scholarly journals Exploratory factor analysis with structured residuals for brain network data

2020 ◽  
pp. 1-27
Author(s):  
Erik-Jan van Kesteren ◽  
Rogier A. Kievit
Keyword(s):  
Factor Analysis ◽  
Dimension Reduction ◽  
Exploratory Factor Analysis ◽  
A Priori ◽  
Brain Regions ◽  
Brain Network ◽  
R Software ◽  
Network Analyses ◽  
Number Of Factors ◽  
The Brain

Dimension reduction is widely used and often necessary to make network analyses and their interpretation tractable by reducing high-dimensional data to a small number of underlying variables. Techniques such as exploratory factor analysis (EFA) are used by neuroscientists to reduce measurements from a large number of brain regions to a tractable number of factors. However, dimension reduction often ignores relevant a priori knowledge about the structure of the data. For example, it is well established that the brain is highly symmetric. In this paper, we (a) show the adverse consequences of ignoring a priori structure in factor analysis, (b) propose a technique to accommodate structure in EFA by using structured residuals (EFAST), and (c) apply this technique to three large and varied brain-imaging network datasets, demonstrating the superior fit and interpretability of our approach. We provide an R software package to enable researchers to apply EFAST to other suitable datasets.

scholarly journals Exploratory Factor Analysis with Structured Residuals for Brain Imaging Data

2020 ◽  
Author(s):  
Erik-Jan van Kesteren ◽  
Rogier A. Kievit
Keyword(s):  
Factor Analysis ◽  
Dimension Reduction ◽  
Brain Imaging ◽  
Exploratory Factor Analysis ◽  
A Priori ◽  
Brain Regions ◽  
Imaging Data ◽  
Number Of Factors ◽  
Brain Imaging Data ◽  
The Brain

AbstractDimension reduction is widely used and often necessary to reduce high dimensional data to a small number of underlying variables, making subsequent analyses and their interpretation tractable. One popular technique is Exploratory Factor Analysis (EFA), used by cognitive neuroscientists to reduce measurements from a large number of brain regions to a tractable number of factors. However, dimension reduction often ignores relevant a priori knowledge about the structure of the data. For example, it is well established that the brain is highly symmetric. In this paper, we (a) show the adverse consequences of ignoring a priori structure in factor analysis, (b) propose a technique to accommodate structure in EFA using structured residuals (EFAST), and (c) apply this technique to three large and varied brain imaging datasets, demonstrating the superior fit and interpretability of our approach. We provide an R software package to enable researchers to apply EFAST to other suitable datasets.

scholarly journals A Computational Network Control Theory Analysis of Depression Symptoms

2018 ◽  
Vol 1 ◽  
Author(s):  
Yoed N. Kenett ◽  
Roger E. Beaty ◽  
John D. Medaglia
Keyword(s):  
Control Theory ◽  
Diffusion Tensor ◽  
Brain Regions ◽  
Brain Network ◽  
Network Control ◽  
Depression Symptoms ◽  
Theory Approach ◽  
Imaging Data ◽  
The Brain ◽  
Subclinical Depression

AbstractRumination and impaired inhibition are considered core characteristics of depression. However, the neurocognitive mechanisms that contribute to these atypical cognitive processes remain unclear. To address this question, we apply a computational network control theory approach to structural brain imaging data acquired via diffusion tensor imaging in a large sample of participants, to examine how network control theory relates to individual differences in subclinical depression. Recent application of this theory at the neural level is built on a model of brain dynamics, which mathematically models patterns of inter-region activity propagated along the structure of an underlying network. The strength of this approach is its ability to characterize the potential role of each brain region in regulating whole-brain network function based on its anatomical fingerprint and a simplified model of node dynamics. We find that subclinical depression is negatively related to higher integration abilities in the right anterior insula, replicating and extending previous studies implicating atypical switching between the default mode and Executive Control Networks in depression. We also find that subclinical depression is related to the ability to “drive” the brain system into easy to reach neural states in several brain regions, including the bilateral lingual gyrus and lateral occipital gyrus. These findings highlight brain regions less known in their role in depression, and clarify their roles in driving the brain into different neural states related to depression symptoms.

