arXiv subjects

Reka Albert

Publications and source records attributed to Reka Albert.

At least 19 recordsLinked to original sources

arXiv2026

Percolation and Criticality in Hyperuniform Networks

Hyperuniform many-particle systems, which encompass crystals, quasicrystals and certain exotic disordered systems, exhibit an anomalous suppression of density fluctuations on macroscopic length scales relative to those of conventional disordered systems. Here we investigate the percolation behaviors of disordered stealthy hyperuniform systems (SHU), a subclass of hyperuniform configurations for which the structure factor vanishes for a finite range of wavevectors near the origin, with the degree of stealthiness controlled via a parameter $\chi$. We construct Delaunay triangulation networks derived from SHU configurations with varying $\chi$ as well as Poisson point configurations for the purpose of comparison. We investigate a non-uniform bond percolation process, in which bond occupation probabilities decrease with the Euclidean distance between the connected vertices. In this setting, percolation is induced by varying a tuning parameter $z$. We estimate the percolation thresholds $z_c$ and critical exponents of the networks via finite-size scaling and the Newman-Ziff algorithm. We find that SHU networks exhibit lower percolation thresholds than Poisson networks. Notably, the percolation threshold of SHU networks decreases with the stealthiness parameter $\chi$, indicating that global connectivity emerges more readily as short-range order increases. Moreover, we show that SHU networks with large $\chi$ belong to the same universality class as lattices, while Poisson and low-$\chi$ systems show deviations. We relate the shift in critical exponents to the degree of suppression of density fluctuations in the point configurations. Our work extends previous studies on transport properties of SHU systems from continuum two-phase media to networks. These results open new avenues for optimizing the resilience of statistically homogeneous disordered networks.

cond-mat.stat-mech↗

arXiv2025

Finding Influential Cores via Normalized Ricci Flows in Directed and Undirected Hypergraphs with Applications

Many biological and social systems are naturally represented as edge-weighted directed or undirected hypergraphs since they exhibit group interactions involving three or more system units as opposed to pairwise interactions that can be incorporated in graph-theoretic representations. However, finding influential cores in hypergraphs is still not as extensively studied as their graph-theoretic counter-parts. To this end, we develop and implement a hypergraph-curvature guided discrete time diffusion process with suitable topological surgeries and edge-weight re-normalization procedures for both undirected and directed weighted hypergraphs to find influential cores. We successfully apply our framework for directed hypergraphs to seven metabolic hypergraphs and our framework for undirected hypergraphs to two social (co-authorship) hypergraphs to find influential cores, thereby demonstrating the practical feasibility of our approach. In addition, we prove a theorem showing that a certain edge weight re-normalization procedure in a prior research work for Ricci flows for edge-weighted graphs has the undesirable outcome of modifying the edge-weights to negative numbers, thereby rendering the procedure impossible to use. To the best of our knowledge, this seems to be one of the first articles that formulates algorithmic approaches for finding core(s) of (weighted or unweighted) directed hypergraphs.

cs.SI↗

arXiv2024

Structural Properties of Hyperuniform Networks

Disordered hyperuniform many-particle systems are recently discovered exotic states of matter, characterized by a complete suppression of normalized infinite-wavelength density fluctuations and lack of conventional long-range order. Here, we begin a program to quantify the structural properties of nonhyperuniform and hyperuniform networks. In particular, large two-dimensional (2D) Voronoi networks (graphs) containing approximately 10,000 nodes are created from a variety of different point configurations, including the antihyperuniform HIP, nonhyperuniform Poisson process, nonhyperuniform RSA saturated packing, and both non-stealthy and stealthy hyperuniform point processes. We carry out an extensive study of the Voronoi-cell area distribution of each of the networks through determining multiple metrics that characterize the distribution, including their higher-cumulants. We show that the HIP distribution is far from Gaussian; the Poisson and non-stealthy hyperuniform distributions are Gaussian-like distributions, the RSA and the highest stealthy hyperuniform distributions are also non-Gaussian, with diametrically opposite non-Gaussian behavior of the HIP. Moreover, we compute the Voronoi-area correlation functions $C_{00}(r)$ for the networks [M. A. Klatt and S. Torquato, Phys. Rev. E {\bf 90}, 052120 (2014)]. We show that the correlation functions $C_{00}(r)$ qualitatively distinguish the antihyperuniform, nonhyperuniform and hyperuniform Voronoi networks. We find strong anticorrelations in $C_{00}(r)$ (i.e., negative values) for the hyperuniform networks.

