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Danielle Bassett

Publications and source records attributed to Danielle Bassett.

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Spatial Embedding Imposes Constraints on the Network Architectures of Neural Systems

A fundamental understanding of the network architecture of the brain is necessary for the further development of theories explicating circuit function. Perhaps as a derivative of its initial application to abstract informational systems, network science provides many methods and summary statistics that address the network's topological characteristics with little or no thought to its physical instantiation. Recent progress has capitalized on quantitative tools from network science to parsimoniously describe and predict neural activity and connectivity across multiple spatial and temporal scales. Yet, for embedded systems, physical laws can directly constrain processes of network growth, development, and function, and an appreciation of those physical laws is therefore critical to an understanding of the system. Recent evidence demonstrates that the constraints imposed by the physical shape of the brain, and by the mechanical forces at play in its development, have marked effects on the observed network topology and function. Here, we review the rules imposed by space on the development of neural networks and show that these rules give rise to a specific set of complex topologies. We present evidence that these fundamental wiring rules affect the repertoire of neural dynamics that can emerge from the system, and thereby inform our understanding of network dysfunction in disease. We also discuss several computational tools, mathematical models, and algorithms that have proven useful in delineating the effects of spatial embedding on a given networked system and are important considerations for addressing future problems in network neuroscience. Finally, we outline several open questions regarding the network architectures that support circuit function, the answers to which will require a thorough and honest appraisal of the role of physical space in brain network anatomy and physiology.

q-bio.NC

Classification of weighted networks through mesoscale homological features

As complex networks find applications in a growing range of disciplines, the diversity of naturally occurring and model networks being studied is exploding. The adoption of a well-developed collection of network taxonomies is a natural method for both organizing this data and understanding deeper relationships between networks. Most existing metrics for network structure rely on classical graph-theoretic measures, extracting characteristics primarily related to individual vertices or paths between them, and thus classify networks from the perspective of local features. Here, we describe an alternative approach to studying structure in networks that relies on an algebraic-topological metric called persistent homology, which studies intrinsically mesoscale structures called cycles, constructed from cliques in the network. We present a classification of 14 commonly studied weighted network models into four groups or classes, and discuss the structural themes arising in each class. Finally, we compute the persistent homology of two real-world networks and one network constructed by a common dynamical systems model, and we compare the results with the three classes to obtain a better understanding of those networks.

math.CO