arXiv subjects

Danielle S. Bassett

Publications and source records attributed to Danielle S. Bassett.

At least 145 records · Page 8Linked to original sources

arXiv2016

Topological and geometric measurements of force chain structure

Developing quantitative methods for characterizing structural properties of force chains in densely packed granular media is an important step toward understanding or predicting large-scale physical properties of a packing. A promising framework in which to develop such methods is network science, which can be used to translate particle locations and force contacts to a graph in which particles are represented by nodes and forces between particles are represented by weighted edges. Applying network-based community-detection techniques to extract force chains opens the door to developing statistics of force chain structure, with the goal of identifying shape differences across packings, and providing a foundation on which to build predictions of bulk material properties from mesoscale network features. Here, we discuss a trio of related but fundamentally distinct measurements of mesoscale structure of force chains in arbitrary 2D packings, including a novel statistic derived using tools from algebraic topology, which together provide a tool set for the analysis of force chain architecture. We demonstrate the utility of this tool set by detecting variations in force chain architecture with pressure. Collectively, these techniques can be generalized to 3D packings, and to the assessment of continuous deformations of packings under stress or strain.

cond-mat.soft↗

arXiv2016

Graph Frequency Analysis of Brain Signals

This paper presents methods to analyze functional brain networks and signals from graph spectral perspectives. The notion of frequency and filters traditionally defined for signals supported on regular domains such as discrete time and image grids has been recently generalized to irregular graph domains, and defines brain graph frequencies associated with different levels of spatial smoothness across the brain regions. Brain network frequency also enables the decomposition of brain signals into pieces corresponding to smooth or rapid variations. We relate graph frequency with principal component analysis when the networks of interest denote functional connectivity. The methods are utilized to analyze brain networks and signals as subjects master a simple motor skill. We observe that brain signals corresponding to different graph frequencies exhibit different levels of adaptability throughout learning. Further, we notice a strong association between graph spectral properties of brain networks and the level of exposure to tasks performed, and recognize the most contributing and important frequency signatures at different task familiarity.

q-bio.NC↗

arXiv2016

Accurately Predicting Functional Connectivity from Diffusion Imaging

Understanding the relationship between the dynamics of neural processes and the anatomical substrate of the brain is a central question in neuroscience. On the one hand, modern neuroimaging technologies, such as diffusion tensor imaging, can be used to construct structural graphs representing the architecture of white matter streamlines linking cortical and subcortical structures. On the other hand, temporal patterns of neural activity can be used to construct functional graphs representing temporal correlations between brain regions. Although some studies provide evidence that whole-brain functional connectivity is shaped by the underlying anatomy, the observed relationship between function and structure is weak, and the rules by which anatomy constrains brain dynamics remain elusive. In this article, we introduce a methodology to predict with high accuracy the functional connectivity of a subject at rest from his or her structural graph. Using our methodology, we are able to systematically unveil the role of structural paths in the formation of functional correlations. Furthermore, in our empirical evaluations, we observe that the eigen-modes of the predicted functional connectivity are aligned with activity patterns associated with different cognitive systems. Our work offers the potential to infer properties of brain dynamics in clinical or developmental populations with low tolerance for functional neuroimaging.

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arXiv2016

Evolution of network architecture in a granular material under compression

As a granular material is compressed, the particles and forces within the system arrange to form complex heterogeneous structures. Force chains are a prime example and are thought to constrain bulk properties such as mechanical stability and acoustic transmission. However, characterizing the dynamic nature of mesoscale architectures in granular systems can be challenging. A growing body of work has shown that graph theoretic approaches may provide a useful foundation for tackling these problems. Here, we extend current approaches by utilizing multilayer networks as a framework for directly quantifying the evolution of mesoscale architecture in a compressed granular system. We examine a quasi-two-dimensional aggregate of photoelastic disks, subject to biaxial compression through a series of small, quasistatic steps. Treating particles as network nodes and inter-particle forces as network edges, we construct a multilayer network by linking together the series of static force networks that exist at each strain step. We then extract the inherent mesoscale structure from the system by using a generalization of community detection methods, and we define quantitative measures to characterize the reconfiguration and evolution of this structure throughout compression. By separately considering the network of normal and tangential forces, we find that they display different structural evolution. To test the sensitivity of the network model to particle properties, we examine whether the method can distinguish a subsystem of low-friction particles within a bath of higher-friction particles. We find that this can be done by considering the network of tangential forces. The results discussed throughout this study suggest that these novel network science techniques may provide a direct way to compare and classify data from systems under different external conditions or with different physical makeup.

