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Researchers in many fields use networks to represent interactions between entities in complex systems. To study the large-scale behavior of complex systems, it is useful to examine mesoscale structures in networks as building blocks that influence such behavior. In this paper, we present an approach to describe low-rank mesoscale structures in networks. We find that many real-world networks possess a small set of latent motifs that effectively approximate most subgraphs at a fixed mesoscale. Such low-rank mesoscale structures allow one to reconstruct networks by approximating subgraphs of a network using combinations of latent motifs. Employing subgraph sampling and nonnegative matrix factorization enables the discovery of these latent motifs. The ability to encode and reconstruct networks using a small set of latent motifs has many applications in network analysis, including network comparison, network denoising, and edge inference. Network structures can be examined at different scales, and subnetworks in the form of motifs can provide insights into global network properties. The authors propose an approach to decompose a network into a set of latent motifs, which can be used for network comparison, network denoising, and edge inference. [ABSTRACT FROM AUTHOR]

Susceptibility to infectious diseases such as COVID-19 depends on how those diseases spread. Many studies have examined the decrease in COVID-19 spread due to reduction in travel. However, less is known about how much functional geographic regions, which capture natural movements and social interactions, limit the spread of COVID-19. To determine boundaries between functional regions, we apply community-detection algorithms to large networks of mobility and social-media connections to construct geographic regions that reflect natural human movement and relationships at the county level in the coterminous United States. We measure COVID-19 case counts, case rates, and case-rate variations across adjacent counties and examine how often COVID-19 crosses the boundaries of these functional regions. We find that regions that we construct using GPS-trace networks and especially commute networks have the lowest COVID-19 case rates along the boundaries, so these regions may reflect natural partitions in COVID-19 transmission. Conversely, regions that we construct from geolocated Facebook friendships and Twitter connections yield less effective partitions. Our analysis reveals that regions that are derived from movement flows are more appropriate geographic units than states for making policy decisions about opening areas for activity, assessing vulnerability of populations, and allocating resources. Our insights are also relevant for policy decisions and public messaging in future emergency situations. [ABSTRACT FROM AUTHOR]

Ideological divisions in the United States have become increasingly prominent in daily communication. Accordingly, there has been much research on political polarization, including many recent efforts that take a computational perspective. By detecting political biases in a text document, one can attempt to discern and describe its polarity. Intuitively, the named entities (i.e., the nouns and the phrases that act as nouns) and hashtags in text often carry information about political views. For example, people who use the term "pro-choice" are likely to be liberal and people who use the term "pro-life" are likely to be conservative. In this paper, we seek to reveal political polarities in social-media text data and to quantify these polarities by explicitly assigning a polarity score to entities and hashtags. Although this idea is straightforward, it is difficult to perform such inference in a trustworthy quantitative way. Key challenges include the small number of known labels, the continuous spectrum of political views, and the preservation of both a polarity score and a polarity-neutral semantic meaning in an embedding vector of words. To attempt to overcome these challenges, we propose the Polarity-aware Embedding Multi-task learning (PEM) model. This model consists of (1) a self-supervised context-preservation task, (2) an attention-based tweet-level polarity-inference task, and (3) an adversarial learning task that promotes independence between an embedding's polarity component and its semantic component. Our experimental results demonstrate that our PEM model can successfully learn polarity-aware embeddings that perform well at tweet-level and account-level classification tasks. We examine a variety of applications—including a study of spatial and temporal distributions of polarities and a comparison between tweets from Twitter and posts from Parler—and we thereby demonstrate the effectiveness of our PEM model. We also discuss important limitations of our work and encourage caution when applying the PEM model to real-world scenarios. [ABSTRACT FROM AUTHOR]

We consider generalizations of nonlinear Schrödinger equations, which we call “Karpman equations,” that include additional linear higher-order derivatives. Singularly-perturbed Karpman equations produce generalized solitary waves (GSWs) in the form of solitary waves with exponentially small oscillatory tails. Nanoptera are a special type of GSW in which the oscillatory tails do not decay. Previous research on continuous third-order and fourth-order Karpman equations has shown that nanoptera occur in specific settings. We use exponential asymptotic techniques to identify traveling nanoptera in singularly-perturbed continuous Karpman equations. We then study the effect of discretization on nanoptera by applying a finite-difference discretization to continuous Karpman equations and examining traveling-wave solutions. The finite-difference discretization turns a continuous Karpman equation into an advance–delay equation, which we study using exponential asymptotic analysis. By comparing nanoptera in these discrete Karpman equations with nanoptera in their continuous counterparts, we show that the oscillation amplitudes and periods in the nanoptera tails differ in the continuous and discrete equations. We also show that the parameter values at which there is a bifurcation between nanopteron solutions and decaying oscillatory solutions depends on the choice of discretization. Finally, by comparing different higher-order discretizations of the fourth-order Karpman equation, we show that the bifurcation value tends to a nonzero constant for large orders, rather than to 0 as in the associated continuous Karpman equation. [ABSTRACT FROM AUTHOR]

