SparseICA: Sparse Independent Component Analysis

Sparse ICA (Sparse Independent Component Analysis) is a novel ICA method that enables sparse estimation of independent source components.

Installation

We assume you are running R 4.1.0 or newer. There is no guarantee for backward or forward comparability. Please raise the issue on GitHub if something breaks.

The following R packages are required:

RcppArmadillo (>= 14.2.2),
Rcpp (>= 1.0.13),
MASS (>= 7.3-58),
irlba (>= 2.3.5),
clue (>= 0.3),
ciftiTools (>= 0.16),
parallel (>= 4.1),
devtools

You can install them by running this code:

if(!require(c("Rcpp","RcppArmadillo","MASS","irlba","clue","ciftiTools","parallel","devtools"))){
    install.packages(c("Rcpp","RcppArmadillo","MASS","irlba","clue","ciftiTools","parallel","devtools"))
}

Then you can install Sparse ICA from github with:

library(devtools)
# install_github("thebrisklab/SparseICA")
install.packages("SparseICA", repos = c('https://thebrisklab.r-universe.dev', 'https://cloud.r-project.org'))
# Load the package
library(SparseICA)

Tutorial

The sparseICA() is the main function of our Sparse ICA algorithm. It is implemented in both pure R and Rcpp.

Explanation of Arguments

sparseICA(
    xData, n.comp, nu = "BIC", nu_list = seq(0.1, 4, 0.1), U.list = NULL,
    whiten = c('eigenvec', 'sqrtprec', 'none'), lngca = FALSE,
    orth.method = c('svd', 'givens'), method = c("C", "R"),
    restarts = 40, use_irlba = TRUE, eps = 1e-06, maxit = 500,
    verbose = TRUE, BIC_verbose = FALSE, converge_plot = FALSE, col.stand = TRUE,
    row.stand = FALSE, iter.stand = 5, positive_skewness = TRUE
)

xData: A numeric matrix of input data with dimensions P x T, where P is the number of features and T is the number of samples.
n.comp: An integer specifying the number of components to estimate.
nu: A positive numeric value or a character "BIC" specifying the tuning parameter controlling the balance between accuracy and sparsity of the results. It can be selected using a BIC-like criterion ("BIC") or based on expert knowledge (a positive number). Default is "BIC".
nu_list: A numeric vector specifying the list of candidate tuning parameters. Default is seq(0.1, 4, 0.1).
U.list: An optional matrix specifying the initialization of the U matrix. Default is NULL.
whiten: A character string specifying the method for whitening the input xData. Options are eigenvec, sqrtprec, lngca, or none. Default is eigenvec.
lngca: A logical value indicating whether to perform Linear Non-Gaussian Component Analysis (LNGCA). Default is FALSE.
orth.method: A character string specifying the method used for generating initial values for the U matrix. Default is svd.
method: A character string specifying the computation method. If C (default), C code is used for most computations for better performance. If R, computations are performed entirely in R.
restarts: An integer specifying the number of random initializations for optimization. Default is 40.
use_irlba: A logical value indicating whether to use the irlba method for fast truncated Singular Value Decomposition (SVD) during whitening. This can improve memory efficiency for intermediate datasets. Default is TRUE.
eps: A numeric value specifying the convergence threshold. Default is 1e-6.
maxit: An integer specifying the maximum number of iterations for the Sparse ICA method using Laplace density. Default is 500.
verbose: A logical value indicating whether to print convergence information during execution. Default is TRUE.
BIC_verbose: A logical value indicating whether to print BIC selection information. Default is FALSE.
converge_plot: A logical value indicating whether to generate a line plot showing the convergence trace. Default is FALSE.
col.stand: A logical value indicating whether to standardize columns. For each column, the mean of the entries in the column equals 0, and the variance of the entries in the column equals 1. Default is TRUE.
row.stand: A logical value indicating whether to standardize rows. For each row, the mean of the entries in the row equals 0, and the variance of the entries in the row equals 1. Default is FALSE.
iter.stand: An integer specifying the number of iterations for achieving both row and column standardization when col.stand = TRUE and row.stand = TRUE. Default is 5.
positive_skewness: A logical value indicating whether to enforce positive skewness on the estimated components. Default is TRUE.

