arXiv subjects

Kausar Abbas

Publications and source records attributed to Kausar Abbas.

10 recordsLinked to original sources

arXiv2023

Tangent functional connectomes uncover more unique phenotypic traits

Functional connectomes (FCs) contain pairwise estimations of functional couplings based on pairs of brain regions activity. FCs are commonly represented as correlation matrices that are symmetric positive definite (SPD) lying on or inside the SPD manifold. Since the geometry on the SPD manifold is non-Euclidean, the inter-related entries of FCs undermine the use of Euclidean-based distances. By projecting FCs into a tangent space, we can obtain tangent functional connectomes (tangent-FCs). Tangent-FCs have shown a higher predictive power of behavior and cognition, but no studies have evaluated the effect of such projections with respect to fingerprinting. We hypothesize that tangent-FCs have a higher fingerprint than regular FCs. Fingerprinting was measured by identification rates (ID rates) on test-retest FCs as well as on monozygotic and dizygotic twins. Our results showed that identification rates are systematically higher when using tangent-FCs. Specifically, we found: (i) Riemann and log-Euclidean matrix references systematically led to higher ID rates. (ii) In tangent-FCs, Main-diagonal regularization prior to tangent space projection was critical for ID rate when using Euclidean distance, whereas barely affected ID rates when using correlation distance. (iii) ID rates were dependent on condition and fMRI scan length. (iv) Parcellation granularity was key for ID rates in FCs, as well as in tangent-FCs with fixed regularization, whereas optimal regularization of tangent-FCs mostly removed this effect. (v) Correlation distance in tangent-FCs outperformed any other configuration of distance on FCs or on tangent-FCs across the fingerprint gradient (here sampled by assessing test-retest, Monozygotic and Dizygotic twins). (vi)ID rates tended to be higher in task scans compared to resting-state scans when accounting for fMRI scan length.

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arXiv2021

Geodesic distance on optimally regularized functional connectomes uncovers individual fingerprints

Background: Functional connectomes (FCs), have been shown to provide a reproducible individual fingerprint, which has opened the possibility of personalized medicine for neuro/psychiatric disorders. Thus, developing accurate ways to compare FCs is essential to establish associations with behavior and/or cognition at the individual-level. Methods: Canonically, FCs are compared using Pearson's correlation coefficient of the entire functional connectivity profiles. Recently, it has been proposed that the use of geodesic distance is a more accurate way of comparing functional connectomes, one which reflects the underlying non-Euclidean geometry of the data. Computing geodesic distance requires FCs to be positive-definite and hence invertible matrices. As this requirement depends on the fMRI scanning length and the parcellation used, it is not always attainable and sometimes a regularization procedure is required. Results: In the present work, we show that regularization is not only an algebraic operation for making FCs invertible, but also that an optimal magnitude of regularization leads to systematically higher fingerprints. We also show evidence that optimal regularization is dataset-dependent, and varies as a function of condition, parcellation, scanning length, and the number of frames used to compute the FCs. Discussion: We demonstrate that a universally fixed regularization does not fully uncover the potential of geodesic distance on individual fingerprinting, and indeed could severely diminish it. Thus, an optimal regularization must be estimated on each dataset to uncover the most differentiable across-subject and reproducible within-subject geodesic distances between FCs. The resulting pairwise geodesic distances at the optimal regularization level constitute a very reliable quantification of differences between subjects.

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arXiv2021

Functional Connectome Fingerprint Gradients in Young Adults

The assessment of brain fingerprints has emerged in the recent years as an important tool to study individual differences and to infer quality of neuroimaging datasets. Studies so far have mainly focused on connectivity fingerprints between different brain scans of the same individual. Here, we extend the concept of brain connectivity fingerprints beyond test/retest and assess fingerprint gradients in young adults by developing an extension of the differential identifiability framework. To do so, we look at the similarity between not only the multiple scans of an individual (subject fingerprint), but also between the scans of monozygotic and dizygotic twins (twin fingerprint). We have carried out this analysis on the 8 fMRI conditions present in the Human Connectome Project -- Young Adult dataset, which we processed into functional connectomes (FCs) and timeseries parcellated according to the Schaefer Atlas scheme, which has multiple levels of resolution. Our differential identifiability results show that the fingerprint gradients based on genetic and environmental similarities are indeed present when comparing FCs for all parcellations and fMRI conditions. Importantly, only when assessing optimally reconstructed FCs, we fully uncover fingerprints present in higher resolution atlases. We also study the effect of scanning length on subject fingerprint of resting-state FCs to analyze the effect of scanning length and parcellation. In the pursuit of open science, we have also made available the processed and parcellated FCs and timeseries for all conditions for ~1200 subjects part of the HCP-YA dataset to the scientific community.