cond-mat.stat-mech↗

arXiv2024

An open problem: Why are motif-avoidant attractors so rare in asynchronous Boolean networks?

Asynchronous Boolean networks are a type of discrete dynamical system in which each variable can take one of two states, and a single variable state is updated in each time step according to pre-selected rules. Boolean networks are popular in systems biology due to their ability to model long-term biological phenotypes within a qualitative, predictive framework. Boolean networks model phenotypes as attractors, which are closely linked to minimal trap spaces (inescapable hypercubes in the system's state space). In biological applications, attractors and minimal trap spaces are typically in one-to-one correspondence. However, this correspondence is not guaranteed: motif-avoidant attractors (MAAs) that lie outside minimal trap spaces are possible. MAAs are rare and (despite recent efforts) poorly understood. Here we summarize the current state of knowledge regarding MAAs and present several novel observations regarding their response to node deletion reductions and linear extensions of edges. We conduct large-scale computational studies on an ensemble of 14,000 models derived from published Boolean models of biological systems, and more than 100 million Random Boolean Networks. Our findings quantify the rarity of MAAs (in particular, we found no MAAs in the biological models), but highlight the role of network reduction in introducing MAAs into the dynamics. We also show that MAAs are fragile to linear extensions: in sparse networks, even a single linear node can disrupt virtually all MAAs. Motivated by this observation, we improve the upper bound on the number of delays needed to disrupt a motif-avoidant attractor.

q-bio.MN↗

arXiv2023

Boolean Networks as Predictive Models of Emergent Biological Behaviors

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory networks to species in ecological networks) and the often-incomplete state of system knowledge (e.g., the unknown values of kinetic parameters for biochemical reactions). Boolean networks have emerged as a powerful tool for modeling these systems. We provide a methodological overview of Boolean network models of biological systems. After a brief introduction, we describe the process of building, analyzing, and validating a Boolean model. We then present the use of the model to make predictions about the system's response to perturbations and about how to control (or at least influence) its behavior. We emphasize the interplay between structural and dynamical properties of Boolean networks and illustrate them in three case studies from disparate levels of biological organization.

q-bio.MN↗

arXiv2018

Introduction to the Special Issue on Approaches to Control Biological and Biologically Inspired Networks

The emerging field at the intersection of quantitative biology, network modeling, and control theory has enjoyed significant progress in recent years. This Special Issue brings together a selection of papers on complementary approaches to observe, identify, and control biological and biologically inspired networks. These approaches advance the state of the art in the field by addressing challenges common to many such networks, including high dimensionality, strong nonlinearity, uncertainty, and limited opportunities for observation and intervention. Because these challenges are not unique to biological systems, it is expected that many of the results presented in these contributions will also find applications in other domains, including physical, social, and technological networks.

q-bio.MN↗

arXiv2014

Topological implications of negative curvature for biological and social networks

Network measures that reflect the most salient properties of complex large-scale networks are in high demand in the network research community. In this paper we adapt a combinatorial measure of negative curvature (also called hyperbolicity) to parameterized finite networks, and show that a variety of biological and social networks are hyperbolic. This hyperbolicity property has strong implications on the higher-order connectivity and other topological properties of these networks. Specifically, we derive and prove bounds on the distance among shortest or approximately shortest paths in hyperbolic networks. We describe two implications of these bounds to cross-talk in biological networks, and to the existence of central, influential neighborhoods in both biological and social networks.