Explanation of Output

The output will be a list with the following components as such:

loglik: The minimal log-likelihood value among the random initializations.
estS: A numeric matrix of estimated sparse independent components with dimensions P x Q.
estM: The estimated mixing matrix with dimensions Q x T.
estU: The estimated U matrix with dimensions Q x Q.
whitener: The whitener matrix used for data whitening.
converge: The convergence trace of the difference norm of the U matrix.
BIC: A numeric vector of BIC values corresponding to each candidate nu in nu_list.
nu_list: A numeric vector of candidate tuning parameter values.
best_nu: The optimal nu selected based on the BIC-like criterion.

Example

Load the example data:

data(example_sim123)

1. Visualization of example data

The true "source signals" - smat:

par(mfrow=c(1,3))
image(matrix(-example_sim123$smat[,1],33))
image(matrix(-example_sim123$smat[,2],33))
image(matrix(-example_sim123$smat[,3],33))

The true time series in the mixing matrix - mmat:

par(mfrow=c(3,1))
plot(example_sim123$mmat[1,],type = "l",xlab = "Time",ylab = "")
plot(example_sim123$mmat[2,],type = "l",xlab = "Time",ylab = "")
plot(example_sim123$mmat[3,],type = "l",xlab = "Time",ylab = "")

The simulated data matrix at time points T = 12, 23, and 35 - xmat:

par(mfrow=c(1,3))
image(matrix(example_sim123$xmat[,12],33))
image(matrix(example_sim123$xmat[,23],33))
image(matrix(example_sim123$xmat[,35],33))

2. Run Sparse ICA

Perform our Sparse ICA algorithm using sparseICA function. The tuning parameter nu is selected using the BIC-like criterion.

my_sparseICA = sparseICA(xData = example_sim123$xmat, n.comp = 3, nu = "BIC", method = "C",restarts = 40,
                           eps = 1e-6, maxit = 500, verbose=TRUE)

The selected optimal nu is 1.1.

3. Visualization of Sparse ICA results

Match the order of the estimated components with the truth.

matched_res=matchICA(my_sparseICA$estS,example_sim123$smat,my_sparseICA$estM)

Check the estimated source signals.

par(mfrow=c(1,3))
image(matrix(-matched_res$S[,1],33,33))
image(matrix(-matched_res$S[,2],33,33))
image(matrix(-matched_res$S[,3],33,33))

Check the estimated time series in the mixing matrix.

par(mfrow=c(3,1))
plot(matched_res$M[1,],type = "l",xlab = "Time",ylab = "")
plot(matched_res$M[2,],type = "l",xlab = "Time",ylab = "")
plot(matched_res$M[3,],type = "l",xlab = "Time",ylab = "")

Check the correlations.

> cor(example_sim123$smat[,1],matched_res$S[,1])
[1] 0.9970362
> cor(example_sim123$smat[,2],matched_res$S[,2])
[1] 0.9962684
> cor(example_sim123$smat[,3],matched_res$S[,3])
[1] 0.9856885

> cor(example_sim123$mmat[1,],matched_res$M[1,])
[1] 0.964416
> cor(example_sim123$mmat[2,],matched_res$M[2,])
[1] 0.9910054
> cor(example_sim123$mmat[3,],matched_res$M[3,])
[1] 0.9922269

Citation

Those using the SparseICA software should cite:
Wang Z., Gaynanova, I., Aravkin, A., Risk, B. B. (2024). Sparse Independent Component Analysis with an Application to Cortical Surface fMRI Data in Autism. Journal of the American Statistical Association, 119(548), 2508-2520.