A, B, 1L, lambda = lambda, use.C = TRUE)
rm(A, B)
gc()
# Set fold index.
poi$index = index
folds[[i]] <- poi
}
cat('\n')
# Save complete 10 fold results.
file <- sprintf('eeg_analysis_poi.rds')
saveRDS(folds, file = file)