Clusterwise Independent Component Analysis (C-ICA): An R package for clustering subjects based on ICA patterns underlying three-way (brain) data

Neurocomputing, vol. 606, pp. 128396

Abstract

In many areas of science, like neuroscience, genomics and text mining, several important and challenging research questions imply the study of (subject) heterogeneity present in three-way data. In clinical neuroscience, for example, disclosing differences or heterogeneity between subjects in resting state networks (RSNs) underlying multi-subject fMRI data (i.e., time by voxel by subject three-way data) may advance the subtyping of psychiatric and mental diseases. Recently, the Clusterwise Independent Component Analysis (C-ICA) method was proposed that enables the disclosure of heterogeneity between subjects in RSNs that is present in multi-subject rs-fMRI data [1]. Up to now, however, no publicly available software exists that allows to fit C-ICA to empirical data at hand. The goal of this paper, therefore, is to present the CICA R package, which contains the necessary functions to estimate the C-ICA parameters and to interpret and visualize the analysis output. Further, the package also includes functions to select suitable initial values for the C-ICA model parameters and to determine the optimal number of clusters and components for a given empirical data set (i.e., model selection). The use of the main functions of the package is discussed and demonstrated with simulated data. Herewith, the necessary analytical choices that have to be made by the user (e.g., starting values) are explained and showed step by step. The rich functionality of the package is further illustrated by applying C-ICA to empirical rs-fMRI data from a group of Alzheimer patients and elderly control subjects and to multi-country stock market data. Finally, extensions regarding the C-ICA algorithm and procedures for model selection that could be implemented in future releases of the package are discussed.

Authors 5

1. Jeffrey Durieux corresponding Aachen Leiden Institute for Brain and Cognition Methodology and Statistics Unit Institute of Psychology, Leiden University

   Leiden University · Erasmus University Rotterdam

   Affiliation as printed

   Econometrics Institute, Erasmus School of Economics, Erasmus University, Burgermeester Oudlaan 50, Rotterdam, 3062 PA, The Netherlands

   Leiden Institute for Brain and Cognition, Leiden University, The Netherlands

   Methodology and Statistics Unit, Institute of Psychology, Leiden University, Wassenaarseweg 52, Leiden, 2333 AK, The Netherlands

2. Serge A.R.B. Rombouts Aachen Department of Radiology, Leiden University Medical Center Leiden Institute for Brain and Cognition Methodology and Statistics Unit Institute of Psychology, Leiden University

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, Albinusdreef 2, Leiden, 2300 RC, The Netherlands

   Leiden Institute for Brain and Cognition, Leiden University, The Netherlands

   Methodology and Statistics Unit, Institute of Psychology, Leiden University, Wassenaarseweg 52, Leiden, 2333 AK, The Netherlands

3. Marisa Koini

   Medical University of Graz

   Affiliation as printed

   Department of Neurology, Medical University of Graz, Neue Stifingtalstrasse 6, Graz, 8010, Austria

4. Juan Claramunt González Aachen Methodology and Statistics Unit Institute of Psychology, Leiden University

   Leiden University

   Affiliation as printed

   Methodology and Statistics Unit, Institute of Psychology, Leiden University, Wassenaarseweg 52, Leiden, 2333 AK, The Netherlands

5. Tom F. Wilderjans Aachen Leiden Institute for Brain and Cognition Methodology and Statistics Unit Institute of Psychology, Leiden University

   Leiden University · Vrije Universiteit Amsterdam · KU Leuven

   Affiliation as printed

   Department of Clinical Psychology, Vrije Universiteit Amsterdam, van der Boechorstraat 7, Amsterdam, 1081 BT, The Netherlands

   Leiden Institute for Brain and Cognition, Leiden University, The Netherlands

   Methodology and Statistics Unit, Institute of Psychology, Leiden University, Wassenaarseweg 52, Leiden, 2333 AK, The Netherlands

   Research Group of Quantitative Psychology and Individual Differences, Faculty of Psychology and Educational Sciences, KU Leuven, Tiensestraat 102, Leuven, 3000, Belgium