1
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Begga A, Escolano Ruiz F, Lozano MÁ. Edge-Centric Embeddings of Digraphs: Properties and Stability Under Sparsification. ENTROPY (BASEL, SWITZERLAND) 2025; 27:304. [PMID: 40149228 PMCID: PMC11941605 DOI: 10.3390/e27030304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 02/28/2025] [Accepted: 03/11/2025] [Indexed: 03/29/2025]
Abstract
In this paper, we define and characterize the embedding of edges and higher-order entities in directed graphs (digraphs) and relate these embeddings to those of nodes. Our edge-centric approach consists of the following: (a) Embedding line digraphs (or their iterated versions); (b) Exploiting the rank properties of these embeddings to show that edge/path similarity can be posed as a linear combination of node similarities; (c) Solving scalability issues through digraph sparsification; (d) Evaluating the performance of these embeddings for classification and clustering. We commence by identifying the motive behind the need for edge-centric approaches. Then we proceed to introduce all the elements of the approach, and finally, we validate it. Our edge-centric embedding entails a top-down mining of links, instead of inferring them from the similarities of node embeddings. This analysis is key to discovering inter-subgraph links that hold the whole graph connected, i.e., central edges. Using directed graphs (digraphs) allows us to cluster edge-like hubs and authorities. In addition, since directed edges inherit their labels from destination (origin) nodes, their embedding provides a proxy representation for node classification and clustering as well. This representation is obtained by embedding the line digraph of the original one. The line digraph provides nice formal properties with respect to the original graph; in particular, it produces more entropic latent spaces. With these properties at hand, we can relate edge embeddings to node embeddings. The main contribution of this paper is to set and prove the linearity theorem, which poses each element of the transition matrix for an edge embedding as a linear combination of the elements of the transition matrix for the node embedding. As a result, the rank preservation property explains why embedding the line digraph and using the labels of the destination nodes provides better classification and clustering performances than embedding the nodes of the original graph. In other words, we do not only facilitate edge mining but enforce node classification and clustering. However, computing the line digraph is challenging, and a sparsification strategy is implemented for the sake of scalability. Our experimental results show that the line digraph representation of the sparsified input graph is quite stable as we increase the sparsification level, and also that it outperforms the original (node-centric) representation. For the sake of simplicity, our theorem relies on node2vec-like (factorization) embeddings. However, we also include several experiments showing how line digraphs may improve the performance of Graph Neural Networks (GNNs), also following the principle of maximum entropy.
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Affiliation(s)
- Ahmed Begga
- Department of Computer Science and Artificial Intelligence, University of Alicante, 03690 Alicante, Spain; (F.E.R.); (M.Á.L.)
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2
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Li A, Sun X, Zhu S, Zhu F. Random walks on scale-free flowers with stochastic resetting. CHAOS (WOODBURY, N.Y.) 2025; 35:013124. [PMID: 39792698 DOI: 10.1063/5.0242793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 12/06/2024] [Indexed: 01/12/2025]
Abstract
This study explores the impact of stochastic resetting on the random walk dynamics within scale-free (u,v)-flowers. Utilizing the generating function technique, we develop a recursive relationship for the generating function of the first passage time and establish a connection between the mean first passage time with and without resetting. Our investigation spans multiple scenarios, with the random walker starting from various positions and aiming to reach different target nodes, allowing us to identify the optimal resetting probability that minimizes the mean first passage time for each case. We demonstrate that stochastic resetting significantly improves search efficiency, especially in larger networks. These findings underscore the effectiveness of stochastic resetting as a strategy for optimizing search algorithms in complex networks, offering valuable applications in domains such as biological transport, data networks, and search processes where rapid and efficient exploration is vital.
