Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Concurrency and reachability in treelike temporal networks.

ABSTRACT: Network properties govern the rate and extent of various spreading processes, from simple contagions to complex cascades. Recently, the analysis of spreading processes has been extended from static networks to temporal networks, where nodes and links appear and disappear. We focus on the effects of accessibility, whether there is a temporally consistent path from one node to another, and reachability, the density of the corresponding accessibility graph representation of the temporal network. The level of reachability thus inherently limits the possible extent of any spreading process on the temporal network. We study reachability in terms of the overall levels of temporal concurrency between edges and the structural cohesion of the network agglomerating over all edges. We use simulation results and develop heterogeneous mean-field model predictions for random networks to better quantify how the properties of the underlying temporal network regulate reachability.

SUBMITTER: Lee E

PROVIDER: S-EPMC6989038 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Concurrency and reachability in treelike temporal networks.

Lee Eun E Emmons Scott S Gibson Ryan R Moody James J Mucha Peter J PJ

Physical review. E 20191201 6-1

Network properties govern the rate and extent of various spreading processes, from simple contagions to complex cascades. Recently, the analysis of spreading processes has been extended from static networks to temporal networks, where nodes and links appear and disappear. We focus on the effects of accessibility, whether there is a temporally consistent path from one node to another, and reachability, the density of the corresponding accessibility graph representation of the temporal network. Th ...[more]

PMID: 31962508

Similar Datasets

Spatio-temporal networks: reachability, centrality and robustness.

Project description:Recent advances in spatial and temporal networks have enabled researchers to more-accurately describe many real-world systems such as urban transport networks. In this paper, we study the response of real-world spatio-temporal networks to random error and systematic attack, taking a unified view of their spatial and temporal performance. We propose a model of spatio-temporal paths in time-varying spatially embedded networks which captures the property that, as in many real-world systems, interaction between nodes is non-instantaneous and governed by the space in which they are embedded. Through numerical experiments on three real-world urban transport systems, we study the effect of node failure on a network's topological, temporal and spatial structure. We also demonstrate the broader applicability of this framework to three other classes of network. To identify weaknesses specific to the behaviour of a spatio-temporal system, we introduce centrality measures that evaluate the importance of a node as a structural bridge and its role in supporting spatio-temporally efficient flows through the network. This exposes the complex nature of fragility in a spatio-temporal system, showing that there is a variety of failure modes when a network is subject to systematic attacks.

| S-EPMC4929911 | biostudies-literature

Signal reachability facilitates characterization of probabilistic signaling networks.

Project description:Studying biological networks is of extreme importance in understanding cellular functions. These networks model interactions between molecules in each cell. A large volume of research has been done to uncover different characteristics of biological networks, such as large-scale organization, node centrality and network robustness. Nevertheless, the vast majority of research done in this area assume that biological networks have deterministic topologies. Biological interactions are however probabilistic events that may or may not appear at different cells or even in the same cell at different times.In this paper, we present novel methods for characterizing probabilistic signaling networks. Our methods do this by computing the probability that a signal propagates successfully from receptor to reporter genes through interactions in the network. We characterize such networks with respect to (i) centrality of individual nodes, (ii) stability of the entire network, and (iii) important functions served by the network. We use these methods to characterize major H. sapiens signaling networks including Wnt, ErbB and MAPK.

| S-EPMC4674881 | biostudies-literature

The reachability of contagion in temporal contact networks: how disease latency can exploit the rhythm of human behavior.

Project description:BACKGROUND:The symptoms of many infectious diseases influence their host to withdraw from social activity limiting their potential to spread. Successful transmission therefore requires the onset of infectiousness to coincide with a time when the host is socially active. Since social activity and infectiousness are both temporal phenomena, we hypothesize that diseases are most pervasive when these two processes are synchronized. METHODS:We consider disease dynamics that incorporate behavioral responses that effectively shorten the infectious period of the pathogen. Using data collected from face-to-face social interactions and synthetic contact networks constructed from empirical demographic data, we measure the reachability of this disease model and perform disease simulations over a range of latent period durations. RESULTS:We find that maximum transmission risk results when the disease latent period (and thus the generation time) are synchronized with human circadian rhythms of 24 h, and minimum transmission risk when latent periods are out of phase with circadian rhythms by 12 h. The effect of this synchronization is present for a range of disease models with realistic disease parameters and host behavioral responses. CONCLUSIONS:The reproductive potential of pathogens is linked inextricably to the host social behavior required for transmission. We propose that future work should consider contact periodicity in models of disease dynamics, and suggest the possibility that disease control strategies may be designed to optimize against the effects of synchronization.

| S-EPMC5952858 | biostudies-literature

Reachability bounds for chemical reaction networks and strand displacement systems.

Project description:Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

| S-EPMC4224742 | biostudies-other

Revisiting Underapproximate Reachability for Multipushdown Systems

Project description:Boolean programs with multiple recursive threads can be captured as pushdown automata with multiple stacks. This model is Turing complete, and hence, one is often interested in analyzing a restricted class which still captures useful behaviors. In this paper, we propose a new class of bounded underapproximations for multi-pushdown systems, which subsumes most existing classes. We develop an efficient algorithm for solving the under-approximate reachability problem, which is based on efficient fix-point computations. We implement it in our tool BHIM and illustrate its applicability by generating a set of relevant benchmarks and examining its performance. As an additional takeaway BHIM solves the binary reachability problem in pushdown automata. To show the versatility of our approach, we then extend our algorithm to the timed setting and provide the first implementation that can handle timed multi-pushdown automata with closed guards.

| S-EPMC7439744 | biostudies-literature

Partnership concurrency and coital frequency.

