Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous differential network analysis and classification for matrix-variate data with application to brain connectivity.

ABSTRACT: Growing evidence has shown that the brain connectivity network experiences alterations for complex diseases such as Alzheimer's disease (AD). Network comparison, also known as differential network analysis, is thus particularly powerful to reveal the disease pathologies and identify clinical biomarkers for medical diagnoses (classification). Data from neurophysiological measurements are multidimensional and in matrix-form. Naive vectorization method is not sufficient as it ignores the structural information within the matrix. In the article, we adopt the Kronecker product covariance matrices framework to capture both spatial and temporal correlations of the matrix-variate data while the temporal covariance matrix is treated as a nuisance parameter. By recognizing that the strengths of network connections may vary across subjects, we develop an ensemble-learning procedure, which identifies the differential interaction patterns of brain regions between the case group and the control group and conducts medical diagnosis (classification) of the disease simultaneously. Simulation studies are conducted to assess the performance of the proposed method. We apply the proposed procedure to the functional connectivity analysis of an functional magnetic resonance imaging study on AD. The hub nodes and differential interaction patterns identified are consistent with existing experimental studies, and satisfactory out-of-sample classification performance is achieved for medical diagnosis of AD.

SUBMITTER: Chen H

PROVIDER: S-EPMC9295187 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Brain connectivity alteration detection via matrix-variate differential network model.

Project description:Brain functional connectivity reveals the synchronization of brain systems through correlations in neurophysiological measures of brain activities. Growing evidence now suggests that the brain connectivity network experiences alterations with the presence of numerous neurological disorders, thus differential brain network analysis may provide new insights into disease pathologies. The data from neurophysiological measurement are often multidimensional and in a matrix form, posing a challenge in brain connectivity analysis. Existing graphical model estimation methods either assume a vector normal distribution that in essence requires the columns of the matrix data to be independent or fail to address the estimation of differential networks across different populations. To tackle these issues, we propose an innovative matrix-variate differential network (MVDN) model. We exploit the D-trace loss function and a Lasso-type penalty to directly estimate the spatial differential partial correlation matrix and use an alternating direction method of multipliers algorithm for the optimization problem. Theoretical and simulation studies demonstrate that MVDN significantly outperforms other state-of-the-art methods in dynamic differential network analysis. We illustrate with a functional connectivity analysis of an attention deficit hyperactivity disorder dataset. The hub nodes and differential interaction patterns identified are consistent with existing experimental studies.

| S-EPMC7900256 | biostudies-literature

Classification with the matrix-variate-<i>t</i> distribution.

Project description:Matrix-variate distributions can intuitively model the dependence structure of matrix-valued observations that arise in applications with multivariate time series, spatio-temporal or repeated measures. This paper develops an Expectation-Maximization algorithm for discriminant analysis and classification with matrix-variate t-distributions. The methodology shows promise on simulated datasets or when applied to the forensic matching of fractured surfaces or the classification of functional Magnetic Resonance, satellite or hand gestures images.

| S-EPMC7954198 | biostudies-literature

Two-way principal component analysis for matrix-variate data, with an application to functional magnetic resonance imaging data.

Project description:Many modern neuroimaging studies acquire large spatial images of the brain observed sequentially over time. Such data are often stored in the forms of matrices. To model these matrix-variate data we introduce a class of separable processes using explicit latent process modeling. To account for the size and two-way structure of the data, we extend principal component analysis to achieve dimensionality reduction at the individual level. We introduce necessary identifiability conditions for each model and develop scalable estimation procedures. The method is motivated by and applied to a functional magnetic resonance imaging study designed to analyze the relationship between pain and brain activity.

| S-EPMC6075629 | biostudies-literature

A graphical model for skewed matrix-variate non-randomly missing data.