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Affiliation(s)
- Anlin Li
- School of Mathematical Science, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaohan Sun
- School of Mathematical Science, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shaoxiang Zhu
- School of Mathematical Science, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Feng Zhu
- School of Mathematical Science, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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3
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Zhou D, Patankar S, Lydon-Staley DM, Zurn P, Gerlach M, Bassett DS. Architectural styles of curiosity in global Wikipedia mobile app readership. SCIENCE ADVANCES 2024; 10:eadn3268. [PMID: 39454011 PMCID: PMC11506172 DOI: 10.1126/sciadv.adn3268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 09/23/2024] [Indexed: 10/27/2024]
Abstract
Intrinsically motivated information seeking is an expression of curiosity believed to be central to human nature. However, most curiosity research relies on small, Western convenience samples. Here, we analyze a naturalistic population of 482,760 readers using Wikipedia's mobile app in 14 languages from 50 countries or territories. By measuring the structure of knowledge networks constructed by readers weaving a thread through articles in Wikipedia, we replicate two styles of curiosity previously identified in laboratory studies: the nomadic "busybody" and the targeted "hunter." Further, we find evidence for another style-the "dancer"-which was previously predicted by a historico-philosophical examination of texts over two millennia and is characterized by creative modes of knowledge production. We identify associations, globally, between the structure of knowledge networks and population-level indicators of spatial navigation, education, mood, well-being, and inequality. These results advance our understanding of Wikipedia's global readership and demonstrate how cultural and geographical properties of the digital environment relate to different styles of curiosity.
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Affiliation(s)
- Dale Zhou
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Shubhankar Patankar
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - David M. Lydon-Staley
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
- Annenberg School of Communication, University of Pennsylvania, 3620 Walnut St, Philadelphia, PA 19104, USA
| | - Perry Zurn
- Department of Philosophy, American University, 4400 Massachusetts Ave NW, Washington, DC 20016, USA
| | - Martin Gerlach
- Wikimedia Foundation, 1 Montgomery St, San Francisco, CA 94104, USA
| | - Dani S. Bassett
- Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
- Department of Electrical and Systems Engineering, University of Pennsylvania, 200 S 33rd St, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, 3400 Spruce St, Philadelphia, PA 19104, USA
- Department of Psychiatry, University of Pennsylvania, 800 Spruce St, Philadelphia, PA 19104, USA
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
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4
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Di Gaetano L, Carugno G, Battiston F, Coghi F. Dynamical Fluctuations of Random Walks in Higher-Order Networks. PHYSICAL REVIEW LETTERS 2024; 133:107401. [PMID: 39303236 DOI: 10.1103/physrevlett.133.107401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/04/2024] [Accepted: 07/26/2024] [Indexed: 09/22/2024]
Abstract
Although higher-order interactions are known to affect the typical state of dynamical processes giving rise to new collective behavior, how they drive the emergence of rare events and fluctuations is still an open problem. We investigate how fluctuations of a dynamical quantity of a random walk exploring a higher-order network arise over time. In the quenched case, where the hypergraph structure is fixed, through large deviation theory we show that the appearance of rare events is hampered in nodes with many higher-order interactions, and promoted elsewhere. Dynamical fluctuations are further boosted in an annealed scenario, where both the diffusion process and higher-order interactions evolve in time. Here, extreme fluctuations generated by optimal higher-order configurations can be predicted in the limit of a saddle-point approximation. Our study lays the groundwork for a wide and general theory of fluctuations and rare events in higher-order networks.
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Affiliation(s)
| | | | | | - Francesco Coghi
- Nordita, KTH Royal Institute of Technology and Stockholm University, Hannes Alfvéns väg 12, SEa-106 91 Stockholm, Sweden
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5
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Traversa P, de Arruda GF, Moreno Y. From unbiased to maximal-entropy random walks on hypergraphs. Phys Rev E 2024; 109:054309. [PMID: 38907415 DOI: 10.1103/physreve.109.054309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/11/2024] [Indexed: 06/24/2024]
Abstract
Random walks have been intensively studied on regular and complex networks, which are used to represent pairwise interactions. Nonetheless, recent works have demonstrated that many real-world processes are better captured by higher-order relationships, which are naturally represented by hypergraphs. Here we study random walks on hypergraphs. Due to the higher-order nature of these mathematical objects, one can define more than one type of walks. In particular, we study the unbiased and the maximal entropy random walk on hypergraphs with two types of steps, emphasizing their similarities and differences. We characterize these dynamic processes by examining their stationary distributions and associated hitting times. To illustrate our findings, we present a toy example and conduct extensive analyses of artificial and real hypergraphs, providing insights into both their structural and dynamical properties. We hope that our findings motivate further research extending the analysis to different classes of random walks as well as to practical applications.