cond-mat.soft↗

arXiv2016

Optimally controlling the human connectome: the role of network topology

To meet ongoing cognitive demands, the human brain must seamlessly transition from one brain state to another, in the process drawing on different cognitive systems. How does the brain's network of anatomical connections help facilitate such transitions? Which features of this network contribute to making one transition easy and another transition difficult? Here, we address these questions using network control theory. We calculate the optimal input signals to drive the brain to and from states dominated by different cognitive systems. The input signals allow us to assess the contributions made by different brain regions. We show that such contributions, which we measure as energy, are correlated with regions' weighted degrees. We also show that the network communicability, a measure of direct and indirect connectedness between brain regions, predicts the extent to which brain regions compensate when input to another region is suppressed. Finally, we identify optimal states in which the brain should start (and finish) in order to minimize transition energy. We show that the optimal target states display high activity in hub regions, implicating the brain's rich club. Furthermore, when rich club organization is destroyed, the energy cost associated with state transitions increases significantly, demonstrating that it is the richness of brain regions that makes them ideal targets.

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arXiv2016

Brain network efficiency is influenced by pathological source of corticobasal syndrome

Multimodal neuroimaging studies of corticobasal syndrome using volumetric MRI and DTI successfully discriminate between Alzheimer's disease and frontotemporal lobar degeneration but this evidence has typically included clinically heterogeneous patient cohorts and has rarely assessed the network structure of these distinct sources of pathology. Using structural MRI data, we identify areas in fronto-temporo-parietal cortex with reduced gray matter density in corticobasal syndrome relative to age matched controls. A support vector machine procedure demonstrates that gray matter density poorly discriminates between frontotemporal lobar degeneration and Alzheimer's disease pathology subgroups with low sensitivity and specificity. In contrast, a statistic of local network efficiency demonstrates excellent discriminatory power, with high sensitivity and specificity. Our results indicate that the underlying pathological sources of corticobasal syndrome can be classified more accurately using graph theoretical statistics of white matter microstructure in association cortex than by regional gray matter density alone. These results highlight the importance of a multimodal neuroimaging approach to diagnostic analyses of corticobasal syndrome and suggest that distinct sources of pathology mediate the circuitry of brain regions affected by corticobasal syndrome.

q-bio.NC↗

arXiv2016

A positive mood, a flexible brain

Flexible reconfiguration of human brain networks supports cognitive flexibility and learning. However, modulating flexibility to enhance learning requires an understanding of the relationship between flexibility and brain state. In an unprecedented longitudinal data set, we investigate the relationship between flexibility and mood, demonstrating that flexibility is positively correlated with emotional state. Our results inform the modulation of brain state to enhance response to training in health and injury.

q-bio.NC↗

arXiv2016

Two's company, three (or more) is a simplex: Algebraic-topological tools for understanding higher-order structure in neural data

The language of graph theory, or network science, has proven to be an exceptional tool for addressing myriad problems in neuroscience. Yet, the use of networks is predicated on a critical simplifying assumption: that the quintessential unit of interest in a brain is a dyad -- two nodes (neurons or brain regions) connected by an edge. While rarely mentioned, this fundamental assumption inherently limits the types of neural structure and function that graphs can be used to model. Here, we describe a generalization of graphs that overcomes these limitations, thereby offering a broad range of new possibilities in terms of modeling and measuring neural phenomena. Specifically, we explore the use of \emph{simplicial complexes}, a theoretical notion developed in the field of mathematics known as algebraic topology, which is now becoming applicable to real data due to a rapidly growing computational toolset. We review the underlying mathematical formalism as well as the budding literature applying simplicial complexes to neural data, from electrophysiological recordings in animal models to hemodynamic fluctuations in humans. Based on the exceptional flexibility of the tools and recent ground-breaking insights into neural function, we posit that this framework has the potential to eclipse graph theory in unraveling the fundamental mysteries of cognition.

q-bio.NC↗

arXiv2016

Stimulation-based control of dynamic brain networks

The ability to modulate brain states using targeted stimulation is increasingly being employed to treat neurological disorders and to enhance human performance. Despite the growing interest in brain stimulation as a form of neuromodulation, much remains unknown about the network-level impact of these focal perturbations. To study the system wide impact of regional stimulation, we employ a data-driven computational model of nonlinear brain dynamics to systematically explore the effects of targeted stimulation. Validating predictions from network control theory, we uncover the relationship between regional controllability and the focal versus global impact of stimulation, and we relate these findings to differences in the underlying network architecture. Finally, by mapping brain regions to cognitive systems, we observe that the default mode system imparts large global change despite being highly constrained by structural connectivity. This work forms an important step towards the development of personalized stimulation protocols for medical treatment or performance enhancement.

