Showing papers on "Modularity (networks) published in 2018"

From hairballs to hypotheses-biological insights from microbial networks.

Abstract: Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these networks is not straightforward, and the biological implications of network properties are unclear. Analysis of microbial networks allows researchers to predict hub species and species interactions. Additionally, such analyses can help identify alternative community states and niches. Here, we review factors that can result in spurious predictions and address emergent properties that may be meaningful in the context of the microbiome. We also give an overview of studies that analyse microbial networks to identify new hypotheses. Moreover, we show in a simulation how network properties are affected by tool choice and environmental factors. For example, hub species are not consistent across tools, and environmental heterogeneity induces modularity. We highlight the need for robust microbial network inference and suggest strategies to infer networks more reliably.

General Resilience to Cope with Extreme Events

Abstract: Resilience to specified kinds of disasters is an active area of research and practice. However, rare or unprecedented disturbances that are unusually intense or extensive require a more broad-spectrum type of resilience. General resilience is the capacity of social-ecological systems to adapt or transform in response to unfamiliar, unexpected and extreme shocks. Conditions that enable general resilience include diversity, modularity, openness, reserves, feedbacks, nestedness, monitoring, leadership, and trust. Processes for building general resilience are an emerging and crucially important area of research.

A mechanistic model of connector hubs, modularity and cognition

Abstract: The human brain network is modular-comprised of communities of tightly interconnected nodes1. This network contains local hubs, which have many connections within their own communities, and connector hubs, which have connections diversely distributed across communities2,3. A mechanistic understanding of these hubs and how they support cognition has not been demonstrated. Here, we leveraged individual differences in hub connectivity and cognition. We show that a model of hub connectivity accurately predicts the cognitive performance of 476 individuals in four distinct tasks. Moreover, there is a general optimal network structure for cognitive performance-individuals with diversely connected hubs and consequent modular brain networks exhibit increased cognitive performance, regardless of the task. Critically, we find evidence consistent with a mechanistic model in which connector hubs tune the connectivity of their neighbors to be more modular while allowing for task appropriate information integration across communities, which increases global modularity and cognitive performance.

Multiresolution Consensus Clustering in Networks

Abstract: Networks often exhibit structure at disparate scales. We propose a method for identifying community structure at different scales based on multiresolution modularity and consensus clustering. Our contribution consists of two parts. First, we propose a strategy for sampling the entire range of possible resolutions for the multiresolution modularity quality function. Our approach is directly based on the properties of modularity and, in particular, provides a natural way of avoiding the need to increase the resolution parameter by several orders of magnitude to break a few remaining small communities, necessitating the introduction of ad-hoc limits to the resolution range with standard sampling approaches. Second, we propose a hierarchical consensus clustering procedure, based on a modified modularity, that allows one to construct a hierarchical consensus structure given a set of input partitions. While here we are interested in its application to partitions sampled using multiresolution modularity, this consensus clustering procedure can be applied to the output of any clustering algorithm. As such, we see many potential applications of the individual parts of our multiresolution consensus clustering procedure in addition to using the procedure itself to identify hierarchical structure in networks.

A mechanistic model of connector hubs, modularity, and cognition

Abstract: The human brain network is modular--comprised of communities of tightly interconnected nodes. This network contains local hubs, which have many connections within their own communities, and connector hubs, which have connections diversely distributed across communities. A mechanistic understanding of these hubs and how they support cognition has not been demonstrated. Here, we leveraged individual differences in hub connectivity and cognition. We show that a model of hub connectivity accurately predicts the cognitive performance of 476 individuals in four distinct tasks. Moreover, there is a general optimal network structure for cognitive performance--individuals with diversely connected hubs and consequent modular brain networks exhibit increased cognitive performance, regardless of the task. Critically, we find evidence consistent with a mechanistic model in which connector hubs tune the connectivity of their neighbors to be more modular while allowing for task appropriate information integration across communities, which increases global modularity and cognitive performance.

Detecting hierarchical genome folding with network modularity.

Abstract: Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease.

