Hervé Abdi’s research while affiliated with The University of Texas at Dallas and other places

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Publications (254)


Figure 1. CovSTATIS is used to analyze multiple correlation/covariance matrices obtained either within or between individuals. We provide an example using functional connectivity matrices, collected on several individuals, as input to covSTATIS. (1) First, covSTATIS combines all connectivity matrices by quantifying their overall similarity via their R V coefficients. These coefficients are then stored in the R V matrix (C). Next, covSTATIS uses the first eigenvector ( u 1 ) of the R V matrix to derive weights for each connectivity matrix. (2) With these weights, covSTATIS computes the linear combination of all matrices to generate a common space, the compromise, which best represents the connectivity pattern across the sample. (3) The compromise then undergoes eigenvalue decomposition and orthogonal components are extracted to characterize the variance in the whole-sample connectivity pattern. (4) The variables of the compromise (illustrated by different shapes of green dots; i.e., individual brain regions) are represented as global factor scores in the component space. Global factor scores represent the connectivity pattern of each brain region across the entire sample. The same variables from each individual matrix can also be back projected onto the same space as partial factor scores (indicated by points with the same shape of different colors). Partial factor scores represent the connectivity pattern of each brain region for a specific individual. Importantly, the weighted means of all partial factor scores of a given variable equal to their global factor scores (i.e., barycentric property). In this component space, the distance between factor scores provides meaningful and interpretable information about the similarity in the connectivity profile of any two brain regions. The closer the (global or partial) factor scores of two brain regions, the more similar their connectivity profiles.
Figure 2. Top panel: examples of applications of covSTATIS in network neuroscience. Bottom panel: examples of extractable features from covSTATIS. For instance, (A) illustrates how we can extract, from global factor scores, group means of partial factor scores, derive their bootstrap confidence intervals, and use them to interpret group differences in network configurations. (B) demonstrates how we can quantify the overall heterogeneity among all partial factor scores via computing the area of the hull. (C) shows how such heterogeneity can also be evaluated for different groups separately.
covSTATIS: A multi-table technique for network neuroscience
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November 2024

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24 Reads

Aperture Neuro

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Jenny R. Rieck

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Robert N. Spreng

Similarity analyses between multiple correlation or covariance tables constitute the cornerstone of network neuroscience. Here, we introduce covSTATIS, a versatile, linear, unsupervised multi-table method designed to identify structured patterns in multi-table data, and allow for the simultaneous extraction and interpretation of both individual and group-level features. With covSTATIS, multiple similarity tables can now be easily integrated, without requiring a priori data simplification, complex black-box implementations, user-dependent specifications, or supervised frameworks. Applications of covSTATIS, a tutorial with Open Data and source code are provided. CovSTATIS offers a promising avenue for advancing the theoretical and analytic landscape of network neuroscience.

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How do speech language pathologists use the Schwarz et al. (2015) rubric for read-aloud storybook selection?

September 2024

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22 Reads

Speech Language and Hearing

Reading storybooks aloud to prereaders helps them develop oral language skills; but educators struggle to select appropriate storybooks for read alouds. To better understand this selection process, we evaluated how experienced speech language pathologists (SLPs) apply the storybook selection rubric in Schwarz et al.'s (2015). A read-aloud storybook selection system for prereaders at the preschool language level: A pilot study.. That rubric includes: eight book characteristics, one four-level difficulty scale, and exemplar storybooks for each scale level. Using this rubric, 38 SLPs-who had served children at the preschool language level-rated 63 storybooks based on how difficult they thought the storybooks would be for children at the preschool language level to understand when the storybooks were read aloud to them. A principal component analysis identified-among the original eight characteristics a subset of five highly correlated characteristics related to overall text difficulty: vocabulary, story structure, sentence length, book length, and density. We revised the original rubric to include only four storybook characteristics: (a) text difficulty, (b) amount of inferencing, problem-solving, and abstract concepts, (c) familiarity of activities/experiences, and (d) level of support provided by the illustrations. Using quartile values of the text difficulty characteristic, we derived a four-level difficulty scale for the 63 storybooks. The revised storybook selection rubric simplifies the process of selecting appropriate storybooks for read alouds. The revised rubric and SLPs' difficulty ratings of 63 storybooks provide clinicians with a resource ready-made for clinical practice. ARTICLE HISTORY


Sparse Factor Analysis for Categorical Data with the Group-Sparse Generalized Singular Value Decomposition

