arXiv subjects

Petter Holme

Publications and source records attributed to Petter Holme.

At least 109 records · Page 6Linked to original sources

arXiv2011

Temporal Networks

A great variety of systems in nature, society and technology -- from the web of sexual contacts to the Internet, from the nervous system to power grids -- can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via email, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks.

nlin.AO↗

arXiv2011

Cooperation, structure and hierarchy in multiadaptive games

Game-theoretical models where the rules of the game and the interaction structure both coevolves with the game dynamics -- multiadaptive games -- capture very flexible situations where cooperation among selfish agents can emerge. In this work, we will discuss a multiadaptive model presented in a recent Letter [Phys. Rev. Lett. 106, 028702 (2011)], and generalizations of it. The model captures a non-equilibrium situation where social unrest increases the incentive to cooperate and, simultaneously, agents are partly free to influence with whom they interact. First, we investigate the details of how the feedback from the behavior of agents determines the emergence of cooperation and hierarchical contact structures. We also study the stability of the system to different types of noise, and find that different regions of parameter space show very different response. Some types of noise can destroy an all-cooperator state. If, on the other hand, hubs are stable, then so is the all-C state. Finally, we investigate the dependence of the ratio between the timescales of strategy updates and the evolution of the interaction structure. We find that a comparatively fast strategy dynamics is a prerequisite for the emergence of cooperation.

q-bio.PE↗

arXiv2011

Pathlength scaling in graphs with incomplete navigational information

The graph-navigability problem concerns how one can find as short paths as possible between a pair of vertices, given an incomplete picture of a graph. We study the navigability of graphs where the vertices are tagged by a number (between 1 and the total number of vertices) in a way to aid navigation. This information is too little to ensure errorfree navigation but enough, as we will show, for the agents to do significantly better than a random walk. In our setup, given a graph, we first assign information to the vertices that agents can utilize for their navigation. To evaluate the navigation, we calculate the average distance traveled over random pairs of source and target and different graph realizations. We show that this type of embedding can be made quite efficiently; the more information is embedded, the more efficient it gets. We also investigate the embedded navigational information in a standard graph layout algorithm and find that although this information does not make algorithms as efficient as the above-mentioned schemes, it is significantly helpful.

physics.soc-ph↗

arXiv2011

Onion structure and network robustness

In a recent work [Proc. Natl. Acad. Sci. USA 108, 3838 (2011)], Schneider et al. proposed a new measure for network robustness and investigated optimal networks with respect to this quantity. For networks with a power-law degree distribution, the optimized networks have an onion structure-high-degree vertices forming a core with radially decreasing degrees and an over-representation of edges within the same radial layer. In this paper we relate the onion structure to graphs with good expander properties (another characterization of robust network) and argue that networks of skewed degree distributions with large spectral gaps (and thus good expander properties) are typically onion structured. Furthermore, we propose a generative algorithm producing synthetic scale-free networks with onion structure, circumventing the optimization procedure of Schneider et al. We validate the robustness of our generated networks against malicious attacks and random removals.

physics.soc-ph↗

arXiv2011

Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

q-bio.MN↗

arXiv2011

Emergent Hierarchical Structures in Multiadaptive Games

We investigate a game-theoretic model of a social system where both the rules of the game and the interaction structure are shaped by the behavior of the agents. We call this type of model, with several types of feedback couplings from the behavior of the agents to their environment, a multiadaptive game. Our model has a complex behavior with several regimes of different dynamic behavior accompanied by different network topological properties. Some of these regimes are characterized by heterogeneous, hierarchical interaction networks, where cooperation and network topology coemerge from the dynamics.

q-bio.PE↗

arXiv2010

Metabolic robustness and network modularity: A model study

[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic robustness. In this paper we measure the relation between network modularity and several aspects of robustness directly in a model system of metabolism. [Methodology/Principal Findings] By using a model for generating chemical reaction systems where one can tune the network modularity, we find that robustness increases with modularity for changes in the concentrations of metabolites, whereas it decreases with changes in the expression of enzymes. The same modularity scaling is true for the speed of relaxation after the perturbations. [Conclusions/Significance] Modularity is not a general principle for making metabolism either more or less robust; this question needs to be addressed specifically for different types of perturbations of the system.

q-bio.MN↗

arXiv2010

Exploiting temporal network structures of human interaction to effectively immunize populations