HomotopyContinuation.jl: A Package for Homotopy Continuation in Julia

Abstract: We present the Julia package HomotopyContinuation.jl, which provides an algorithmic framework for solving polynomial systems by numerical homotopy continuation. We introduce the basic capabilities of the package and demonstrate the software on an illustrative example. We motivate our choice of Julia and how its features allow us to improve upon existing software packages with respect to usability, modularity and performance. Furthermore, we compare the performance of HomotopyContinuation.jl to the existing packages Bertini and PHCpack.

Deep Logic Networks: Inserting and Extracting Knowledge From Deep Belief Networks

Abstract: Developments in deep learning have seen the use of layerwise unsupervised learning combined with supervised learning for fine-tuning. With this layerwise approach, a deep network can be seen as a more modular system that lends itself well to learning representations. In this paper, we investigate whether such modularity can be useful to the insertion of background knowledge into deep networks, whether it can improve learning performance when it is available, and to the extraction of knowledge from trained deep networks, and whether it can offer a better understanding of the representations learned by such networks. To this end, we use a simple symbolic language—a set of logical rules that we call confidence rules —and show that it is suitable for the representation of quantitative reasoning in deep networks. We show by knowledge extraction that confidence rules can offer a low-cost representation for layerwise networks (or restricted Boltzmann machines). We also show that layerwise extraction can produce an improvement in the accuracy of deep belief networks. Furthermore, the proposed symbolic characterization of deep networks provides a novel method for the insertion of prior knowledge and training of deep networks. With the use of this method, a deep neural–symbolic system is proposed and evaluated, with the experimental results indicating that modularity through the use of confidence rules and knowledge insertion can be beneficial to network performance.

Modularity assessment in reconfigurable manufacturing system (RMS) design: an Archived Multi-Objective Simulated Annealing-based approach

Abstract: Enhancing productivity, reducing inaccuracy and avoiding time waste at changeover are considered major drivers in manufacturing system design. One of the emerging paradigms concerned with these characteristics is reconfigurable manufacturing systems (RMSs). The high responsiveness and performance efficiencies of RMS make it a convenient manufacturing paradigm for and flexible enabler of mass customization. The RMS offers customized flexibility and a variety of alternatives as features thanks to its reconfigurable machine tool (RMT). These machines represent a major component of RMS and are based on an adjustable, modular and reconfigurable structure. Hence, the system modularity is of great importance. This paper outlines a multi-objective approach to optimize the RMS design. Three objectives are considered: the maximization of the system modularity, the minimization of the system completion time and the minimization of the system cost. We developed a modularity-based multi-objective approach that uses an adapted version of the “Archived Multi-Objective Simulated Annealing” (AMOSA) method to solve the optimization problem by selecting from a set of candidate machines the most suitable ones. Implemented, the decision maker can use a multi-objective decision making tool based on the well-known “Technique for Order of Preference by Similarity to Ideal Solution” (TOPSIS) to choose the best solution in the Pareto front according to his preferences. We demonstrated the applicability of the proposed approach through an illustrative example and an analysis of the obtained numerical results.

Epidemic spreading in modular time-varying networks.

Abstract: We investigate the effects of modular and temporal connectivity patterns on epidemic spreading. To this end, we introduce and analytically characterise a model of time-varying networks with tunable modularity. Within this framework, we study the epidemic size of Susceptible-Infected-Recovered, SIR, models and the epidemic threshold of Susceptible-Infected-Susceptible, SIS, models. Interestingly, we find that while the presence of tightly connected clusters inhibits SIR processes, it speeds up SIS phenomena. In this case, we observe that modular structures induce a reduction of the threshold with respect to time-varying networks without communities. We confirm the theoretical results by means of extensive numerical simulations both on synthetic graphs as well as on a real modular and temporal network.