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Affiliation(s)
- Pietro Traversa
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
| | | | - Yamir Moreno
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain
- Department of Theoretical Physics, University of Zaragoza, 50018 Zaragoza, Spain
- CENTAI Institute, 10138 Turin, Italy
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6
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Zelenkovski K, Sandev T, Metzler R, Kocarev L, Basnarkov L. Random Walks on Networks with Centrality-Based Stochastic Resetting. ENTROPY (BASEL, SWITZERLAND) 2023; 25:293. [PMID: 36832659 PMCID: PMC9955709 DOI: 10.3390/e25020293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
We introduce a refined way to diffusely explore complex networks with stochastic resetting where the resetting site is derived from node centrality measures. This approach differs from previous ones, since it not only allows the random walker with a certain probability to jump from the current node to a deliberately chosen resetting node, rather it enables the walker to jump to the node that can reach all other nodes faster. Following this strategy, we consider the resetting site to be the geometric center, the node that minimizes the average travel time to all the other nodes. Using the established Markov chain theory, we calculate the Global Mean First Passage Time (GMFPT) to determine the search performance of the random walk with resetting for different resetting node candidates individually. Furthermore, we compare which nodes are better resetting node sites by comparing the GMFPT for each node. We study this approach for different topologies of generic and real-life networks. We show that, for directed networks extracted for real-life relationships, this centrality focused resetting can improve the search to a greater extent than for the generated undirected networks. This resetting to the center advocated here can minimize the average travel time to all other nodes in real networks as well. We also present a relationship between the longest shortest path (the diameter), the average node degree and the GMFPT when the starting node is the center. We show that, for undirected scale-free networks, stochastic resetting is effective only for networks that are extremely sparse with tree-like structures as they have larger diameters and smaller average node degrees. For directed networks, the resetting is beneficial even for networks that have loops. The numerical results are confirmed by analytic solutions. Our study demonstrates that the proposed random walk approach with resetting based on centrality measures reduces the memoryless search time for targets in the examined network topologies.
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Affiliation(s)
- Kiril Zelenkovski
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
| | - Trifce Sandev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, Arhimedova 3, 1000 Skopje, Macedonia
- Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam, Germany
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam, Germany
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Ljupco Kocarev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, 1000 Skopje, Macedonia
| | - Lasko Basnarkov
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, 1000 Skopje, Macedonia
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7
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Wang Y, Chen H. Entropy rate of random walks on complex networks under stochastic resetting. Phys Rev E 2022; 106:054137. [PMID: 36559349 DOI: 10.1103/physreve.106.054137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
Abstract
Stochastic processes under resetting at random times have attracted a lot of attention in recent years and served as illustrations of nontrivial and interesting static and dynamic features of stochastic dynamics. In this paper, we aim to address how the entropy rate is affected by stochastic resetting in discrete-time Markovian processes, and we explore nontrivial effects of the resetting in the mixing properties of a stochastic process. In particular, we consider resetting random walks (RRWs) with a single resetting node on three different types of networks: degree-regular random networks, a finite-size Cayley tree, and a Barabási-Albert (BA) scale-free network, and we compute the entropy rate as a function of the resetting probability γ. Interestingly, for the first two types of networks, the entropy rate shows a nonmonotonic dependence on γ. There exists an optimal value of γ at which the entropy rate reaches a maximum. Such a maximum is larger than that of maximal-entropy random walks (MREWs) and standard random walks (SRWs) on the same topology, while for the BA network the entropy rate of RRWs either shows a unique maximum or decreases monotonically with γ, depending upon the choice of the resetting node. When the maximum entropy rate of RRWs exists, it can be higher or lower than that of MREWs or SRWs. Our study reveals a nontrivial effect of stochastic resetting on nonequilibrium statistical physics.