q-bio.NC↗

arXiv2015

Choosing Wavelet Methods, Filters, and Lengths for Functional Brain Network Construction

Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into time series representing neurophysiological activity in fixed frequency bands. Using these time series, one can estimate frequency-band specific functional connectivity between sensors or regions of interest, and thereby construct functional brain networks that can be examined from a graph theoretic perspective. Despite their common use, however, practical guidelines for the choice of wavelet method, filter, and length have remained largely undelineated. Here, we explicitly explore the effects of wavelet method (MODWT vs. DWT), wavelet filter (Daubechies Extremal Phase, Daubechies Least Asymmetric, and Coiflet families), and wavelet length (2 to 24) - each essential parameters in wavelet-based methods - on the estimated values of network diagnostics and in their sensitivity to alterations in psychiatric disease. We observe that the MODWT method produces less variable estimates than the DWT method. We also observe that the length of the wavelet filter chosen has a greater impact on the estimated values of network diagnostics than the type of wavelet chosen. Furthermore, wavelet length impacts the sensitivity of the method to detect differences between health and disease and tunes classification accuracy. Collectively, our results suggest that the choice of wavelet method and length significantly alters the reliability and sensitivity of these methods in estimating values of network diagnostics drawn from graph theory. They furthermore demonstrate the importance of reporting the choices utilized in neuroimaging studies and support the utility of exploring wavelet parameters to maximize classification accuracy in the development of biomarkers of psychiatric disease and neurological disorders.

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arXiv2015

Flexible Traversal Through Diverse Brain States Underlies Executive Function in Normative Neurodevelopment

Adolescence is marked by rapid development of executive function. Mounting evidence suggests that executive function in adults may be driven by dynamic control of neurophysiological processes. Yet, how these dynamics evolve over adolescence and contribute to cognitive development is unknown. Using a novel dynamic graph approach in which each moment in time is a node and the similarity in brain states at two different times is an edge, we identify two primary brain states reminiscent of intrinsic and task-evoked systems. We demonstrate that time spent in these two states increases over development, as does the flexibility with which the brain switches between them. Increasing time spent in primary states and flexibility among states relates to increased executive performance over adolescence. Indeed, flexibility is increasingly advantageous for performance toward early adulthood. These findings demonstrate that brain state dynamics underlie the development of executive function during the critical period of adolescence.

q-bio.NC↗

arXiv2015

Small-World Propensity in Weighted, Real-World Networks

Quantitative descriptions of network structure in big data can provide fundamental insights into the function of interconnected complex systems. Small-world structure, commonly diagnosed by high local clustering yet short average path length between any two nodes, directly enables information flow in coupled systems, a key function that can differ across conditions or between groups. However, current techniques to quantify small-world structure are dependent on nuisance variables such as density and agnostic to critical variables such as the strengths of connections between nodes, thereby hampering accurate and comparable assessments of small-world structure in different networks. Here, we address both limitations with a novel metric called the Small-World Propensity (SWP). In its binary instantiation, the SWP provides an unbiased assessment of small-world structure in networks of varying densities. We extend this concept to the case of weighted networks by developing (i) a standardized procedure for generating weighted small-world networks, (ii) a weighted extension of the SWP, and (iii) a stringent and generalizable method for mapping real-world data onto the theoretical model. In applying these techniques to real world brain networks, we uncover the surprising fact that the canonical example of a biological small-world network, the C. elegans neuronal network, has strikingly low SWP in comparison to other examined brain networks. These metrics, models, and maps form a coherent toolbox for the assessment of architectural properties in real-world networks and their statistical comparison across conditions.

q-bio.NC↗

arXiv2015

Extraction of Force-Chain Network Architecture in Granular Materials Using Community Detection

Force chains form heterogeneous physical structures that can constrain the mechanical stability and acoustic transmission of granular media. However, despite their relevance for predicting bulk properties of materials, there is no agreement on a quantitative description of force chains. Consequently, it is difficult to compare the force-chain structures in different materials or experimental conditions. To address this challenge, we treat granular materials as spatially-embedded networks in which the nodes (particles) are connected by weighted edges that represent contact forces. We use techniques from community detection, which is a type of clustering, to find sets of closely connected particles. By using a geographical null model that is constrained by the particles' contact network, we extract chain-like structures that are reminiscent of force chains. We propose three diagnostics to measure these chain-like structures, and we demonstrate the utility of these diagnostics for identifying and characterizing classes of force-chain network architectures in various materials. To illustrate our methods, we describe how force-chain architecture depends on pressure for two very different types of packings: (1) ones derived from laboratory experiments and (2) ones derived from idealized, numerically-generated frictionless packings. By resolving individual force chains, we quantify statistical properties of force-chain shape and strength, which are potentially crucial diagnostics of bulk properties (including material stability). These methods facilitate quantitative comparisons between different particulate systems, regardless of whether they are measured experimentally or numerically.