September 2024

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16 Reads

Correspondence analysis, multiple correspondence analysis and their discriminant counterparts (i.e., discriminant simple correspondence analysis and discriminant multiple correspondence analysis) are methods of choice for analyzing multivariate categorical data. In these methods, variables are integrated into optimal components computed as linear combinations whose weights are obtained from a generalized singular value decomposition (GSVD) that integrates specific metric constraints on the rows and columns of the original data matrix. The weights of the linear combinations are, in turn, used to interpret the components, and this interpretation is facilitated when components are 1) pairwise orthogonal and 2) when the values of the weights are either large or small but not intermediate-a pattern called a simple or a sparse structure. To obtain such simple configurations, the optimization problem solved by the GSVD is extended to include new constraints that implement component orthogonality and sparse weights. Because multiple correspondence analysis represents qualitative variables by a set of binary variables, an additional group constraint is added to the optimization problem in order to sparsify the whole set representing one qualitative variable. This new algorithm-called group-sparse GSVD (gsGSVD)-integrates these constraints via an iterative projection scheme onto the intersection of subspaces where each subspace implements a specific constraint. In this paper, we expose this new algorithm and show how it can be adapted to the sparsification of simple and multiple correspondence analysis, and illustrate its applications with the analysis of four different data sets-each illustrating the sparsification of a particular CA-based analysis.



Overview of the analytical pipeline used in the current study. (A) The main CCA and PLS analysis: the decomposition of the cross-product matrices to produce singular values and loadings (reweighted singular vectors in the case of CCA). (B) The sum of squares permutation analysis to assess the statistical significance of each LV. (C) The split-half analysis used to assess the similarity between respective loadings from each split-half. In this analysis, the brain and behavioral data are both split into two different matrices (resulting in X1, X2, Y1, Y2) for each of the 10,000 iterations. Each respective split pair (e.g., X1 and Y1) then undergoes the CCA or PLS analysis shown in panel A. The resulting loadings from the respective split pairs are correlated (e.g., X1 and X2) to provide a distribution of Pearson correlation coefficients between each respective brain and behavior loading across the 10,000 iterations. (D) The train-test resampling analysis that assesses how well the singular values from the training sample can predict the singular values of the test sample. For each of the 10,000 iterations, the dataset was split into an 80% train set (X80, Y80) and 20% test set (X20, Y20). The train set underwent the CCA or PLS analysis shown in panel A. The respective loadings from the SVD of the training set were used to solve for the singular values (S) of the test set. The resulting predicted singular values of each of the 10,000 train/test analyses were plotted as a distribution. Importantly, each analysis is independent from one another (i.e., the results of one analysis are not used in another) and not sequential (i.e., the permutation test in panel B did not necessarily need to happen prior to the split-half or train-test analysis). The bootstrap confidence interval estimation, not shown here, was used to assess the stability of the parameter estimates of variable weights in the loadings. SVD = singular value decomposition.
Unthresholded behavior and brain loadings from the PLS and CCA analysis performed in the CBCL brain analysis (N = 9,191). The highest PLS-derived behavior loadings were aggressive behavior, thought problems, and stress problems. The highest PLS-derived brain loadings were right pars triangularis, right inferior parietal cortex, and left posterior cingulate cortex. The highest CCA-derived behavior loadings were social problems, anxious/depressive symptoms, and stress problems. The highest CCA-derived brain loadings were the right superior temporal gyrus, left fusiform gyrus, and right lingual gyrus. Panel B shows the latent scores between XU and YV for LV1. Prior to calculating the latent scores, the brain and behavioral loadings have been standardized by the singular values. Panel C depicts the train-test distributions of the predicted singular values of the test sample for each iteration. Asterisks indicate the LVs that showed a distribution with a Z-score greater than 1.96. LV1 from CCA was found to be reliable (i.e., LV1 of the training sample can reliably predict the singular values of LV1 from the test sample). The lack of any other significant distributions of predicted singular values suggest that the 80% train set does not reliably and consistently predict the singular values from the 20% test set. OCD = obsessive compulsive symptoms; withdep = withdrawn/depression symptoms; sct = sluggish-cognitive-tempo; anxdep = anxious/depressive symptoms; rulebreak = rule-breaking behavior.
Unthresholded behavior and brain loadings of LV1 from the PLS and CCA analysis performed between NIH Cognitive Toolbox scores and cortical thickness. The largest PLS- and CCA-derived loadings were found for the list sorting task and the picture vocabulary task. The highest CCA-derived brain loadings were the left pars opercularis, superior frontal gyrus, and parahippocampal gyrus. The highest PLS-derived brain loadings were the left pars opercularis, parahippocampal gyrus, and medial orbitofrontal gyrus. Panel B shows the latent scores between XU and YV for LV1. Prior to calculating the latent scores, the brain and behavioral loadings have been standardized by the singular values. Overall, there is a similar relationship between the brain and behavioral latent scores when comparing CCA and PLS. Panel C shows the results of the train-test resampling analysis. Asterisks indicate the LVs that showed a distribution with a Z-score greater than 1.96. LV1 (Z-score: PLS = 4.8, CCA = 7.8) and LV3 (Z-score: PLS = 2.6, CCA = 2.2) for both PLS and CCA, and LV2 (Z-score: CCA = 2.02) for CCA, were found to be reliable (i.e., singular values of these LVs of the training sample can reliably predict the singular values from the test sample). Flanker = Flanker task; pattern = pattern comparison processing speed task; cardsort = dimensional change card sort task; reading = oral reading recognition task; picture = picture vocabulary task; list = list sorting working memory task; picvocab = picture vocabulary task.
This figure depicts the distributions of the resampled loadings from the split-half analysis for the CBCL brain and NIH brain analyses. The x-axis from the split-half distributions are the Pearson correlation coefficients between respective loadings from each split-half analysis (e.g., U1 and U2 from the analysis comparing X1 and Y1 and separately, X2 and Y2). In the CBCL brain analysis, the distribution of Pearson correlation coefficients centered around 0 for the majority of LVs, indicating minimal correspondence between respective loadings from the split-halves. This suggests that characteristics of participants are highly influential in the loadings derived from CCA or PLS models in the CBCL brain analysis. In the NIH brain analysis, the distribution of Pearson correlation coefficients are centered around r = 0.6–0.8, indicating high correspondence between respective split-halves and that loadings from CCA and PLS models remain similar regardless of which participants are included in each iteration. Asterisks indicate the LVs which showed a distribution with a Z-score greater than 1.96.
Demographic Characteristics of the ABCD subsample included in the current study and the acquired ABCD sample
Comparing the stability and reproducibility of brain-behavior relationships found using canonical correlation analysis and partial least squares within the ABCD sample