scholarly journals A Graphlet-Based Topological Characterization of the Resting-State Network in Healthy People

2021 ◽  
Vol 15 ◽  
Author(s):  
Paolo Finotelli ◽  
Carlo Piccardi ◽  
Edie Miglio ◽  
Paolo Dulio
Keyword(s):  
Resting State ◽  
Brain Regions ◽  
Brain Network ◽  
Induced Subgraphs ◽  
Topological Characterization ◽  
Network Information ◽  
The Subject ◽  
Euclidean Distances ◽  
The Brain

In this paper, we propose a graphlet-based topological algorithm for the investigation of the brain network at resting state (RS). To this aim, we model the brain as a graph, where (labeled) nodes correspond to specific cerebral areas and links are weighted connections determined by the intensity of the functional magnetic resonance imaging (fMRI). Then, we select a number of working graphlets, namely, connected and non-isomorphic induced subgraphs. We compute, for each labeled node, its Graphlet Degree Vector (GDV), which allows us to associate a GDV matrix to each one of the 133 subjects of the considered sample, reporting how many times each node of the atlas “touches” the independent orbits defined by the graphlet set. We focus on the 56 independent columns (i.e., non-redundant orbits) of the GDV matrices. By aggregating their count all over the 133 subjects and then by sorting each column independently, we obtain a sorted node table, whose top-level entries highlight the nodes (i.e., brain regions) most frequently touching each of the 56 independent graphlet orbits. Then, by pairwise comparing the columns of the sorted node table in the top-k entries for various values of k, we identify sets of nodes that are consistently involved with high frequency in the 56 independent graphlet orbits all over the 133 subjects. It turns out that these sets consist of labeled nodes directly belonging to the default mode network (DMN) or strongly interacting with it at the RS, indicating that graphlet analysis provides a viable tool for the topological characterization of such brain regions. We finally provide a validation of the graphlet approach by testing its power in catching network differences. To this aim, we encode in a Graphlet Correlation Matrix (GCM) the network information associated with each subject then construct a subject-to-subject Graphlet Correlation Distance (GCD) matrix based on the Euclidean distances between all possible pairs of GCM. The analysis of the clusters induced by the GCD matrix shows a clear separation of the subjects in two groups, whose relationship with the subject characteristics is investigated.

scholarly journals Likert scale and change in range of response categories vs. the factors extraction in EFA model

2015 ◽  
Vol 1 (311) ◽  
Author(s):  
Piotr Tarka
Keyword(s):  
Factor Analysis ◽  
Exploratory Factor Analysis ◽  
Rating Scale ◽  
Likert Scale ◽  
Optimal Number ◽  
Number Of Factors ◽  
Scale Experiment ◽  
Methodological Aspects ◽  
The Impact ◽  
Selection Of

Abstract: The objective article is the comparative analysis of Likert rating scale based on the following range of response categories, i.e. 5, 7, 9 and 11 in context of the appropriate process of factors extraction in exploratory factor analysis (EFA). The problem which is being addressed in article relates primarily to the methodological aspects, both in selection of the optimal number of response categories of the measured items (constituting the Likert scale) and identification of possible changes, differences or similarities associated (as a result of the impact of four types of scales) with extraction and determination the appropriate number of factors in EFA model.Keywords: Exploratory factor analysis, Likert scale, experiment research, marketing

Graph Theory-Based Brain Network Connectivity Analysis and Classification of Alzheimer’s Disease

2021 ◽  
Author(s):  
A. Thushara ◽  
C. Ushadevi Amma ◽  
Ansamma John
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Graph Theory ◽  
Neurodegenerative Disorder ◽  
Brain Networks ◽  
Network Connectivity ◽  
Brain Regions ◽  
Brain Network ◽  
Fiber Tracts ◽  
The Brain