Project description:Epidemiological studies on periodontal disease (PD) collect relevant bio-markers, such as the clinical attachment level (CAL) and the probed pocket depth (PPD), at pre-specified tooth sites clustered within a subject's mouth, along with various other demographic and biological risk factors. Routine cross-sectional evaluation are conducted under a linear mixed model (LMM) framework with underlying normality assumptions on the random terms. However, a careful investigation reveals considerable non-normality manifested in those random terms, in the form of skewness and tail behavior. In addition, PD progression is hypothesized to be spatially-referenced, i.e. disease status at proximal tooth-sites may be different from distally located sites, and tooth missingness is non-random (or informative), given that the number and location of missing teeth informs about the periodontal health in that region. To mitigate these complexities, we consider a matrix-variate skew-$t$ formulation of the LMM with a Markov graphical embedding to handle the site-level spatial associations of the bivariate (PPD and CAL) responses. Within the same framework, the non-randomly missing responses are imputed via a latent probit regression of the missingness indicator over the responses. Our hierarchical Bayesian framework powered by relevant Markov chain Monte Carlo steps addresses the aforementioned complexities within an unified paradigm, and estimates model parameters with seamless sharing of information across various stages of the hierarchy. Using both synthetic and real clinical data assessing PD status, we demonstrate a significantly improved fit of our proposition over various other alternative models.

| S-EPMC7672691 | biostudies-literature

Classification of amyotrophic lateral sclerosis by brain volume, connectivity, and network dynamics.

Project description:Emerging studies corroborate the importance of neuroimaging biomarkers and machine learning to improve diagnostic classification of amyotrophic lateral sclerosis (ALS). While most studies focus on structural data, recent studies assessing functional connectivity between brain regions by linear methods highlight the role of brain function. These studies have yet to be combined with brain structure and nonlinear functional features. We investigate the role of linear and nonlinear functional brain features, and the benefit of combining brain structure and function for ALS classification. ALS patients (N = 97) and healthy controls (N = 59) underwent structural and functional resting state magnetic resonance imaging. Based on key hubs of resting state networks, we defined three feature sets comprising brain volume, resting state functional connectivity (rsFC), as well as (nonlinear) resting state dynamics assessed via recurrent neural networks. Unimodal and multimodal random forest classifiers were built to classify ALS. Out-of-sample prediction errors were assessed via five-fold cross-validation. Unimodal classifiers achieved a classification accuracy of 56.35-61.66%. Multimodal classifiers outperformed unimodal classifiers achieving accuracies of 62.85-66.82%. Evaluating the ranking of individual features' importance scores across all classifiers revealed that rsFC features were most dominant in classification. While univariate analyses revealed reduced rsFC in ALS patients, functional features more generally indicated deficits in information integration across resting state brain networks in ALS. The present work undermines that combining brain structure and function provides an additional benefit to diagnostic classification, as indicated by multimodal classifiers, while emphasizing the importance of capturing both linear and nonlinear functional brain properties to identify discriminative biomarkers of ALS.

| S-EPMC8720197 | biostudies-literature

Data Driven Classification Using fMRI Network Measures: Application to Schizophrenia.

Project description:Using classification to identify biomarkers for various brain disorders has become a common practice among the functional MR imaging community. Typical classification pipeline includes taking the time series, extracting features from them, and using them to classify a set of patients and healthy controls. The most informative features are then presented as novel biomarkers. In this paper, we compared the results of single and double cross validation schemes on a cohort of 170 subjects with schizophrenia and healthy control subjects. We used graph theoretic measures as our features, comparing the use of functional and anatomical atlases to define nodes and the effect of prewhitening to remove autocorrelation trends. We found that double cross validation resulted in a 20% decrease in classification performance compared to single cross validation. The anatomical atlas resulted in higher classification results. Prewhitening resulted in a 10% boost in classification performance. Overall, a classification performance of 80% was obtained with a double-cross validation scheme using prewhitened time series and an anatomical brain atlas. However, reproducibility of classification within subjects across scans was surprisingly low and comparable to across subject classification rates, indicating that subject state during the short scan significantly influences the estimated features and classification performance.

| S-EPMC6218612 | biostudies-literature

Differential deactivation during mentalizing and classification of autism based on default mode network connectivity.