If we can lower the number of people needed to vaccinate for a community to be immune against contagious diseases, we can save resources and life. A key to reach such a lower threshold of immunization is to find and vaccinate people who, through their behavior, are more likely to become infected and effective to spread the disease than the average. Fortunately, the very behavior that makes these people important to vaccinate can help us finding them. People you have met recently are more likely to be socially active and thus central in the contact pattern, and important to vaccinate. We propose two immunization schemes exploiting temporal contact patterns. Both of these rely only on obtainable, local information and could implemented in practice. We show that these schemes outperform benchmark protocols in four real data sets under various epidemic scenarios. The data sets are dynamic, which enables us to make more realistic evaluations than other studies - we use information only about the past to perform the vaccination and the future to simulate disease outbreaks. We also use models to elucidate the mechanisms behind how the temporal structures make our immunization protocols efficient.

q-bio.PE↗

arXiv2010

Emergence of collective memories

We understand the dynamics of the world around us as by associating pairs of events, where one event has some influence on the other. These pairs of events can be aggregated into a web of memories representing our understanding of an episode of history. The events and the associations between them need not be directly experienced-they can also be acquired by communication. In this paper we take a network approach to study the dynamics of memories of history. First we investigate the network structure of a data set consisting of reported events by several individuals and how associations connect them. We focus our measurement on degree distributions, degree correlations, cycles (which represent inconsistencies as they would break the time ordering) and community structure. We proceed to model effects of communication using an agent-based model. We investigate the conditions for the memory webs of different individuals to converge to collective memories, how groups where the individuals have similar memories (but different from other groups) can form. Our work outlines how the cognitive representation of memories and social structure can co-evolve as a contagious process. We generate some testable hypotheses including that the number of groups is limited as a function of the total population size.

physics.soc-ph↗

arXiv2010

The network organisation of consumer complaints

Interaction between consumers and companies can create conflict. When a consensus is unreachable there are legal authorities to resolve the case. This letter is a study of data from the Brazilian Department of Justice from which we build a bipartite network of categories of complaints linked to the companies receiving those complaints. We find the complaint categories organised in an hierarchical way where companies only get complaints of lower degree if they already got complaints of higher degree. The fraction of resolved complaints for a company appears to be nearly independent on the equity of the company but is positively correlated with the total number of complaints received. We construct feature vectors based on the edge-weight - the weight of an edge represents the times complaints of a category have been filed against that company - and use these vectors to study the similarity between the categories of complaints. From this analysis, we obtain trees mapping the hierarchical organisation of the complaints. We also apply principal component analysis to the set of feature vectors concluding that a reduction of the dimensionality of these from 8827 to 27 gives an optimal hierarchical representation.

physics.soc-ph↗

arXiv2010

Simulated epidemics in an empirical spatiotemporal network of 50,185 sexual contacts

We study implications of the dynamical and spatial contact structure between Brazilian escorts and sex-buyers for the spreading of sexually transmitted infections (STI). Despite a highly skewed degree distribution diseases spreading in this contact structure have rather well-defined epidemic thresholds. Temporal effects create a broad distribution of outbreak sizes even if the transmission probability is taken to the hypothetical value of 100%. Temporal correlations speed up outbreaks, especially in the early phase, compared to randomized contact structures. The time-ordering and the network topology, on the other hand, slow down the epidemics. Studying compartmental models we show that the contact structure can probably not support the spread of HIV, not even if individuals were sexually active during the acute infection. We investigate hypothetical means of containing an outbreak and find that travel restrictions are about as efficient as removal of the vertices of highest degree. In general, the type of commercial sex we study seems not like a major factor in STI epidemics.

physics.soc-ph↗

arXiv2010

Local interaction scale controls the existence of a non-trivial optimal critical mass in opinion spreading

We study a model of opinion formation where the collective decision of group is said to happen if the fraction of agents having the most common opinion exceeds a threshold value, a \textit{critical mass}. We find that there exists a unique, non-trivial critical mass giving the most efficient convergence to consensus. In addition, we observe that for small critical masses, the characteristic time scale for the relaxation to consensus splits into two. The shorter time scale corresponds to a direct relaxation and the longer can be explained by the existence of intermediate, metastable states similar to those found in [P.\ Chen and S.\ Redner, Phys.\ Rev.\ E \textbf{71}, 036101 (2005)]. This longer time-scale is dependent on the precise condition for consensus---with a modification of the condition it can go away.

physics.soc-ph↗

arXiv2010

Information dynamics shape the networks of Internet-mediated prostitution

Like many other social phenomena, prostitution is increasingly coordinated over the Internet. The online behavior affects the offline activity; the reverse is also true. We investigated the reported sexual contacts between 6,624 anonymous escorts and 10,106 sex-buyers extracted from an online community from its beginning and six years on. These sexual encounters were also graded and categorized (in terms of the type of sexual activities performed) by the buyers. From the temporal, bipartite network of posts, we found a full feedback loop in which high grades on previous posts affect the future commercial success of the sex-worker, and vice versa. We also found a peculiar growth pattern in which the turnover of community members and sex workers causes a sublinear preferential attachment. There is, moreover, a strong geographic influence on network structure-the network is geographically clustered but still close to connected, the contacts consistent with the inverse-square law observed in trading patterns. We also found that the number of sellers scales sublinearly with city size, so this type of prostitution does not, comparatively speaking, benefit much from an increasing concentration of people.