q-bio.MN↗

arXiv2013

Some Perspectives on Network Modeling in Therapeutic Target Prediction

Drug target identification is of significant commercial interest to pharmaceutical companies, and there is a vast amount of research done related to the topic of therapeutic target identification. Interdisciplinary research in this area involves both the biological network community and the graph algorithms community. Key steps of a typical therapeutic target identification problem include synthesizing or inferring the complex network of interactions relevant to the disease, connecting this network to the disease-specific behavior, and predicting which components are key mediators of the behavior. All of these steps involve graph theoretical or graph algorithmic aspects. In this perspective, we provide modelling and algorithmic perspectives for therapeutic target identification and highlight a number of algorithmic advances, which have gotten relatively little attention so far, with the hope of strengthening the ties between these two research communities.

q-bio.MN↗

arXiv2012

Networks in Motion

Feature article on how networks that govern communication, growth, herd behavior, and other key processes in nature and society are becoming increasingly amenable to modeling, forecast, and control.

physics.soc-ph↗

arXiv2011

A New Computationally Efficient Measure of Topological Redundancy of Biological and Social Networks

It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this paper, we introduce a topological redundancy measure for labeled directed networks that is formal, computationally efficient and applicable to a variety of directed networks such as cellular signaling, metabolic and social interaction networks. We demonstrate the computational efficiency of our measure by computing its value and statistical significance on a number of biological and social networks with up to several thousands of nodes and edges. Our results suggest a number of interesting observations: (1) social networks are more redundant that their biological counterparts, (2) transcriptional networks are less redundant than signaling networks, (3) the topological redundancy of the C. elegans metabolic network is largely due to its inclusion of currency metabolites, and (4) the redundancy of signaling networks is highly (negatively) correlated with the monotonicity of their dynamics.

physics.soc-ph↗

arXiv2009

Mapping Complex Networks: Exploring Boolean Modeling of Signal Transduction Pathways

In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield oscillatory activity patterns for both the endoplasmic reticulum resident inositol-1,4,5-trisphosphate receptor (IP3R) and the plasma-membrane resident canonical transient receptor potential channel 3 (TRPC3). These results are specific as randomization of the Boolean operators ablates oscillatory pattern formation. Furthermore, knock-out simulations of the IP3R, TRPC3, and multiple other proteins recapitulate experimentally derived results. The potential of this approach can be observed by its ability to predict previously undescribed cellular phenotypes using in vitro experimental data. Indeed our cellular analysis of the developmental and calcium-regulatory protein, DANGER1a, confirms the counter-intuitive predictions from our Boolean models in two highly relevant cellular models. Based on these results, we theorize that with sufficient legacy knowledge and/or computational biology predictions, Boolean networks provide a robust method for predictive-modeling of any biological system.

q-bio.MN↗

arXiv2007

Near linear time algorithm to detect community structures in large-scale networks

Community detection and analysis is an important methodology for understanding the organization of various real-world networks and has applications in problems as diverse as consensus formation in social communities or the identification of functional modules in biochemical networks. Currently used algorithms that identify the community structures in large-scale real-world networks require a priori information such as the number and sizes of communities or are computationally expensive. In this paper we investigate a simple label propagation algorithm that uses the network structure alone as its guide and requires neither optimization of a pre-defined objective function nor prior information about the communities. In our algorithm every node is initialized with a unique label and at every step each node adopts the label that most of its neighbors currently have. In this iterative process densely connected groups of nodes form a consensus on a unique label to form communities. We validate the algorithm by applying it to networks whose community structures are known. We also demonstrate that the algorithm takes an almost linear time and hence it is computationally less expensive than what was possible so far.