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arXiv2020

Improving Functional Connectome Fingerprinting with Degree-Normalization

Functional connectivity quantifies the statistical dependencies between the activity of brain regions, measured using neuroimaging data such as functional MRI BOLD time series. The network representation of functional connectivity, called a Functional Connectome (FC), has been shown to contain an individual fingerprint allowing participants identification across consecutive testing sessions. Recently, researchers have focused on the extraction of these fingerprints, with potential applications in personalized medicine. Here, we show that a mathematical operation denominated degree-normalization can improve the extraction of FC fingerprints. Degree-normalization has the effect of reducing the excessive influence of strongly connected brain areas in the whole-brain network. We adopt the differential identifiability framework and apply it to both original and degree-normalized FCs of 409 individuals from the Human Connectome Project, in resting-state and 7 fMRI tasks. Our results indicate that degree-normalization systematically improves three fingerprinting metrics, namely differential identifiability, identification rate and matching rate. Moreover, the results related to the matching rate metric suggest that individual fingerprints are embedded in a low-dimensional space. The results suggest that low-dimensional functional fingerprints lie in part in weakly connected subnetworks of the brain, and that degree-normalization helps uncovering them. This work introduces a simple mathematical operation that could lead to significant improvements in future FCs fingerprinting studies.

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arXiv2020

A morphospace of functional configuration to assess configural breadth based on brain functional networks

The best approach to quantify human brain functional reconfigurations in response to varying cognitive demands remains an unresolved topic in network neuroscience. We propose that such functional reconfigurations may be categorized into three different types: i) Network Configural Breadth, ii) Task-to-Task transitional reconfiguration, and iii) Within-Task reconfiguration. In order to quantify these reconfigurations, we propose a mesoscopic framework focused on functional networks (FNs) or communities. To do so, we introduce a 2D network morphospace that relies on two novel mesoscopic metrics, Trapping Efficiency (TE) and Exit Entropy (EE), which capture topology and integration of information within and between a reference set of FNs. In this study, we use this framework to quantify the Network Configural Breadth across different tasks. We show that the metrics defining this morphospace can differentiate FNs, cognitive tasks and subjects. We also show that network configural breadth significantly predicts behavioral measures, such as episodic memory, verbal episodic memory, fluid intelligence and general intelligence. In essence, we put forth a framework to explore the cognitive space in a comprehensive manner, for each individual separately, and at different levels of granularity. This tool that can also quantify the FN reconfigurations that result from the brain switching between mental states.

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arXiv2020

Towards an information theoretical description of communication in brain networks

Modeling communication dynamics in the brain is a key challenge in network neuroscience. We present here a framework that combines two measurements for any system where different communication processes are taking place on top of a fixed structural topology: Path Processing Score (PPS) estimates how much the brain signal has changed or has been transformed between any two brain regions (source and target); Path Broadcasting Strength (PBS) estimates the propagation of the signal through edges adjacent to the path being assessed. We use PPS and PBS to explore communication dynamics in large-scale brain networks. We show that brain communication dynamics can be divided into three main 'communication regimes' of information transfer: absent communication (no communication happening); relay communication (information is being transferred almost intact); transducted communication (the information is being transformed). We use PBS to categorize brain regions based on the way they broadcast information. Subcortical regions are mainly direct broadcasters to multiple receivers; Temporal and frontal nodes mainly operate as broadcast relay brain stations; Visual and somato-motor cortices act as multi-channel transducted broadcasters. This work paves the way towards the field of brain network information theory by providing a principled methodology to explore communication dynamics in large-scale brain networks.