physics.soc-ph↗

arXiv2009

Majority-vote model on hyperbolic lattices

We study the critical properties of a non-equilibrium statistical model, the majority-vote model, on heptagonal and dual heptagonal lattices. Such lattices have the special feature that they only can be embedded in negatively curved surfaces. We find, by using Monte Carlo simulations and finite-size analysis, that the critical exponents $1/ν$, $β/ν$ and $γ/ν$ are different from those of the majority-vote model on regular lattices with periodic boundary condition, which belongs to the same universality class as the equilibrium Ising model. The exponents are also from those of the Ising model on a hyperbolic lattice. We argue that the disagreement is caused by the effective dimensionality of the hyperbolic lattices. By comparative studies, we find that the critical exponents of the majority-vote model on hyperbolic lattices satisfy the hyperscaling relation $2β/ν+γ/ν=D_{\mathrm{eff}}$, where $D_{\mathrm{eff}}$ is an effective dimension of the lattice. We also investigate the effect of boundary nodes on the ordering process of the model.

cond-mat.stat-mech↗

arXiv2009

Modeling scientific-citation patterns and other triangle-rich acyclic networks

We propose a model of the evolution of the networks of scientific citations. The model takes an out-degree distribution (distribution of number of citations) and two parameters as input. The parameters capture the two main ingredients of the model, the aging of the relevance of papers and the formation of triangles when new papers cite old. We compare our model with three network structural quantities of an empirical citation network. We find that an unique point in parameter space optimizing the match between the real and model data for all quantities. The optimal parameter values suggest that the impact of scientific papers, at least in the empirical data set we model is proportional to the inverse of the number of papers since they were published.

physics.soc-ph↗

arXiv2009

Diversity of reproduction time scale promotes cooperation in spatial prisoner's dilemma games

We study an evolutionary spatial prisoner's dilemma game where the fitness of the players is determined by both the payoffs from the current interaction and their history. We consider the situation where the selection timescale is slower than the interaction timescale. This is done by implementing probabilistic reproduction on an individual level. We observe that both too fast and too slow reproduction rates hamper the emergence of cooperation. In other words, there exists an intermediate selection timescale that maximizes cooperation. Another factor we find to promote cooperation is a diversity of reproduction timescales.

physics.soc-ph↗

arXiv2009

Three faces of metabolites: Pathways, localizations and network positions

To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed description of the organization of metabolism. In this study, we investigate the relative organization of three categorizations of metabolites -- pathways, subcellular localizations and network clusters, by block-model techniques borrowed from social-network studies and further characterize the categories from topological point of view. The picture of the metabolism we obtain is that of peripheral modules, characterized both by being dense network clusters and localized to organelles, connected by a central, highly connected core. Pathways typically run through several network clusters and localizations, connecting them laterally. The strong overlap between organelles and network clusters suggest that these are natural "modules" -- relatively independent sub-systems. The different categorizations divide the core metabolism differently suggesting that this, if possible, should be not be treated as a module on par with the organelles. Although overlapping more than chance, none of the pathways correspond very closely to a network cluster or localization. This, we believe, highlights the benefits of different orthogonal classifications and future experimental categorizations based on simple principles.

q-bio.MN↗

arXiv2009

Effects of strategy-migration direction and noise in the evolutionary spatial prisoner's dilemma

Spatial games are crucial for understanding patterns of cooperation in nature (and to some extent society). They are known to be more sensitive to local symmetries than e.g. spin models. This paper concerns the evolution of the prisoner's dilemma game on regular lattices with three different types of neighborhoods -- the von Neumann-, Moore-, and kagome types. We investigate two kinds of dynamics for the players to update their strategies (that can be unconditional cooperator or defector). Depending on the payoff difference, an individual can adopt the strategy of a random neighbor (a voter-model-like dynamics, VMLD), or impose its strategy on a random neighbor, i.e., invasion-like dynamics (IPLD). In particular, we focus on the effects of noise, in combination with the strategy dynamics, on the evolution of cooperation. We find that VMLD, compared to IPLD, better supports the spreading and sustaining of cooperation. We see that noise has nontrivial effects on the evolution of cooperation: maximum cooperation density can be realized either at a medium noise level, in the limit of zero noise, or in both these regions. The temptation to defect and the local interaction structure determine the outcome. Especially, in the low noise limit, the local interaction plays a crucial role in determining the fate of cooperators. We elucidate these both by numerical simulations and mean-field cluster approximation methods.

physics.soc-ph↗