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Affiliation(s)
- Yating Wang
- School of Physics and Optoelectronic Engineering, Anhui University, Hefei 230601, China
| | - Hanshuang Chen
- School of Physics and Optoelectronic Engineering, Anhui University, Hefei 230601, China
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8
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Falcó C. From random walks on networks to nonlinear diffusion. Phys Rev E 2022; 106:054103. [PMID: 36559369 DOI: 10.1103/physreve.106.054103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great impact on the collective movement of the group. For this reason, many models in mathematical biology have incorporated crowding effects and managed to understand their implications. Here, we build on a previously developed framework for random walks on networks to show that in the continuum limit, the underlying stochastic process can be identified with a diffusion partial differential equation. The diffusion coefficient of the emerging equation is, in general, density dependent, and can be directly related to the transition probabilities of the random walk. Moreover, the relaxation time of the stochastic process is directly linked to the diffusion coefficient and also to the network structure, as it usually happens in the case of linear diffusion. As a specific example, we study the equivalent of a porous-medium-type equation on networks, which shows similar properties to its continuum equivalent. For this equation, self-similar solutions on a lattice and on homogeneous trees can be found, showing finite speed of propagation in contrast to commonly used linear diffusion equations. These findings also provide insights into reaction-diffusion systems with general diffusion operators, which have appeared recently in some applications.
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Affiliation(s)
- Carles Falcó
- Mathematical Institute, University of Oxford, OX2 6GG Oxford, United Kingdom
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9
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Benigni B, Gallotti R, De Domenico M. Potential-driven random walks on interconnected systems. Phys Rev E 2021; 104:024120. [PMID: 34525567 DOI: 10.1103/physreve.104.024120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022]
Abstract
Interconnected systems have to route information to function properly: At the lowest scale neural cells exchange electrochemical signals to communicate, while at larger scales animals and humans move between distinct spatial patches and machines exchange information via the Internet through communication protocols. Nontrivial patterns emerge from the analysis of information flows, which are not captured either by broadcasting, such as in random walks, or by geodesic routing, such as shortest paths. In fact, alternative models between those extreme protocols are still eluding us. Here we propose a class of stochastic processes, based on biased random walks, where agents are driven by a physical potential pervading the underlying network topology. By considering a generalized Coulomb dependence on the distance on destination(s), we show that it is possible to interpolate between random walk and geodesic routing in a simple and effective way. We demonstrate that it is not possible to find a one-size-fit-all solution to efficient navigation and that network heterogeneity or modularity has measurable effects. We illustrate how our framework can describe the movements of animals and humans, capturing with a stylized model some measurable features of the latter. From a methodological perspective, our potential-driven random walks open the doors to a broad spectrum of analytical tools, ranging from random-walk centralities to geometry induced by potential-driven network processes.
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Affiliation(s)
- Barbara Benigni
- Department of Information Engineering and Computer Science, University of Trento, Via Sommarive, 9, 38123 Povo, Trento, Italy and CoMuNe Lab, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo, Trento, Italy
| | - Riccardo Gallotti
- CoMuNe Lab, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo, Trento, Italy
| | - Manlio De Domenico
- CoMuNe Lab, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo, Trento, Italy
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10
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Riascos AP, Sanders DP. Mean encounter times for multiple random walkers on networks. Phys Rev E 2021; 103:042312. [PMID: 34005853 DOI: 10.1103/physreve.103.042312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/23/2021] [Indexed: 01/18/2023]
Abstract
We introduce a general approach for the study of the collective dynamics of noninteracting random walkers on connected networks. We analyze the movement of R independent (Markovian) walkers, each defined by its own transition matrix. By using the eigenvalues and eigenvectors of the R independent transition matrices, we deduce analytical expressions for the collective stationary distribution and the average number of steps needed by the random walkers to start in a particular configuration and reach specific nodes the first time (mean first-passage times), as well as global times that characterize the global activity. We apply these results to the study of mean first-encounter times for local and nonlocal random walk strategies on different types of networks, with both synchronous and asynchronous motion.