Weighted Stochastic Block Models of the Human Connectome across the Life Span

Abstract: The human brain can be described as a complex network of anatomical connections between distinct areas, referred to as the human connectome. Fundamental characteristics of connectome organization can be revealed using the tools of network science and graph theory. Of particular interest is the network's community structure, commonly identified by modularity maximization, where communities are conceptualized as densely intra-connected and sparsely inter-connected. Here we adopt a generative modeling approach called weighted stochastic block models (WSBM) that can describe a wider range of community structure topologies by explicitly considering patterned interactions between communities. We apply this method to the study of changes in the human connectome that occur across the life span (between 6-85 years old). We find that WSBM communities exhibit greater hemispheric symmetry and are spatially less compact than those derived from modularity maximization. We identify several network blocks that exhibit significant linear and non-linear changes across age, with the most significant changes involving subregions of prefrontal cortex. Overall, we show that the WSBM generative modeling approach can be an effective tool for describing types of community structure in brain networks that go beyond modularity.

Developmental pathways inferred from modularity, morphological integration and fluctuating asymmetry patterns in the human face

Abstract: Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds. To do so, 4104 individuals were analyzed using 3D photogrammetry reconstructions and a set of 34 facial landmarks placed on each individual. We found a pattern of modularity and integration that is conserved across sub-samples differing in their genomic ancestry background. Specifically, a signal of modularity based on functional demands and organization of the face is regularly observed across the whole sample. Our results shed more light on previous evidence obtained from Genome Wide Association Studies performed on the same samples, indicating the action of different genomic regions contributing to the expression of the nose and mouth facial phenotypes. Our results also indicate that large samples including phenotypic and genomic metadata enable a better understanding of the developmental and genetic architecture of craniofacial phenotypes.

Brain Network Modularity Predicts Exercise-Related Executive Function Gains in Older Adults.

Abstract: Recent work suggests that the brain can be conceptualized as a network comprised of groups of sub-networks or modules. The extent of segregation between modules can be quantified with a modularity metric, where networks with high modularity have dense connections within modules and sparser connections between modules. Previous work has shown that higher modularity predicts greater improvements after cognitive training in patients with traumatic brain injury and in healthy older and young adults. It is not known, however, whether modularity can also predict cognitive gains after a physical exercise intervention. Here, we quantified modularity in older adults (N = 128, mean age = 64.74) who underwent one of the following interventions for 6 months (NCT01472744 on ClinicalTrials.gov): (1) aerobic exercise in the form of brisk walking (Walk), (2) aerobic exercise in the form of brisk walking plus nutritional supplement (Walk+), (3) stretching, strengthening and stability (SSS), or (4) dance instruction. After the intervention, the Walk, Walk+ and SSS groups showed gains in cardiorespiratory fitness (CRF), with larger effects in both walking groups compared to the SSS and Dance groups. The Walk, Walk+ and SSS groups also improved in executive function (EF) as measured by reasoning, working memory, and task-switching tests. In the Walk, Walk+, and SSS groups that improved in EF, higher baseline modularity was positively related to EF gains, even after controlling for age, in-scanner motion and baseline EF. No relationship between modularity and EF gains was observed in the Dance group, which did not show training-related gains in CRF or EF control. These results are consistent with previous studies demonstrating that individuals with a more modular brain network organization are more responsive to cognitive training. These findings suggest that the predictive power of modularity may be generalizable across interventions aimed to enhance aspects of cognition and that, especially in low-performing individuals, global network properties can capture individual differences in neuroplasticity.

Multiscale mixing patterns in networks.

Abstract: Assortative mixing in networks is the tendency for nodes with the same attributes, or metadata, to link to each other. It is a property often found in social networks, manifesting as a higher tendency of links occurring between people of the same age, race, or political belief. Quantifying the level of assortativity or disassortativity (the preference of linking to nodes with different attributes) can shed light on the organization of complex networks. It is common practice to measure the level of assortativity according to the assortativity coefficient, or modularity in the case of categorical metadata. This global value is the average level of assortativity across the network and may not be a representative statistic when mixing patterns are heterogeneous. For example, a social network spanning the globe may exhibit local differences in mixing patterns as a consequence of differences in cultural norms. Here, we introduce an approach to localize this global measure so that we can describe the assortativity, across multiple scales, at the node level. Consequently, we are able to capture and qualitatively evaluate the distribution of mixing patterns in the network. We find that, for many real-world networks, the distribution of assortativity is skewed, overdispersed, and multimodal. Our method provides a clearer lens through which we can more closely examine mixing patterns in networks.