Project description:The default mode network (DMN) is a collection of brain areas found to be consistently deactivated during task performance. Previous neuroimaging studies of resting state have revealed reduced task-related deactivation of this network in autism. We investigated the DMN in 13 high-functioning adults with autism spectrum disorders (ASD) and 14 typically developing control participants during three fMRI studies (two language tasks and a Theory-of-Mind (ToM) task). Each study had separate blocks of fixation/resting baseline. The data from the task blocks and fixation blocks were collated to examine deactivation and functional connectivity. Deficits in the deactivation of the DMN in individuals with ASD were specific only to the ToM task, with no group differences in deactivation during the language tasks or a combined language and self-other discrimination task. During rest blocks following the ToM task, the ASD group showed less deactivation than the control group in a number of DMN regions, including medial prefrontal cortex (MPFC), anterior cingulate cortex, and posterior cingulate gyrus/precuneus. In addition, we found weaker functional connectivity of the MPFC in individuals with ASD compared to controls. Furthermore, we were able to reliably classify participants into ASD or typically developing control groups based on both the whole-brain and seed-based connectivity patterns with accuracy up to 96.3%. These findings indicate that deactivation and connectivity of the DMN were altered in individuals with ASD. In addition, these findings suggest that the deficits in DMN connectivity could be a neural signature that can be used for classifying an individual as belonging to the ASD group.

| S-EPMC3501481 | biostudies-literature

Connectivity strength-weighted sparse group representation-based brain network construction for MCI classification.

Project description:Brain functional network analysis has shown great potential in understanding brain functions and also in identifying biomarkers for brain diseases, such as Alzheimer's disease (AD) and its early stage, mild cognitive impairment (MCI). In these applications, accurate construction of biologically meaningful brain network is critical. Sparse learning has been widely used for brain network construction; however, its l1 -norm penalty simply penalizes each edge of a brain network equally, without considering the original connectivity strength which is one of the most important inherent linkwise characters. Besides, based on the similarity of the linkwise connectivity, brain network shows prominent group structure (i.e., a set of edges sharing similar attributes). In this article, we propose a novel brain functional network modeling framework with a "connectivity strength-weighted sparse group constraint." In particular, the network modeling can be optimized by considering both raw connectivity strength and its group structure, without losing the merit of sparsity. Our proposed method is applied to MCI classification, a challenging task for early AD diagnosis. Experimental results based on the resting-state functional MRI, from 50 MCI patients and 49 healthy controls, show that our proposed method is more effective (i.e., achieving a significantly higher classification accuracy, 84.8%) than other competing methods (e.g., sparse representation, accuracy = 65.6%). Post hoc inspection of the informative features further shows more biologically meaningful brain functional connectivities obtained by our proposed method. Hum Brain Mapp 38:2370-2383, 2017. © 2017 Wiley Periodicals, Inc.

| S-EPMC5488335 | biostudies-literature

Mixed-Effect Time-Varying Network Model and Application in Brain Connectivity Analysis.

Project description:Time-varying networks are fast emerging in a wide range of scientific and business applications. Most existing dynamic network models are limited to a single-subject and discrete-time setting. In this article, we propose a mixed-effect network model that characterizes the continuous time-varying behavior of the network at the population level, meanwhile taking into account both the individual subject variability as well as the prior module information. We develop a multistep optimization procedure for a constrained likelihood estimation and derive the associated asymptotic properties. We demonstrate the effectiveness of our method through both simulations and an application to a study of brain development in youth. Supplementary materials for this article are available online.

| S-EPMC8314561 | biostudies-literature

A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models.

Project description:RNA sequencing of time-course experiments results in three-way count data where the dimensions are the genes, the time points and the biological units. Clustering RNA-seq data allows to extract groups of co-expressed genes over time. After standardisation, the normalised counts of individual genes across time points and biological units have similar properties as compositional data. We propose the following procedure to suitably cluster three-way RNA-seq data: (1) pre-process the RNA-seq data by calculating the normalised expression profiles, (2) transform the data using the additive log ratio transform to map the composition in the D-part Aitchison simplex to a D-1 -dimensional Euclidean vector, (3) cluster the transformed RNA-seq data using matrix-variate Gaussian mixture models and (4) assess the quality of the overall cluster solution and of individual clusters based on cluster separation in the transformed space using density-based silhouette information and on compactness of the cluster in the original space using cluster maps as a suitable visualisation. The proposed procedure is illustrated on RNA-seq data from fission yeast and results are also compared to an analogous two-way approach after flattening out the biological units.

| S-EPMC10905927 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data