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Register a new userDiffusion map for clustering fMRI spatial maps extracted by independent component analysis
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Tuomo Sipola
Publication date
2013
fields
Informatics Engineering
and research's language is
English
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Functional magnetic resonance imaging (fMRI) produces data about activity inside the brain, from which spatial maps can be extracted by independent component analysis (ICA). In datasets, there are n spatial maps that contain p voxels. The number of voxels is very high compared to the number of analyzed spatial maps. Clustering of the spatial maps is usually based on correlation matrices. This usually works well, although such a similarity matrix inherently can explain only a certain amount of the total variance contained in the high-dimensional data where n is relatively small but p is large. For high-dimensional space, it is reasonable to perform dimensionality reduction before clustering. In this research, we used the recently developed diffusion map for dimensionality reduction in conjunction with spectral clustering. This research revealed that the diffusion map based clustering worked as well as the more traditional methods, and produced more compact clusters when needed.
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Independent component analysis (ICA) has been widely used for blind source separation in many fields such as brain imaging analysis, signal processing and telecommunication. Many statistical techniques based on M-estimates have been proposed for estimating the mixing matrix. Recently, several nonparametric methods have been developed, but in-depth analysis of asymptotic efficiency has not been available. We analyze ICA using semiparametric theories and propose a straightforward estimate based on the efficient score function by using B-spline approximations. The estimate is asymptotically efficient under moderate conditions and exhibits better performance than standard ICA methods in a variety of simulations.
We introduce coroICA, confounding-robust independent component analysis, a novel ICA algorithm which decomposes linearly mixed multivariate observations into independent components that are corrupted (and rendered dependent) by hidden group-wise stationary confounding. It extends the ordinary ICA model in a theoretically sound and explicit way to incorporate group-wise (or environment-wise) confounding. We show that our proposed general noise model allows to perform ICA in settings where other noisy ICA procedures fail. Additionally, it can be used for applications with grouped data by adjusting for different stationary noise within each group. Our proposed noise model has a natural relation to causality and we explain how it can be applied in the context of causal inference. In addition to our theoretical framework, we provide an efficient estimation procedure and prove identifiability of the unmixing matrix under mild assumptions. Finally, we illustrate the performance and robustness of our method on simulated data, provide audible and visual examples, and demonstrate the applicability to real-world scenarios by experiments on publicly available Antarctic ice core data as well as two EEG data sets. We provide a scikit-learn compatible pip-installable Python package coroICA as well as R and Matlab implementations accompanied by a documentation at https://sweichwald.de/coroICA/
Independent component analysis (ICA) has been a popular dimension reduction tool in statistical machine learning and signal processing. In this paper, we present a convergence analysis for an online tensorial ICA algorithm, by viewing the problem as a nonconvex stochastic approximation problem. For estimating one component, we provide a dynamics-based analysis to prove that our online tensorial ICA algorithm with a specific choice of stepsize achieves a sharp finite-sample error bound. In particular, under a mild assumption on the data-generating distribution and a scaling condition such that $d^4/T$ is sufficiently small up to a polylogarithmic factor of data dimension $d$ and sample size $T$, a sharp finite-sample error bound of $tilde{O}(sqrt{d/T})$ can be obtained.
Understanding how certain brain regions relate to a specific neurological disorder has been an important area of neuroimaging research. A promising approach to identify the salient regions is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, e.g. brain networks constructed by functional magnetic resonance imaging (fMRI). We propose an interpretable GNN framework with a novel salient region selection mechanism to determine neurological brain biomarkers associated with disorders. Specifically, we design novel regularized pooling layers that highlight salient regions of interests (ROIs) so that we can infer which ROIs are important to identify a certain disease based on the node pooling scores calculated by the pooling layers. Our proposed framework, Pooling Regularized-GNN (PR-GNN), encourages reasonable ROI-selection and provides flexibility to preserve either individual- or group-level patterns. We apply the PR-GNN framework on a Biopoint Autism Spectral Disorder (ASD) fMRI dataset. We investigate different choices of the hyperparameters and show that PR-GNN outperforms baseline methods in terms of classification accuracy. The salient ROI detection results show high correspondence with the previous neuroimaging-derived biomarkers for ASD.
Compositional data represent a specific family of multivariate data, where the information of interest is contained in the ratios between parts rather than in absolute values of single parts. The analysis of such specific data is challenging as the application of standard multivariate analysis tools on the raw observations can lead to spurious results. Hence, it is appropriate to apply certain transformations prior further analysis. One popular multivariate data analysis tool is independent component analysis. Independent component analysis aims to find statistically independent components in the data and as such might be seen as an extension to principal component analysis. In this paper we examine an approach of how to apply independent component analysis on compositional data by respecting the nature of the former and demonstrate the usefulness of this procedure on a metabolomic data set.
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