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Affiliation(s)
- Alejandro P Riascos
- Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - David P Sanders
- Departamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México 04510, Mexico and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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11
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Smerlak M. Neutral quasispecies evolution and the maximal entropy random walk. SCIENCE ADVANCES 2021; 7:7/16/eabb2376. [PMID: 33853768 PMCID: PMC8046360 DOI: 10.1126/sciadv.abb2376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
Even if they have no impact on phenotype, neutral mutations are not equivalent in the eyes of evolution: A robust neutral variant-one which remains functional after further mutations-is more likely to spread in a large, diverse population than a fragile one. Quasispecies theory shows that the equilibrium frequency of a genotype is proportional to its eigenvector centrality in the neutral network. This paper explores the link between the selection for mutational robustness and the navigability of neutral networks. I show that sequences of neutral mutations follow a "maximal entropy random walk," a canonical Markov chain on graphs with nonlocal, nondiffusive dynamics. I revisit M. Smith's word-game model of evolution in this light, finding that the likelihood of certain sequences of substitutions can decrease with the population size. These counterintuitive results underscore the fertility of the interface between evolutionary dynamics, information theory, and physics.
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Affiliation(s)
- M Smerlak
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
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12
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Skardal PS. Quasiperiodic dynamics and a Neimark-Sacker bifurcation in nonlinear random walks on complex networks. Phys Rev E 2020; 101:012307. [PMID: 32069530 DOI: 10.1103/physreve.101.012307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Indexed: 06/10/2023]
Abstract
We study the dynamics of nonlinear random walks on complex networks. In particular, we investigate the role and effect of directed network topologies on long-term dynamics. While a period-doubling bifurcation to alternating patterns occurs at a critical bias parameter value, we find that some directed structures give rise to a different kind of bifurcation that gives rise to quasiperiodic dynamics. This does not occur for all directed network structure, but only when the network structure is sufficiently directed. We find that the onset of quasiperiodic dynamics is the result of a Neimark-Sacker bifurcation, where a pair of complex-conjugate eigenvalues of the system Jacobian pass through the unit circle, destabilizing the stationary distribution with high-dimensional rotations. We investigate the nature of these bifurcations, study the onset of quasiperiodic dynamics as network structure is tuned to be more directed, and present an analytically tractable case of a four-neighbor ring.
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13
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Zhang D, Zhang Y, Niu Q, Qiu X. Mining concise patterns on graph-connected itemsets. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2018.03.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Dawson DE, Farthing TS, Sanderson MW, Lanzas C. Transmission on empirical dynamic contact networks is influenced by data processing decisions. Epidemics 2019; 26:32-42. [PMID: 30528207 PMCID: PMC6613374 DOI: 10.1016/j.epidem.2018.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 11/02/2022] Open
Abstract
Dynamic contact data can be used to inform disease transmission models, providing insight into the dynamics of infectious diseases. Such data often requires extensive processing for use in models or analysis. Therefore, processing decisions can potentially influence the topology of the contact network and the simulated disease transmission dynamics on the network. In this study, we examine how four processing decisions, including temporal sampling window (TSW), spatial threshold of contact (SpTh), minimum contact duration (MCD), and temporal aggregation (daily or hourly) influence the information content of contact data (indicated by changes in entropy) as well as disease transmission model dynamics. We found that changes made to information content by processing decisions translated to significant impacts to the transmission dynamics of disease models using the contact data. In particular, we found that SpTh had the largest independent influence on information content, and that some output metrics (R0, time to peak infection) were more sensitive to changes in information than others (epidemic extent). These findings suggest that insights gained from transmission modeling using dynamic contact data can be influenced by processing decisions alone, emphasizing the need to carefully consideration them prior to using contact-based models to conduct analyses, compare different datasets, or inform policy decisions.
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Affiliation(s)
- Daniel E Dawson
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA.
| | - Trevor S Farthing
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | - Michael W Sanderson
- Center for Outcomes Research and Epidemiology, Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Cristina Lanzas
- Department of Pathobiology and Population Health, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
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15
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Coghi F, Morand J, Touchette H. Large deviations of random walks on random graphs. Phys Rev E 2019; 99:022137. [PMID: 30934304 DOI: 10.1103/physreve.99.022137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Indexed: 06/09/2023]
Abstract
We study the rare fluctuations or large deviations of time-integrated functionals or observables of an unbiased random walk evolving on Erdös-Rényi random graphs, and construct a modified, biased random walk that explains how these fluctuations arise in the long-time limit. Two observables are considered: the sum of the degrees visited by the random walk and the sum of their logarithm, related to the trajectory entropy. The modified random walk is used for both quantities to explain how sudden changes in degree fluctuations, similar to dynamical phase transitions, are related to localization transitions. For the second quantity, we also establish links between the large deviations of the trajectory entropy and the maximum entropy random walk.
