arXiv subjects

Mason A. Porter

Publications and source records attributed to Mason A. Porter.

At least 127 records · Page 7Linked to original sources

arXiv2017

A roadmap for the computation of persistent homology

Persistent homology (PH) is a method used in topological data analysis (TDA) to study qualitative features of data that persist across multiple scales. It is robust to perturbations of input data, independent of dimensions and coordinates, and provides a compact representation of the qualitative features of the input. The computation of PH is an open area with numerous important and fascinating challenges. The field of PH computation is evolving rapidly, and new algorithms and software implementations are being updated and released at a rapid pace. The purposes of our article are to (1) introduce theory and computational methods for PH to a broad range of computational scientists and (2) provide benchmarks of state-of-the-art implementations for the computation of PH. We give a friendly introduction to PH, navigate the pipeline for the computation of PH with an eye towards applications, and use a range of synthetic and real-world data sets to evaluate currently available open-source implementations for the computation of PH. Based on our benchmarking, we indicate which algorithms and implementations are best suited to different types of data sets. In an accompanying tutorial, we provide guidelines for the computation of PH. We make publicly available all scripts that we wrote for the tutorial, and we make available the processed version of the data sets used in the benchmarking.

math.AT↗

arXiv2017

Modeling the lowest-cost splitting of a herd of cows by optimizing a cost function

Animals live in groups to defend against predation and to obtain food. However, for some animals --- especially ones that spend long periods of time feeding --- there are costs if a group chooses to move on before their nutritional needs are satisfied. If the conflict between feeding and keeping up with a group becomes too large, it may be advantageous to some animals to split into subgroups of animals with similar nutritional needs. We model the costs and benefits of splitting by a herd of cows using a cost function (CF) that quantifies individual variation in hunger, desire to lie down, and predation risk. We model the costs associated with hunger and lying desire as the standard deviations of individuals within a group, and we model predation risk as an inverse exponential function of group size. We minimize the cost function over all plausible groups that can arise from a given herd and study the dynamics of group splitting. We explore our model using two examples: (1) we consider group switching and group fission in a herd of relatively homogeneous cows; and (2) we examine a herd with an equal number of adult males (larger animals) and adult females (smaller animals).

q-bio.PE↗

arXiv2017

Layer Communities in Multiplex Networks

Multiplex networks are a type of multilayer network in which entities are connected to each other via multiple types of connections. We propose a method, based on computing pairwise similarities between layers and then doing community detection, for grouping structurally similar layers in multiplex networks. We illustrate our approach using both synthetic and empirical networks, and we are able to find meaningful groups of layers in both cases. For example, we find that airlines that are based in similar geographic locations tend to be grouped together in an airline multiplex network and that related research areas in physics tend to be grouped together in an multiplex collaboration network.

physics.soc-ph↗

arXiv2017

Complex Contagions with Timers

A great deal of effort has gone into trying to model social influence --- including the spread of behavior, norms, and ideas --- on networks. Most models of social influence tend to assume that individuals react to changes in the states of their neighbors without any time delay, but this is often not true in social contexts, where (for various reasons) different agents can have different response times. To examine such situations, we introduce the idea of a timer into threshold models of social influence. The presence of timers on nodes delays the adoption --- i.e., change of state --- of each agent, which in turn delays the adoptions of its neighbors. With a homogeneous-distributed timer, in which all nodes exhibit the same amount of delay, adoption delays are also homogeneous, so the adoption order of nodes remains the same. However, heterogeneously-distributed timers can change the adoption order of nodes and hence the "adoption paths" through which state changes spread in a network. Using a threshold model of social contagions, we illustrate that heterogeneous timers can either accelerate or decelerate the spread of adoptions compared to an analogous situation with homogeneous timers, and we investigate the relationship of such acceleration or deceleration with respect to timer distribution and network structure. We derive an analytical approximation for the temporal evolution of the fraction of adopters by modifying a pair approximation of the Watts threshold model, and we find good agreement with numerical computations. We also examine our new timer model on networks constructed from empirical data.

physics.soc-ph↗

arXiv2017

Direct measurement of superdiffusive and subdiffusive energy transport in disordered granular chains