cond-mat.soft↗

arXiv2014

Cross-Linked Structure of Network Evolution

We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice, and subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

cond-mat.dis-nn↗

arXiv2014

Brain Network Adaptability Across Task States

Activity in the human brain moves between diverse functional states to meet the demands of our dynamic environment, but fundamental principles guiding these transitions remain poorly understood. Here, we capitalize on recent advances in network science to analyze patterns of functional interactions between brain regions. We use dynamic network representations to probe the landscape of brain reconfigurations that accompany task performance both within and between four cognitive states: a task-free resting state, an attention-demanding state, and two memory-demanding states. Using the formalism of hypergraphs, we identify the presence of groups of functional interactions that fluctuate coherently in strength over time both within (task-specific) and across (task-general) brain states. In contrast to prior emphases on the complexity of many dyadic (region-to-region) relationships, these results demonstrate that brain adapt- ability can be described by common processes that drive the dynamic integration of cognitive systems. Moreover, our results establish the hypergraph as an effective measure for understanding functional brain dynamics, which may also prove useful in examining cross-task, cross-age, and cross-cohort functional change.

q-bio.NC↗

arXiv2014

Learning about Learning: Human Brain Sub-Network Biomarkers in fMRI Data

It has become increasingly popular to study the brain as a network due to the realization that functionality cannot be explained exclusively by independent activation of specialized regions. Instead, across a large spectrum of behaviors, function arises due to the dynamic interactions between brain regions. The existing literature on functional brain networks focuses mainly on a battery of network properties characterizing the "resting state" using for example the modularity, clustering, or path length among regions. In contrast, we seek to uncover subgraphs of functional connectivity that predict or drive individual differences in sensorimotor learning across subjects. We employ a principled approach for the discovery of significant subgraphs of functional connectivity, induced by brain activity (measured via fMRI imaging) while subjects perform a motor learning task. Our aim is to uncover patterns of functional connectivity that discriminate between high and low rates of learning among subjects. The discovery of such significant discriminative subgraphs promises a better data-driven understanding of the dynamic brain processes associated with brain plasticity.

q-bio.NC↗

arXiv2014

Dynamic network drivers of seizure generation, propagation and termination in human epilepsy

Drug-resistant epilepsy is traditionally characterized by pathologic cortical tissue comprised of seizure-initiating `foci'. These `foci' are thought to be embedded within an epileptic network whose functional architecture dynamically reorganizes during seizures through synchronous and asynchronous neurophysiologic processes. Critical to understanding these dynamics is identifying the synchronous connections that link foci to surrounding tissue and investigating how these connections facilitate seizure generation and termination. We use intracranial recordings from neocortical epilepsy patients undergoing pre-surgical evaluation to analyze functional connectivity before and during seizures. We develop and apply a novel technique to track network reconfiguration in time and to parse these reconfiguration dynamics into distinct seizure states, each characterized by unique patterns of network connections that differ in their strength and topography. Our approach suggests that seizures are generated when the synchronous relationships that isolate seizure `foci' from the surrounding epileptic network are broken down. As seizures progress, foci reappear as isolated subnetworks, marking a shift in network state that may aid seizure termination. Collectively, our observations have important theoretical implications for understanding the spatial involvement of distributed cortical structures in the dynamics of seizure generation, propagation and termination, and have practical significance in determining which circuits to modulate with implantable devices.

q-bio.NC↗

arXiv2014

Controllability of Brain Networks

Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behavior. Fundamental principles constraining these dynamic network processes have remained elusive. Here we use network control theory to offer a mechanistic explanation for how the brain moves between cognitive states drawn from the network organization of white matter microstructure. Our results suggest that densely connected areas, particularly in the default mode system, facilitate the movement of the brain to many easily-reachable states. Weakly connected areas, particularly in cognitive control systems, facilitate the movement of the brain to difficult-to-reach states. Areas located on the boundary between network communities, particularly in attentional control systems, facilitate the integration or segregation of diverse cognitive systems. Our results suggest that structural network differences between the cognitive circuits dictate their distinct roles in controlling dynamic trajectories of brain network function.

q-bio.NC↗