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arXiv2020

GEFF: Graph Embedding for Functional Fingerprinting

It has been well established that Functional Connectomes (FCs), as estimated from functional MRI (fMRI) data, have an individual fingerprint that can be used to identify an individual from a population (subject-identification). Although identification rate is high when using resting-state FCs, other tasks show moderate to low values. Furthermore, identification rate is task-dependent, and is low when distinct cognitive states, as captured by different fMRI tasks, are compared. Here we propose an embedding framework, GEFF (Graph Embedding for Functional Fingerprinting), based on group-level decomposition of FCs into eigenvectors. GEFF creates an eigenspace representation of a group of subjects using one or more task FCs (Learning Stage). In the Identification Stage, we compare new instances of FCs from the Learning subjects within this eigenspace (validation dataset). The validation dataset contains FCs either from the same tasks as the Learning dataset or from the remaining tasks that were not included in Learning. Assessment of validation FCs within the eigenspace results in significantly increased subject-identification rates for all fMRI tasks tested and potentially task-independent fingerprinting process. It is noteworthy that combining resting-state with one fMRI task for GEFF Learning Stage covers most of the cognitive space for subject identification. In addition to subject-identification, GEFF was also used for identification of cognitive states, i.e. to identify the task associated to a given FC, regardless of the subject being already in the Learning dataset or not (subject-independent task-identification). In addition, we also show that eigenvectors from the Learning Stage can be characterized as task-dominant, subject dominant or neither, providing a deeper insight into the extent of variance in functional connectivity across individuals and cognitive states.

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arXiv2019

Optimizing Differential Identifiability Improves Connectome Predictive Modeling of Cognitive Deficits in Alzheimer's Disease

Functional connectivity, as estimated using resting state fMRI, has shown potential in bridging the gap between pathophysiology and cognition. However, clinical use of functional connectivity biomarkers is impeded by unreliable estimates of individual functional connectomes and lack of generalizability of models predicting cognitive outcomes from connectivity. To address these issues, we combine the frameworks of connectome predictive modeling and differential identifiability. Using the combined framework, we show that enhancing the individual fingerprint of resting state functional connectomes leads to robust identification of functional networks associated to cognitive outcomes and also improves prediction of cognitive outcomes from functional connectomes. Using a comprehensive spectrum of cognitive outcomes associated to Alzheimer's disease, we identify and characterize functional networks associated to specific cognitive deficits exhibited in Alzheimer's disease. This combined framework is an important step in making individual level predictions of cognition from resting state functional connectomes and in understanding the relationship between cognition and connectivity.

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arXiv2019

Uncovering differential identifiability in network properties of human brain functional connectomes

The Identifiability Framework (If) has been shown to improve differential identifiability (reliability across-sessions and -sites, and differentiability across-subjects) of functional connectomes for a variety of fMRI tasks. But having a robust single session/subject functional connectome is just the starting point to subsequently assess network properties for characterizing properties of integration, segregation and communicability, among others. Naturally, one wonders if uncovering identifiability at the connectome level also uncovers identifiability on the derived network properties. This also raises the question of where to apply the If framework: on the connectivity data or directly on each network measurement? Our work answers these questions by exploring the differential identifiability profiles of network measures when If is applied on 1) the functional connectomes, and 2) directly on derived network measurements. Results show that improving across-session reliability of FCs also improves reliability of derived network measures. We also find that, for specific network properties, application of If directly on network properties is more effective. Finally, we discover that applying the framework, either way, increases task sensitivity of network properties. At a time when the neuroscientific community is focused on subject-level inferences, this framework is able to uncover FC fingerprints, which propagates to derived network properties.

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arXiv2019

Alterations in Structural Correlation Networks with Prior Concussion in Collision-Sport Athletes

Several studies have used structural correlation networks, derived from anatomical covariance of brain regions, to analyze neurologic changes associated with multiple sclerosis, schizophrenia and breast cancer [1][2]. Graph-theoretical analyses of human brain structural networks have consistently shown the characteristic of small-worldness that reflects a network with both high segregation and high integration. A large neuroimaging literature on football players, with and without history of concussion, has shown both functional and anatomical changes. Here we use graph-based topological properties of anatomical correlation networks to study the effect of prior concussion in collision-sport athletes. 40 high school collision-sport athletes (23 male football, 17 female soccer; CSA) without self-reported history of concussion (HOC-), 18 athletes (13 male football, 5 female soccer) with self-reported history of concussion (HOC+) and 24 healthy controls (19 male, 5 female; CN) participated in imaging sessions before the beginning of a competition season. The extracted residual volumes for each group were used for building the correlation networks and their small-worldness, , is calculated. The small-worldness of CSA without prior history of concussion, , is significantly greater than that of controls, . CSA with prior history have significantly higher (vs. 95% confidence interval) small-worldness compared to HOC+, over a range of network densities. The longer path lengths in HOC+ group could indicate disrupted neuronal integration relative to healthy controls.

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