The study of energy transport properties in heterogeneous materials has attracted scientific interest for more than a century, and it continues to offer fundamental and rich questions. One of the unanswered challenges is to extend Anderson theory for uncorrelated and fully disordered lattices in condensed-matter systems to physical settings in which additional effects compete with disorder. Specifically, the effect of strong nonlinearity has been largely unexplored experimentally, partly due to the paucity of testbeds that can combine the effect of disorder and nonlinearity in a controllable manner. Here we present the first systematic experimental study of energy transport and localization properties in simultaneously disordered and nonlinear granular crystals. We demonstrate experimentally that disorder and nonlinearity --- which are known from decades of studies to individually favor energy localization --- can in some sense "cancel each other out", resulting in the destruction of wave localization. We also report that the combined effect of disorder and nonlinearity can enable the manipulation of energy transport speed in granular crystals from subdiffusive to superdiffusive ranges.

cond-mat.mtrl-sci↗

arXiv2017

The physics of spreading processes in multilayer networks

The study of networks plays a crucial role in investigating the structure, dynamics, and function of a wide variety of complex systems in myriad disciplines. Despite the success of traditional network analysis, standard networks provide a limited representation of complex systems, which often include different types of relationships (i.e., "multiplexity") among their constituent components and/or multiple interacting subsystems. Such structural complexity has a significant effect on both dynamics and function. Throwing away or aggregating available structural information can generate misleading results and be a major obstacle towards attempts to understand complex systems. The recent "multilayer" approach for modeling networked systems explicitly allows the incorporation of multiplexity and other features of realistic systems. On one hand, it allows one to couple different structural relationships by encoding them in a convenient mathematical object. On the other hand, it also allows one to couple different dynamical processes on top of such interconnected structures. The resulting framework plays a crucial role in helping achieve a thorough, accurate understanding of complex systems. The study of multilayer networks has also revealed new physical phenomena that remain hidden when using ordinary graphs, the traditional network representation. Here we survey progress towards attaining a deeper understanding of spreading processes on multilayer networks, and we highlight some of the physical phenomena related to spreading processes that emerge from multilayer structure.

physics.soc-ph↗

arXiv2017

Message-Passing Methods for Complex Contagions

Message-passing methods provide a powerful approach for calculating the expected size of cascades either on random networks (e.g., drawn from a configuration-model ensemble or its generalizations) asymptotically as the number $N$ of nodes becomes infinite or on specific finite-size networks. We review the message-passing approach and show how to derive it for configuration-model networks using the methods of (Dhar et al., 1997) and (Gleeson, 2008). Using this approach, we explain for such networks how to determine an analytical expression for a "cascade condition", which determines whether a global cascade will occur. We extend this approach to the message-passing methods for specific finite-size networks (Shrestha and Moore, 2014; Lokhov et al., 2015), and we derive a generalized cascade condition. Throughout this chapter, we illustrate these ideas using the Watts threshold model.

physics.soc-ph↗

arXiv2017

Mesoscale analyses of fungal networks as an approach for quantifying phenotypic traits

We investigate the application of mesoscopic response functions (MRFs) to characterize a large set of networks of fungi and slime moulds grown under a wide variety of different experimental treatments, including inter-species competition and attack by fungivores. We construct 'structural networks' by estimating cord conductances (which yield edge weights) from the experimental data, and we construct 'functional networks' by calculating edge weights based on how much nutrient traffic is predicted to occur along each edge. Both types of networks have the same topology, and we compute MRFs for both families of networks to illustrate two different ways of constructing taxonomies to group the networks into clusters of related fungi and slime moulds. Although both network taxonomies generate intuitively sensible groupings of networks across species, treatments and laboratories, we find that clustering using the functional-network measure appears to give groups with lower intra-group variation in species or treatments. We argue that MRFs provide a useful quantitative analysis of network behaviour that can (1) help summarize an expanding set of increasingly complex biological networks and (2) help extract information that captures subtle changes in intra- and inter-specific phenotypic traits that are integral to a mechanistic understanding of fungal behaviour and ecology. As an accompaniment to our paper, we also make a large data set of fungal networks available in the public domain.

q-bio.QM↗

arXiv2017

Time-dependent community structure in legislation cosponsorship networks in the Congress of the Republic of Peru

We study community structure in time-dependent legislation cosponsorship networks in the Peruvian Congress, and we compare them briefly to legislation cosponsorship networks in the US Senate. To study these legislatures, we employ a multilayer representation of temporal networks in which legislators in each layer are connected to each other with a weight that is based on how many bills they cosponsor. We then use multilayer modularity maximization to detect communities in these networks. From our computations, we are able to capture power shifts in the Peruvian Congress during 2006--2011. For example, we observe the emergence of 'opportunists', who switch from one community to another, as well as cohesive legislative communities whose initial component legislators never change communities. Interestingly, many of the opportunists belong to the group that won the majority in Congress.