July 2024

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103 Reads

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10 Citations

Network Neuroscience

Canonical correlation analysis (CCA) and partial least squares correlation (PLS) detect linear associations between two data matrices by computing latent variables (LVs) having maximal correlation (CCA) or covariance (PLS). This study compared the similarity and generalizability of CCA- and PLS-derived brain-behavior relationships. Data were accessed from the baseline Adolescent Brain Cognitive Development (ABCD) dataset (N > 9,000, 9–11 years). The brain matrix consisted of cortical thickness estimates from the Desikan-Killiany atlas. Two phenotypic scales were examined separately as the behavioral matrix; the Child Behavioral Checklist (CBCL) subscale scores and NIH Toolbox performance scores. Resampling methods were used to assess significance and generalizability of LVs. LV1 for the CBCL brain relationships was found to be significant, yet not consistently stable or reproducible, across CCA and PLS models (singular value: CCA = .13, PLS = .39, p < .001). LV1 for the NIH brain relationships showed similar relationships between CCA and PLS and was found to be stable and reproducible (singular value: CCA = .21, PLS = .43, p < .001). The current study suggests that stability and reproducibility of brain-behavior relationships identified by CCA and PLS are influenced by the statistical characteristics of the phenotypic measure used when applied to a large population-based pediatric sample.



Visual imagery and STEM occupational attainment: Gender matters

March 2024

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10 Reads

Science, technology, engineering and mathematical (STEM) occupations are crucial for economic growth and individual financial stability, yet there is a STEM labour shortage, particularly among women. We examined how individual differences in visual imagery relate to characteristics of STEM occupations — specifically those requiring computational abilities. In a discovery cohort of 2357 online participants, we found that — consistent with prior research — spatial thinking was positively associated with STEM occupations for both males and females. Object imagery (mnemonic vividness), however, was negatively associated with STEM occupations that require computational thinking, possibly because efficient analytical reasoning abilities associate with low object imagery. This negative association was present for males, but not for females. We extended these findings to a sample of 1891 individuals with aphantasia (congenitally low imagery) and a sample of 186 university undergraduates. These results suggest that the well-known influence of spatial imagery is evident across genders, whereas an independent influence of non-spatial and non-visual abstract analytic abilities on computational STEM professions is confined to males. These findings have implications for policy in fostering careers in STEM, particularly for females.