physics.soc-ph↗

arXiv2006

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid (ABA) inhibits stomatal opening and promotes stomatal closure, thereby promoting water conservation. Here we synthesize experimental results into a consistent guard cell signal transduction network for ABA-induced stomatal closure, and develop a dynamic model of this process. Our model captures the regulation of more than forty identified network components, and accords well with previous experimental results at both the pathway and whole cell physiological level. Our analysis reveals the novel predictions that the disruption of membrane depolarizability, anion efflux, actin cytoskeleton reorganization, cytosolic pH increase, the phosphatidic acid pathway or of K+ efflux through slowly activating K+ channels at the plasma membrane lead to the strongest reduction in ABA responsiveness. Initial experimental analysis assessing ABA-induced stomatal closure in the presence of cytosolic pH clamp imposed by the weak acid butyrate is consistent with model prediction. Our method can be readily applied to other biological signaling networks to identify key regulatory components in systems where quantitative information is limited.

q-bio.MN↗

arXiv2006

Using graph concepts to understand the organization of complex systems

Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the topologies of different systems. Attempts to explain these similarities have led to the ongoing development and refinement of network models and graph-theoretical analysis techniques with which to characterize and understand complexity. In this tutorial, we demonstrate through illustrative examples, how network measures and models have contributed to the elucidation of the organization of complex systems.

q-bio.OT↗

arXiv2006

Methods of robustness analysis for Boolean models of gene control networks

As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states (expressed or not expressed) for each gene or protein in the network as well as a high level of synchronization among the various regulatory processes. In this paper, we discuss and compare two possible methods of adapting qualitative models to incorporate the continuous-time character of regulatory networks. The first method consists of introducing asynchronous updates in the Boolean model. In the second method, we adopt the approach introduced by L. Glass to obtain a set of piecewise linear differential equations which continuously describe the states of each gene or protein in the network. We apply both methods to a particular example: a Boolean model of the segment polarity gene network of Drosophila melanogaster. We analyze the dynamics of the model, and provide a theoretical characterization of the model's gene pattern prediction as a function of the timescales of the various processes.

q-bio.MN↗

arXiv2006

Search in weighted complex networks

We study trade-offs presented by local search algorithms in complex networks which are heterogeneous in edge weights and node degree. We show that search based on a network measure, local betweenness centrality (LBC), utilizes the heterogeneity of both node degrees and edge weights to perform the best in scale-free weighted networks. The search based on LBC is universal and performs well in a large class of complex networks.

cond-mat.stat-mech↗

arXiv2006

Effects of Noise on Ecological Invasion Processes: Bacteriophage-mediated Competition in Bacteria

Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in nature. Using an experimental system of bacteriophage-mediated competition in bacterial populations and a deterministic model, we have shown in [Joo et al 2005] that the competitive advantage conferred by the phage depends only on the relative phage pathology and is independent of the initial phage concentration and other phage and host parameters such as the infection-causing contact rate, the spontaneous and infection-induced lysis rates, and the phage burst size. Here we investigate the effects of stochastic fluctuations on bacterial invasion facilitated by bacteriophage, and examine the validity of the deterministic approach. We use both numerical and analytical methods of stochastic processes to identify the source of noise and assess its magnitude. We show that the conclusions obtained from the deterministic model are robust against stochastic fluctuations, yet deviations become prominently large when the phage are more pathological to the invading bacterial strain.

q-bio.PE↗

arXiv2005

Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites

We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network inference and network topological analysis approaches for uncovering biological insights. We determine the gene co-expression network of Bacillus subtilis using Affymetrix GeneChip time series data and show how the inferred network topology can be linked to sequence-level information hard-wired in the organism's genome. We propose a systematic way for determining the correlation threshold at which two genes are assessed to be co-expressed by using the clustering coefficient and we expand the scope of the gene co-expression network by proposing the slope ratio metric as a means for incorporating directionality on the edges. We show through specific examples for B. subtilis that by incorporating expression level information in addition to the temporal expression patterns, we can uncover sequence-level biological insights. In particular, we are able to identify a number of cases where (i) the co-expressed genes are part of a single transcriptional unit or operon and (ii) the inferred directionality arises due to the presence of intra-operon transcription termination sites.

q-bio.MN↗