physics.soc-ph↗

arXiv2017

Isomorphisms in Multilayer Networks

We extend the concept of graph isomorphisms to multilayer networks with any number of "aspects" (i.e., types of layering). In developing this generalization, we identify multiple types of isomorphisms. For example, in multilayer networks with a single aspect, permuting vertex labels, layer labels, and both vertex labels and layer labels each yield different isomorphism relations between multilayer networks. Multilayer network isomorphisms lead naturally to defining isomorphisms in any of the numerous types of networks that can be represented as a multilayer network, and we thereby obtain isomorphisms for multiplex networks, temporal networks, networks with both of these features, and more. We reduce each of the multilayer network isomorphism problems to a graph isomorphism problem, where the size of the graph isomorphism problem grows linearly with the size of the multilayer network isomorphism problem. One can thus use software that has been developed to solve graph isomorphism problems as a practical means for solving multilayer network isomorphism problems. Our theory lays a foundation for extending many network analysis methods --- including motifs, graphlets, structural roles, and network alignment --- to any multilayer network.

physics.soc-ph↗

arXiv2017

A Mean-Field Approach to Evolving Spatial Networks, with an Application to Osteocyte Network Formation

We consider evolving networks in which each node can have various associated properties (a state) in addition to those that arise from network structure. For example, each node can have a spatial location and a velocity, or some more abstract internal property that describes something like social trait. Edges between nodes are created and destroyed, and new nodes enter the system. We introduce a "local state degree distribution" (LSDD) as the degree distribution at a particular point in state space. We then make a mean-field assumption and thereby derive an integro-partial differential equation that is satisfied by the LSDD. We perform numerical experiments and find good agreement between solutions of the integro-differential equation and the LSDD from stochastic simulations of the full model. To illustrate our theory, we apply it to a simple continuum model for osteocyte network formation within bones, with a view to understanding changes that may take place during cancer. Our results suggest that increased rates of differentiation lead to higher densities of osteocytes but with a lower number of dendrites. To help provide biological context, we also include an introduction to osteocytes, the formation of osteocyte networks, and the role of osteocytes in bona metastasis.

q-bio.QM↗

arXiv2017

Synergistic effects in threshold models on networks

Network structure can have significant effects on the propagation of diseases, memes, and information on social networks. Such effects depend on the specific type of dynamical process that affects the nodes and edges of a network, and it is important to develop tractable models of spreading processes on networks to explore how network structure affects dynamics. In this paper, we incorporate the idea of \emph{synergy} into a two-state ("active" or "passive") threshold model of social influence on networks. Our model's update rule is deterministic, and the influence of each meme-carrying (i.e., active) neighbor can --- depending on a parameter --- either be enhanced or inhibited by an amount that depends on the number of active neighbors of a node. Such a synergistic system models social behavior in which the willingness to adopt either accelerates or saturates depending on the number of neighbors who have adopted that behavior. We illustrate that the synergy parameter in our model has a crucial effect on system dynamics, as it determines whether degree-$k$ nodes are possible or impossible to activate. We simulate synergistic meme spreading on both random-graph models and networks constructed from empirical data. Using a local-tree approximation, we examine the spreading of synergistic memes and find good agreement on all but one of the networks on which we simulate spreading. We find for any network and for a broad family of synergistic models that one can predict which synergy-parameter values allow degree-$k$ nodes to be activated.

physics.soc-ph↗

arXiv2017

Opinion formation and distribution in a bounded confidence model on various networks

In the social, behavioral, and economic sciences, it is an important problem to predict which individual opinions will eventually dominate in a large population, if there will be a consensus, and how long it takes a consensus to form. This idea has been studied heavily both in physics and in other disciplines, and the answer depends strongly on both the model for opinions and for the network structure on which the opinions evolve. One model that was created to study consensus formation quantitatively is the Deffuant model, in which the opinion distribution of a population evolves via sequential random pairwise encounters. To consider the heterogeneity of interactions in a population due to social influence, we study the Deffuant model on various network structures (deterministic synthetic networks, random synthetic networks, and social networks constructed from Facebook data) using several interaction mechanisms. We numerically simulate the Deffuant model and conduct regression analyses to investigate the dependence of the convergence time to equilibrium on parameters, including a confidence bound for opinion updates, the number of participating entities, and their willingness to compromise. We find that network structure and parameter values both have an effect on the convergence time, and for some network topologies, the convergence time undergoes a transition at a critical value of the confidence bound. We discuss the number of opinion groups that form at equilibrium in terms of a confidence-bound threshold for a transition from consensus to multiple-opinion equilibria.