Project description:National HIV prevalence estimates across sub-Saharan Africa range from less than 1 percent to over 25 percent. Recent research proposes several explanations for the observed variation, including prevalence of male circumcision, levels of condom use, presence of other sexually transmitted infections, and practice of multiple concurrent partnerships. However, the importance of partnership concurrency for HIV transmission may depend on how it affects coital frequency with each partner. The coital dilution hypothesis suggests that coital frequency within a partnership declines with the addition of concurrent partners. Using sexual behavior data from rural Malawi and urban Kenya, we investigate the relationship between partnership concurrency and coital frequency, and find partial support for the coital dilution hypothesis. We conclude the paper with a discussion of our findings in light of the current literature on concurrency.

| S-EPMC3760194 | biostudies-literature

Estimating Attractor Reachability in Asynchronous Logical Models.

Project description:Logical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are associated with model attractors (stable states or cyclic attractors) whose identification and reachability properties are particularly relevant. While synchronous updates assume unlikely instantaneous or identical rates associated with component changes, the consideration of asynchronous updates is more realistic but, for large models, may hinder the analysis of the resulting non-deterministic concurrent dynamics. This complexity hampers the study of asymptotical behaviors, and most existing approaches suffer from efficiency bottlenecks, being generally unable to handle cyclical attractors and quantify attractor reachability. Here, we propose two algorithms providing probability estimates of attractor reachability in asynchronous dynamics. The first algorithm, named Firefront, exhaustively explores the state space from an initial state, and provides quasi-exact evaluations of the reachability probabilities of model attractors. The algorithm progresses in breadth, propagating the probabilities of each encountered state to its successors. Second, Avatar is an adapted Monte Carlo approach, better suited for models with large and intertwined transient and terminal cycles. Avatar iteratively explores the state space by randomly selecting trajectories and by using these random walks to estimate the likelihood of reaching an attractor. Unlike Monte Carlo simulations, Avatar is equipped to avoid getting trapped in transient cycles and to identify cyclic attractors. Firefront and Avatar are validated and compared to related methods, using as test cases logical models of synthetic and biological networks. Both algorithms are implemented as new functionalities of GINsim 3.0, a well-established software tool for logical modeling, providing executable GUI, Java API, and scripting facilities.

| S-EPMC6137237 | biostudies-literature

Predictability of real temporal networks.

Project description:Links in most real networks often change over time. Such temporality of links encodes the ordering and causality of interactions between nodes and has a profound effect on network dynamics and function. Empirical evidence has shown that the temporal nature of links in many real-world networks is not random. Nonetheless, it is challenging to predict temporal link patterns while considering the entanglement between topological and temporal link patterns. Here, we propose an entropy-rate-based framework, based on combined topological-temporal regularities, for quantifying the predictability of any temporal network. We apply our framework on various model networks, demonstrating that it indeed captures the intrinsic topological-temporal regularities whereas previous methods considered only temporal aspects. We also apply our framework on 18 real networks of different types and determine their predictability. Interestingly, we find that, for most real temporal networks, despite the greater complexity of predictability brought by the increase in dimension, the combined topological-temporal predictability is higher than the temporal predictability. Our results demonstrate the necessity for incorporating both temporal and topological aspects of networks in order to improve predictions of dynamical processes.

| S-EPMC8288877 | biostudies-literature

Verified Certification of Reachability Checking for Timed Automata

Project description:Prior research has shown how to construct a mechanically verified model checker for timed automata, a popular formalism for modeling real-time systems. In this paper, we shift the focus from verified model checking to certifying unreachability. This allows us to benefit from better approximation operations for symbolic states, and reduces execution time by exploring fewer states and by exploiting parallelism. Moreover, this gives us the ability to audit results of unverified model checkers that implement a range of further optimizations, including certificate compression. The resulting tool is evaluated on a set of standard benchmarks to demonstrate its practicality, using a new unverified model checker implementation in Standard ML to construct the certificates.

| S-EPMC7439749 | biostudies-literature

Temporal efficiency evaluation and small-worldness characterization in temporal networks.

Project description:Numerous real-world systems can be modeled as networks. To date, most network studies have been conducted assuming stationary network characteristics. Many systems, however, undergo topological changes over time. Temporal networks, which incorporate time into conventional network models, are therefore more accurate representations of such dynamic systems. Here, we introduce a novel generalized analytical framework for temporal networks, which enables 1) robust evaluation of the efficiency of temporal information exchange using two new network metrics and 2) quantitative inspection of the temporal small-worldness. Specifically, we define new robust temporal network efficiency measures by incorporating the time dependency of temporal distance. We propose a temporal regular network model, and based on this plus the redefined temporal efficiency metrics and widely used temporal random network models, we introduce a quantitative approach for identifying temporal small-world architectures (featuring high temporal network efficiency both globally and locally). In addition, within this framework, we can uncover network-specific dynamic structures. Applications to brain networks, international trade networks, and social networks reveal prominent temporal small-world properties with distinct dynamic network structures. We believe that the framework can provide further insight into dynamic changes in the network topology of various real-world systems and significantly promote research on temporal networks.

| S-EPMC5041081 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data