Alzheimer’s Disease (AD) is basically a progressive neurodegenerative disorder associated with abnormal brain networks that affect millions of elderly people and degrades their quality of life. The abnormalities in brain networks are due to the disruption of White Matter (WM) fiber tracts that connect the brain regions. Diffusion-Weighted Imaging (DWI) captures the brain’s WM integrity. Here, the correlation betwixt the WM degeneration and also AD is investigated by utilizing graph theory as well as Machine Learning (ML) algorithms. By using the DW image obtained from Alzheimer’s Disease Neuroimaging Initiative (ADNI) database, the brain graph of each subject is constructed. The features extracted from the brain graph form the basis to differentiate between Mild Cognitive Impairment (MCI), Control Normal (CN) and AD subjects. Performance evaluation is done using binary and multiclass classification algorithms and obtained an accuracy that outperforms the current top-notch DWI-based studies.

scholarly journals EEG Source Network for the Diagnosis of Schizophrenia and the Identification of Subtypes Based on Symptom Severity—A Machine Learning Approach

2020 ◽  
Vol 9 (12) ◽  
pp. 3934
Author(s):  
Jeong-Youn Kim ◽  
Hyun Seo Lee ◽  
Seung-Hwan Lee
Keyword(s):  
Resting State ◽  
Symptom Severity ◽  
Classification Accuracy ◽  
Brain Regions ◽  
Brain Network ◽  
Clustering Coefficient ◽  
Forward Selection ◽  
Linear Discriminant ◽  
Network Analyses ◽  
Local Clustering Coefficient

A precise diagnosis and a comprehensive assessment of symptom severity are important clinical issues in patients with schizophrenia (SZ). We investigated whether electroencephalography (EEG) features obtained from EEG source network analyses could be effectively applied to classify the SZ subtypes based on symptom severity. Sixty-four electrode EEG signals were recorded from 119 patients with SZ (53 males and 66 females) and 119 normal controls (NC, 51 males and 68 females) during resting-state with closed eyes. Brain network features (global and local clustering coefficient and global path length) were calculated from EEG source activities. According to positive, negative, and cognitive/disorganization symptoms, the SZ patients were divided into two groups (high and low) by positive and negative syndrome scale (PANSS). To select features for classification, we used the sequential forward selection (SFS) method. The classification accuracy was evaluated using 10 by 10-fold cross-validation with the linear discriminant analysis (LDA) classifier. The best classification accuracy was 80.66% for estimating SZ patients from the NC group. The best classification accuracy between low and high groups in positive, negative, and cognitive/disorganization symptoms were 88.10%, 75.25%, and 77.78%, respectively. The selected features well-represented the pathological brain regions of SZ. Our study suggested that resting-state EEG network features could successfully classify between SZ patients and the NC, and between low and high SZ groups in positive, negative, and cognitive/disorganization symptoms.

scholarly journals Transient brain networks underlying interpersonal strategies during synchronized action

2020 ◽  
Author(s):  
Ole Adrian Heggli ◽  
Ivana Konvalinka ◽  
Joana Cabral ◽  
Elvira Brattico ◽  
Morten L Kringelbach ◽  
...  
Keyword(s):  
Computational Models ◽  
Brain Activity ◽  
Brain Regions ◽  
Brain Network ◽  
Human Interaction ◽  
Action Perception ◽  
Network Information ◽  
Mutual Adaptation ◽  
Underlying Mechanisms ◽  
The Brain

Abstract Interpersonal coordination is a core part of human interaction, and its underlying mechanisms have been extensively studied using social paradigms such as joint finger-tapping. Here, individual and dyadic differences have been found to yield a range of dyadic synchronization strategies, such as mutual adaptation, leading–leading, and leading–following behaviour, but the brain mechanisms that underlie these strategies remain poorly understood. To identify individual brain mechanisms underlying emergence of these minimal social interaction strategies, we contrasted EEG-recorded brain activity in two groups of musicians exhibiting the mutual adaptation and leading–leading strategies. We found that the individuals coordinating via mutual adaptation exhibited a more frequent occurrence of phase-locked activity within a transient action–perception-related brain network in the alpha range, as compared to the leading–leading group. Furthermore, we identified parietal and temporal brain regions that changed significantly in the directionality of their within-network information flow. Our results suggest that the stronger weight on extrinsic coupling observed in computational models of mutual adaptation as compared to leading–leading might be facilitated by a higher degree of action–perception network coupling in the brain.