physics.soc-ph↗

arXiv2016

Nonlinear Coherent Structures in Granular Crystals

The study of granular crystals, metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals, a type of nonlinear metamaterial, exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures --- which include traveling solitary waves, dispersive shock waves, and discrete breathers --- have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

nlin.PS↗

arXiv2016

Persistent homology of time-dependent functional networks constructed from coupled time series

We use topological data analysis to study "functional networks" that we construct from time-series data from both experimental and synthetic sources. We use persistent homology with a weight rank clique filtration to gain insights into these functional networks, and we use persistence landscapes to interpret our results. Our first example uses time-series output from networks of coupled Kuramoto oscillators. Our second example consists of biological data in the form of functional magnetic resonance imaging (fMRI) data that was acquired from human subjects during a simple motor-learning task in which subjects were monitored on three days in a five-day period. With these examples, we demonstrate that (1) using persistent homology to study functional networks provides fascinating insights into their properties and (2) the position of the features in a filtration can sometimes play a more vital role than persistence in the interpretation of topological features, even though conventionally the latter is used to distinguish between signal and noise. We find that persistent homology can detect differences in synchronization patterns in our data sets over time, giving insight both on changes in community structure in the networks and on increased synchronization between brain regions that form loops in a functional network during motor learning. For the motor-learning data, persistence landscapes also reveal that on average the majority of changes in the network loops take place on the second of the three days of the learning process.

q-bio.QM↗

arXiv2016

The Multilayer Nature of Ecological Networks

Although networks provide a powerful approach to study a large variety of ecological systems, their formulation does not typically account for multiple interaction types, interactions that vary in space and time, and interconnected systems such as networks of networks. The emergent field of `multilayer networks' provides a natural framework for extending analyses of ecological systems to include such multiple layers of complexity, as it specifically allows one to differentiate and model `intralayer' and `interlayer' connectivity. The framework provides a set of concepts and tools that can be adapted and applied to ecology, facilitating research on high-dimensional, heterogeneous systems in nature. Here, we formally define ecological multilayer networks based on a review of previous and related approaches, illustrate their application and potential with analyses of existing data, and discuss limitations, challenges, and future applications. The integration of multilayer network theory into ecology offers largely untapped potential to further address ecological complexity, to ultimately provide new theoretical and empirical insights into the architecture and dynamics of ecological systems.

q-bio.QM↗

arXiv2016

Detection of Core-Periphery Structure in Networks Using Spectral Methods and Geodesic Paths

We introduce several novel and computationally efficient methods for detecting "core--periphery structure" in networks. Core--periphery structure is a type of mesoscale structure that includes densely-connected core vertices and sparsely-connected peripheral vertices. Core vertices tend to be well-connected both among themselves and to peripheral vertices, which tend not to be well-connected to other vertices. Our first method, which is based on transportation in networks, aggregates information from many geodesic paths in a network and yields a score for each vertex that reflects the likelihood that a vertex is a core vertex. Our second method is based on a low-rank approximation of a network's adjacency matrix, which can often be expressed as a tensor-product matrix. Our third approach uses the bottom eigenvector of the random-walk Laplacian to infer a coreness score and a classification into core and peripheral vertices. We also design an objective function to (1) help classify vertices into core or peripheral vertices and (2) provide a goodness-of-fit criterion for classifications into core versus peripheral vertices. To examine the performance of our methods, we apply our algorithms to both synthetically-generated networks and a variety of networks constructed from real-world data sets.

cs.DM↗

arXiv2016

A predator-2 prey fast-slow dynamical system for rapid predator evolution

We consider adaptive change of diet of a predator population that switches its feeding between two prey populations. We develop a novel 1 fast--3 slow dynamical system to describe the dynamics of the three populations amidst continuous but rapid evolution of the predator's diet choice. The two extremes at which the predator's diet is composed solely of one prey correspond to two branches of the three-branch critical manifold of the fast--slow system. By calculating the points at which there is a fast transition between these two feeding choices (i.e., branches of the critical manifold), we prove that the system has a two-parameter family of periodic orbits for sufficiently large separation of the time scales between the evolutionary and ecological dynamics. Using numerical simulations, we show that these periodic orbits exist, and that their phase difference and oscillation patterns persist, when ecological and evolutionary interactions occur on comparable time scales. Our model also exhibits periodic orbits that agree qualitatively with oscillation patterns observed in experimental studies of the coupling between rapid evolution and ecological interactions.

math.DS↗