Old and New Perspectives on Optimal Scaling

January 2024

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5 Reads

Processing in machine learning qualitative variables having a very large number of modalities is an opportunity to revisit the theory of optimal scaling and its applications. This revisitation starts with the pioneers of scaling in statistics, psychometrics and psychology before moving on to more contemporary treatments of scaling that fall within the realm of machine learning and neural networks.


Infants who develop autism show smaller inventories of deictic and symbolic gestures at 12 months of age

January 2024

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49 Reads

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1 Citation

Autism Research

Gestures are an important social communication skill that infants and toddlers use to convey their thoughts, ideas, and intentions. Research suggests that early gesture use has important downstream impacts on developmental processes, such as language learning. However, autistic children are more likely to have challenges in their gestural development. The current study expands upon previous literature on the differences in gesture use between young autistic and non‐autistic toddlers by collecting data using a parent‐report questionnaire called the MCDI–Words and Gestures at three time points, 12, 18, and 24 months of age. Results ( N = 467) showed that high‐likelihood infants who later met diagnostic criteria for ASD ( n = 73 HL‐ASD) have attenuated gesture growth from 12 to 24 months for both deictic gestures and symbolic gestures when compared to high‐likelihood infants who later did not meet criteria for ASD ( n = 249 HL‐Neg) and low‐likelihood infants who did not meet criteria for ASD ( n = 145 LL‐Neg). Other social communicative skills, like play behaviors and imitation, were also found to be impacted in young autistic children when compared to their non‐autistic peers. Understanding early differences in social communication growth before a formal autism diagnosis can provide important insights for early intervention.


Partial Least Squares Regression Analysis of Alzheimer’s Disease Biomarkers, Modifiable Health Variables, and Cognitive Change in Older Adults with Mild Cognitive Impairment

April 2023

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82 Reads

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1 Citation

Journal of Alzheimer's Disease

Background: Prior work has shown that certain modifiable health, Alzheimer's disease (AD) biomarker, and demographic variables are associated with cognitive performance. However, less is known about the relative importance of these different domains of variables in predicting longitudinal change in cognition. Objective: Identify novel relationships between modifiable physical and health variables, AD biomarkers, and slope of cognitive change over two years in a cohort of older adults with mild cognitive impairment (MCI). Methods: Metrics of cardiometabolic risk, stress, inflammation, neurotrophic/growth factors, and AD pathology were assessed in 123 older adults with MCI at baseline from the Alzheimer's Disease Neuroimaging Initiative (mean age = 73.9; SD = 7.6; mean education = 16.0; SD = 3.0). Partial least squares regression (PLSR)-a multivariate method which creates components that best predict an outcome-was used to identify whether these physiological variables were important in predicting slope of change in episodic memory or executive function over two years. Results: At two-year follow-up, the two PLSR models predicted, respectively, 20.0% and 19.6% of the variance in change in episodic memory and executive function. Baseline levels of AD biomarkers were important in predicting change in both episodic memory and executive function. Baseline education and neurotrophic/growth factors were important in predicting change in episodic memory, whereas cardiometabolic variables such as blood pressure and cholesterol were important in predicting change in executive function. Conclusion: These data-driven analyses highlight the impact of AD biomarkers on cognitive change and further clarify potential domain specific relationships with predictors of cognitive change.


Citations (69)


... Finally, while LVs may be significant by permutation testing, it is well established that effect size estimates are crucial for making neurobiological inferences about a finding (Chen et al., 2017), and there are growing concerns that the results from PLS and other multivariate techniques do not necessarily reproduce in held-out samples (Churchill et al., 2013;Nakua et al., 2024;Ji et al., 2021;Helmer et al., 2024;Dinga et al., 2019), regardless of significance McIntosh, 2022). Accordingly, we also evaluated whether alternative PLS outcome metrics, namely LV strength (covariance explained) and stability (across sample splits), offered information beyond significance about LV quality in both simulated and UK Biobank data. ...

Reference:

Evaluating permutation-based inference for partial least squares analysis of neuroimaging data
Comparing the stability and reproducibility of brain-behavior relationships found using canonical correlation analysis and partial least squares within the ABCD sample

Network Neuroscience

... Current research into the brain, aging, and cognition contains important trends that provide a context for the article by Stark et al. [1]. One is the recognition that cognitive trajectories depend upon many factors that are often highly inter-related [2,3]. ...