Seeing and Conceptualizing: Modularity and the Shallow Contents of Perception

Abstract: After presenting evidence about categorization behavior, this paper argues for the following theses: 1) that there is a border between perception and cognition; 2) that the border is to be characterized by perception being modular (and cognition not being so); 3) that perception outputs conceptualized representations, so views that posit that the output of perception is solely non-conceptual are false; and 4) that perceptual content consists of basic-level categories and not richer contents.

Thermodynamics of Modularity: Structural Costs Beyond the Landauer Bound

Abstract: Author(s): Boyd, AB; Mandal, D; Crutchfield, JP | Abstract: Information processing typically occurs via the composition of modular units, such as the universal logic gates found in discrete computation circuits. The benefit of modular information processing, in contrast to globally integrated information processing, is that complex computations are more easily and flexibly implemented via a series of simpler, localized information processing operations that only control and change local degrees of freedom. We show that, despite these benefits, there are unavoidable thermodynamic costs to modularity - costs that arise directly from the operation of localized processing and that go beyond Landauer's bound on the work required to erase information. Localized operations are unable to leverage global correlations, which are a thermodynamic fuel. We quantify the minimum irretrievable dissipation of modular computations in terms of the difference between the change in global nonequilibrium free energy, which captures these global correlations, and the local (marginal) change in nonequilibrium free energy, which bounds modular work production. This modularity dissipation is proportional to the amount of additional work required to perform a computational task modularly, measuring a structural energy cost. It determines the thermodynamic efficiency of different modular implementations of the same computation, and so it has immediate consequences for the architecture of physically embedded transducers, known as information ratchets. Constructively, we show how to circumvent modularity dissipation by designing internal ratchet states that capture the information reservoir's global correlations and patterns. Thus, there are routes to thermodynamic efficiency that circumvent globally integrated protocols and instead reduce modularity dissipation to optimize the architecture of computations composed of a series of localized operations.

Scaling up genetic circuit design for cellular computing: advances and prospects.

Abstract: Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.

A Correlation Clustering Framework for Community Detection

Abstract: Graph clustering, or community detection, is the task of identifying groups of closely related objects in a large network. In this paper we introduce a new community detection framework called LambdaCC that is based on a specially weighted version of correlation clustering. A key component in our methodology is a clustering resolution parameter, lambda, which implicitly controls the size and structure of clusters formed by our framework. We show that, by increasing this parameter, our objective effectively interpolates between two different strategies in graph clustering: finding a sparse cut and forming dense subgraphs. Our methodology unifies and generalizes a number of other important clustering quality functions including modularity, sparsest cut, and cluster deletion, and places them all within the context of an optimization problem that has been well studied from the perspective of approximation algorithms. Our approach to clustering is particularly relevant in the regime of finding dense clusters, as it leads to a 2-approximation for the cluster deletion problem. We use our approach to cluster several graphs, including large collaboration networks and social networks.

Building C( sp 3 )-rich complexity by combining cycloaddition and C–C cross-coupling reactions

Abstract: Prized for their ability to rapidly generate chemical complexity by building new ring systems and stereocentres1, cycloaddition reactions have featured in numerous total syntheses2 and are a key component in the education of chemistry students3. Similarly, carbon-carbon (C-C) cross-coupling methods are integral to synthesis because of their programmability, modularity and reliability4. Within the area of drug discovery, an overreliance on cross-coupling has led to a disproportionate representation of flat architectures that are rich in carbon atoms with orbitals hybridized in an sp2 manner5. Despite the ability of cycloadditions to introduce multiple carbon sp3 centres in a single step, they are less used6. This is probably because of their lack of modularity, stemming from the idiosyncratic steric and electronic rules for each specific type of cycloaddition. Here we demonstrate a strategy for combining the optimal features of these two chemical transformations into one simple sequence, to enable the modular, enantioselective, scalable and programmable preparation of useful building blocks, natural products and lead scaffolds for drug discovery.