Networks, which represent agents and interactions between them, arise in myriad applications throughout the sciences, engineering, and even the humanities. To understand large-scale structure in a network, a common task is to cluster a network's nodes into sets called "communities," such that there are dense connections within communities but sparse connections between them. A popular and statistically principled method to perform such clustering is to use a family of generative models known as stochastic block models (SBMs). In this paper, we show that maximum-likelihood estimation in an SBM is a network analog of a well-known continuum surface-tension problem that arises from an application in metallurgy. To illustrate the utility of this relationship, we implement network analogs of three surface-tension algorithms, with which we successfully recover planted community structure in synthetic networks and which yield fascinating insights on empirical networks that we construct from hyperspectral videos. [ABSTRACT FROM AUTHOR]

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 a multiplex airline network and that related research areas in physics tend to be grouped together in a multiplex collaboration network. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The two most commonly used hypergeometric functions are the confluent hypergeometric function and the Gauss hypergeometric function. We review the available techniques for accurate, fast, and reliable computation of these two hypergeometric functions in different parameter and variable regimes. The methods that we investigate include Taylor and asymptotic series computations, Gauss-Jacobi quadrature, numerical solution of differential equations, recurrence relations, and others. We discuss the results of numerical experiments used to determine the best methods, in practice, for each parameter and variable regime considered. We provide 'roadmaps' with our recommendation for which methods should be used in each situation. [ABSTRACT FROM AUTHOR]

We employ KAM theory to rigorously investigate quasiperiodic dynamics in cigar-shaped Bose-Einstein condensates (BEC) in periodic lattices and superlattices. Toward this end, we apply a coherent structure ansatz to the Gross-Pitaevskii equation to obtain a parametrically forced Duffing equation describing the spatial dynamics of the condensate. For shallow-well, intermediate-well, and deep-well potentials, we find KAM tori and Aubry-Mather sets to prove that one obtains mostly quasiperiodic dynamics for condensate wave functions of sufficiently large amplitude, where the minimal amplitude depends on the experimentally adjustable BEC parameters. We show that this threshold scales with the square root of the inverse of the two-body scattering length, whereas the rotation number of tori above this threshold is proportional to the amplitude. As a consequence, one obtains the same dynamical picture for lattices of all depths, as an increase in depth essentially affects only scaling in phase space. Our approach is applicable to periodic superlattices with an arbitrary number of rationally dependent wave numbers. [ABSTRACT FROM AUTHOR]

The original version of this Article contained an error in second sentence of the Acknowledgements, which incorrectly read ‘J.Y. and P.G.K. also acknowledge support from US-ARO (W911NF-15-1-0604) and US-AFOSR (FA9550-17-1-011), and P.G.K. also gratefully acknowledges support from the Stavros Niarchos Foundation via the Greek Diaspora Fellowship Program.’ The correct version states ‘US-AFOSR (FA9550-17-1-0114)’ in place of ‘US-AFOSR (FA9550-17-1-011)’. This has been corrected in both the PDF and HTML versions of the Article. [ABSTRACT FROM AUTHOR]

Energy transport properties in heterogeneous materials have attracted scientific interest for more than half of a century, and they continue to offer fundamental and rich questions. One of the outstanding 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. Here we present the first systematic experimental study of energy transport and localization properties in simultaneously disordered and nonlinear granular crystals. In line with prior theoretical studies, we observe in our experiments that disorder and nonlinearity—which individually favor energy localization—can effectively cancel each other out, resulting in the destruction of wave localization. We also show that the combined effect of disorder and nonlinearity can enable manipulation of energy transport speed in granular crystals. Specifically, we experimentally demonstrate superdiffusive transport. Furthermore, our numerical computations suggest that subdiffusive transport should be attainable by controlling the strength of the system’s external precompression force. Wave propagation is often nonlinear in character, yet the interplay between disorder and nonlinearity remains elusive. Kim et al. use experiments and corroborating numerical simulations to investigate this phenomenon and demonstrate superdiffusive energy transport in disordered granular chains. [ABSTRACT FROM AUTHOR]

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, 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 investigate ecological complexity and provide new theoretical and empirical insights into the architecture and dynamics of ecological systems.