Partial Least Squares Regression Analysis of Alzheimer’s Disease Biomarkers, Modifiable Health Variables, and Cognitive Change in Older Adults with Mild Cognitive Impairment

Journal of Alzheimer's Disease

... It is also used to assess various neurological conditions, such as acute ischaemic stroke (12), multiple sclerosis (13,14), schizophrenia (15), autism (16) and ageing (17). In anatomical research, it has been used to examine the structure of the language network (18,19), the asymmetry of white matter in twins and siblings (20), and the location, asymmetry, and variability of fibre tracts (21). It has also been applied in neurosurgical planning, navigation (22)(23)(24)(25) and predicting postoperative outcome (26). ...

Language Exposure During Infancy is Negatively Associated with White Matter Microstructure in the Arcuate Fasciculus
  • Citing Article
  • April 2023

Developmental Cognitive Neuroscience

... The Occupational Classification Network (O*NET) data, which indexes detailed occupational attributes for US occupations, has been widely used in grouping occupations and examining the job characteristics' relatedness [33][34][35][36][37][38][39][40][41][42][43]. Hundreds of attributes, termed as descriptors, are divided into different dimensions, such as knowledge, skills, abilities, education, experience, training, interests, work values, work styles, tasks, technology skills & tools, work activities, and work contents. ...

Visualization of latent components assessed in O*Net occupations (VOLCANO): A robust method for standardized conversion of occupational labels to ratio scale format
  • Citing Article
  • January 2023

Behavior Research Methods

... To have a successful read aloud that addresses the oral language development of children at the preschool language level, adults need to select storybooks at an appropriate difficulty level (Damber, 2014;McGee & Schickendanz, 2007;Schwarz et al., 2015;Schwarz et al., 2022;Schwarz, Jurica, Matson, Webb-Culver, & Abdi, 2019). Interventionists struggle to select storybooks at an appropriate difficulty level when serving young children (Damber, 2014;McGee & Schickendanz, 2007;Muhinyi et al., 2020;Nicolopoulou et al., 2023). ...

How Do Teachers of Deaf Pre-Readers Communicating in American Sign Language Select Storybooks for Read-Alouds?
  • Citing Article
  • September 2022

American Annals of the Deaf

... Considering caregiver speech's impact on language development, studies by Ravi et al. and McDaniel et al. have highlighted the significance of parental behaviour during the earliest stages of life on later developmental outcomes for children with ASD (11,22). Furthermore, the work of Alduais et al. and Swanson et al. has brought attention to the importance of pragmatic language skills in communication, suggesting that tools such as the CCC-2 questionnaire could support clinicians in the autism diagnosis process (13,23). ...

Are early social communication skills a harbinger for language development in infants later diagnosed autistic?—A longitudinal study using a standardized social communication assessment

Frontiers in Communication

... Therefore, to sparsify these methods, we developed a sparsification algorithm for the GSVD, called the sparse GSVD (sGSVD; Yu et al., 2023). Further, as some CA-related methods analyze categorical data with qualitative variable being represented by groups of (binary) columns, we also extended the sGSVD to create the group-sparse GSVD (gsGSVD) that, in addition, performs group sparsification where pre-defined groups of columns or rows are kept or eliminated together. ...

Sparse MFA, sparse STATIS, and sparse DiSTATIS with Applications to Sensory Evaluation

Journal of Chemometrics

... Some applications of CA can be seen in the exploration of the relationship between country of residence and the main language used [17], visualization of the relationship between soil physicochemical properties and the composition of soil litter arthropod families [18], and abundance data in ecology [19]. Meanwhile [20] apply Multiblock discriminant correspondence analysis (MUDICA) to psychological problems so that a combined picture of the relationship between observations and variables can be created based on information from large and complex data sets. ...

Multiblock discriminant correspondence analysis: Exploring group differences with structured categorical data
  • Citing Article
  • September 2022

Methods in Psychology

... In this study, we utilized a publicly available functional connectivity dataset provided by J.R. Rieck et al. 76 . The dataset comprises 144 healthy participants, aged 20-86, from the Greater Toronto Area. ...

Dataset of functional connectivity during cognitive control for an adult lifespan sample

Data in Brief

... Task-general FC in adults showed less segregation with higher age across the majority of networks and processing choices, as expected from the rs-fMRI literature (Chan et al., 2014;Setton et al., 2022;Stumme et al., 2020;Varangis et al., 2019;Zonneveld et al., 2019) and background task FC (Grady et al., 2016;Monge et al., 2018;Rieck et al., 2021). In . ...

Reconfiguration and dedifferentiation of functional networks during cognitive control across the adult lifespan
  • Citing Article
  • June 2021

Neurobiology of Aging