A block model for node popularity in networks with community structure

Abstract: Summary The community structure that is observed in empirical networks has been of particular interest in the statistics literature, with a strong emphasis on the study of block models. We study an important network feature called node popularity, which is closely associated with community structure. Neither the classical stochastic block model nor its degree-corrected extension can satisfactorily capture the dynamics of node popularity as observed in empirical networks. We propose a popularity-adjusted block model for flexible and realistic modelling of node popularity. We establish consistency of likelihood modularity for community detection as well as estimation of node popularities and model parameters, and demonstrate the advantages of the new modularity over the degree-corrected block model modularity in simulations. By analysing the political blogs network, the British Members of Parliament network and the ‘Digital bibliography and library project’ bibliographical network, we illustrate that improved empirical insights can be gained through this methodology.

Abelian Surfaces over totally real fields are Potentially Modular

Abstract: We show that abelian surfaces (and consequently curves of genus 2) over totally real fields are potentially modular. As a consequence, we obtain the expected meromorphic continuation and functional equations of their Hasse--Weil zeta functions. We furthermore show the modularity of infinitely many abelian surfaces A over Q with End_C(A)=Z. We also deduce modularity and potential modularity results for genus one curves over (not necessarily CM) quadratic extensions of totally real fields.

A Fast Parallel Community Discovery Model on Complex Networks Through Approximate Optimization

Abstract: Community discovery plays an essential role in the analysis of the structural features of complex networks. Since online networks grow increasingly large and complex over time, the methods traditionally used for community discovery cannot efficiently handle large-scale network data. This introduces the important problem of how to effectively and efficiently discover large communities from complex networks. In this study, we propose a fast parallel community discovery model called picaso (a p arallel commun i ty dis c overy a lgorithm ba s ed on approximate o ptimization), which integrates two new techniques: (1) Mountain model, which works by utilizing graph theory to approximate the selection of nodes needed for merging, and (2) Landslide algorithm, which is used to update the modularity increment based on the approximated optimization. In addition, the GraphX distribution computing framework is employed in order to achieve parallel community detection over complex networks. In the proposed model, clustering on modularity is used to initialize the Mountain model as well as to compute the weight of each edge in the networks. The relationships among the communities are then simplified by applying the Landslide algorithm, which allows us to obtain the community structures of the complex networks. Extensive experiments were conducted on real and synthetic complex network datasets, and the results demonstrate that the proposed algorithm can outperform the state of the art methods, in effectiveness and efficiency, when working to solve the problem of community detection. Moreover, we demonstratively prove that overall time performance approximates to four times faster than similar approaches. Effectively our results suggest a new paradigm for large-scale community discovery of complex networks.

Modularity promotes morphological divergence in ray-finned fishes.

Abstract: Modularity is considered a prerequisite for the evolvability of biological systems. This is because in theory, individual modules can follow quasi-independent evolutionary trajectories or evolve at different rates compared to other aspects of the organism. This may influence the potential of some modules to diverge, leading to differences in disparity. Here, we investigated this relationship between modularity, rates of morphological evolution and disparity using a phylogenetically diverse sample of ray-finned fishes. We compared the support for multiple hypotheses of evolutionary modularity and asked if the partitions delimited by the best-fitting models were also characterized by the highest evolutionary rate differentials. We found that an evolutionary module incorporating the dorsal, anal and paired fins was well supported by the data, and that this module evolves more rapidly and consequently generates more disparity than other modules. This suggests that modularity may indeed promote morphological disparity through differences in evolutionary rates across modules.

Potential automorphy over CM fields

Abstract: Let $F$ be a CM number field. We prove modularity lifting theorems for regular $n$-dimensional Galois representations over $F$ without any self-duality condition. We deduce that all elliptic curves $E$ over $F$ are potentially modular, and furthermore satisfy the Sato--Tate conjecture. As an application of a different sort, we also prove the Ramanujan Conjecture for weight zero cuspidal automorphic representations for $\mathrm{GL}_2(\mathbf{A}_F)$.

Hand exoskeleton for rehabilitation therapies with integrated optical force sensor

Abstract: This article presents the design of a hand exoskeleton that features its modularity and the possibility of integrating a force sensor in its frame. The modularity is achieved by dividing the exoske...