scholarly journals Statistical Method to Extract Evoked Potentials from Noise

2020 ◽  
Vol 170 ◽  
pp. 02005
Author(s):  
Besma Benchabane ◽  
Moncef Benkherrat ◽  
Salah Djelel
Keyword(s):  
Wavelet Transform ◽  
Evoked Potentials ◽  
A Priori ◽  
Brain Regions ◽  
Statistical Test ◽  
A Priori Information ◽  
Time Frequency ◽  
Priori Information ◽  
Electrical Activities ◽  
The Brain

Evoked Potentials are induced by visual or auditory stimulation. The Evoked Potentials represent transient electrical activities of some limited brain regions. The signal-noise ratio (SNR) of the EPs is typically around -10 dB. In order to study brain activities related to information processing in the brain, one has to “extract” the single EPs from the noise. We propose a method does not require a priori information concerning the characteristics (time, frequency) of the signal and does not use a template. The method proposed in this work use the wavelet transform associated with a statistical test.

scholarly journals An exploratory factor analysis of the spontaneous reporting of severe cutaneous adverse reactions

2016 ◽  
Vol 8 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Manfred Hauben ◽  
Eric Hung ◽  
Wen-Yaw Hsieh
Keyword(s):  
Factor Analysis ◽  
T Cell ◽  
Exploratory Factor Analysis ◽  
Adverse Reactions ◽  
Overlap Syndromes ◽  
Number Of Factors ◽  
Shared Variance ◽  
Severe Cutaneous Adverse Reactions ◽  
Cutaneous Adverse Reactions ◽  
Variance Explained

Background: Severe cutaneous adverse reactions (SCARs) are prominent in pharmacovigilance (PhV). They have some commonalities such as nonimmediate nature and T-cell mediation and rare overlap syndromes have been documented, most commonly involving acute generalized exanthematous pustulosis (AGEP) and drug rash with eosinophilia and systemic symptoms (DRESS), and DRESS and toxic epidermal necrolysis (TEN). However, they display diverse clinical phenotypes and variations in specific T-cell immune response profiles, plus some specific genotype–phenotype associations. A question is whether causation of a given SCAR by a given drug supports causality of the same drug for other SCARs. If so, we might expect significant intercorrelations between SCARs with respect to overall drug-reporting patterns. SCARs with significant intercorrelations may reflect a unified underlying concept. Methods: We used exploratory factor analysis (EFA) on data from the United States Food and Drug Administration Adverse Event Reporting System (FAERS) to assess reporting intercorrelations between six SCARs [AGEP, DRESS, erythema multiforme (EM), Stevens–Johnson syndrome (SJS), TEN, exfoliative dermatitis (ExfolDerm)]. We screened the data using visual inspection of scatterplot matrices for problematic data patterns. We assessed factorability via Bartlett’s test of sphericity, Kaiser-Myer-Olkin (KMO) statistic, initial estimates of communality and the anti-image correlation matrix. We extracted factors via principle axis factoring (PAF). The number of factors was determined by scree plot/Kaiser’s rule. We also examined solutions with an additional factor. We applied various oblique rotations. We assessed the strength of the solution by percentage of variance explained, minimum number of factors loading per major factor, the magnitude of the communalities, loadings and crossloadings, and reproduced- and residual correlations. Results: The data were generally adequate for factor analysis but the amount of variance explained, shared variance, and communalities were low, suggesting caution in general against extrapolating causality between SCARs. SJS and TEN displayed most shared variance. AGEP and DRESS, the other SCAR pair most often observed in overlap syndromes, demonstrated modest shared variance, along with maculopapular rash (MPR). DRESS and TEN, another of the more commonly diagnosed pairs in overlap syndromes, did not. EM was uncorrelated with SJS and TEN. Conclusions: The notion that causality of a drug for one SCAR bolsters support for causality of the same drug with other SCARs was generally not supported.

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