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Affiliation(s)
- Francesco Coghi
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jules Morand
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande C8, 1749-016 Lisboa, Portugal
| | - Hugo Touchette
- Department of Mathematical Sciences, Stellenbosch University, Stellenbosch 7600, South Africa
- National Institute for Theoretical Physics (NITheP), Stellenbosch 7600, South Africa
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16
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Fraiberger SP, Sinatra R, Resch M, Riedl C, Barabási AL. Quantifying reputation and success in art. Science 2018; 362:825-829. [PMID: 30409804 DOI: 10.1126/science.aau7224] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/09/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022]
Abstract
In areas of human activity where performance is difficult to quantify in an objective fashion, reputation and networks of influence play a key role in determining access to resources and rewards. To understand the role of these factors, we reconstructed the exhibition history of half a million artists, mapping out the coexhibition network that captures the movement of art between institutions. Centrality within this network captured institutional prestige, allowing us to explore the career trajectory of individual artists in terms of access to coveted institutions. Early access to prestigious central institutions offered life-long access to high-prestige venues and reduced dropout rate. By contrast, starting at the network periphery resulted in a high dropout rate, limiting access to central institutions. A Markov model predicts the career trajectory of individual artists and documents the strong path and history dependence of valuation in art.
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Affiliation(s)
- Samuel P Fraiberger
- Network Science Institute, Northeastern University, Boston, MA, USA.,Harvard Institute for Quantitative Social Sciences, Cambridge, MA, USA
| | - Roberta Sinatra
- Network Science Institute, Northeastern University, Boston, MA, USA.,Department of Mathematics and its Applications and Center for Network Science, Central European University, Budapest, Hungary.,Complexity Science Hub, Vienna, Austria.,ISI Foundation, Turin, Italy
| | - Magnus Resch
- University of St Gallen, St. Gallen, Switzerland.,Zagreb School of Economics and Management, Zagreb, Croatia
| | - Christoph Riedl
- Network Science Institute, Northeastern University, Boston, MA, USA. .,Harvard Institute for Quantitative Social Sciences, Cambridge, MA, USA
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA, USA. .,Department of Mathematics and its Applications and Center for Network Science, Central European University, Budapest, Hungary.,Division of Network Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Network and Data Science, Central European University, Budapest, Hungary
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17
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Niu YW, Liu H, Wang GH, Yan GY. Maximal entropy random walk on heterogenous network for MIRNA-disease Association prediction. Math Biosci 2018; 306:1-9. [PMID: 30336146 DOI: 10.1016/j.mbs.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 12/24/2022]
Abstract
The last few decades have verified the vital roles of microRNAs in the development of human diseases and witnessed the increasing interest in the prediction of potential disease-miRNA associations. Owning to the open access of many miRNA-related databases, up until recently, kinds of feasible in silico models have been proposed. In this work, we developed a computational model of Maximal Entropy Random Walk on heterogenous network for MiRNA-disease Association prediction (MERWMDA). MERWMDA integrated known disease-miRNA association, pair-wise functional relation of miRNAs and pair-wise semantic relation of diseases into a heterogenous network comprised of disease and miRNA nodes full of information. As a kind of widely-applied biased walk process with more randomness, MERW was then implemented on the heterogenous network to reveal potential disease-miRNA associations. Cross validation was further performed to evaluate the performance of MERWMDA. As a result, MERWMDA obtained AUCs of 0.8966 and 0.8491 respectively in the aspect of global and local leave-one-out cross validation. What' more, three different case study strategies on four human complex diseases were conducted to comprehensively assess the quality of the model. Specifically, one kind of case study on Esophageal cancer and Prostate cancer were conducted based on HMDD v2.0 database. 94% and 88% out of the top 50 ranked miRNAs were confirmed by recent literature, respectively. To simulate new disease without known related miRNAs, Lung cancer (confirmed ratio 94%) associated miRNAs were removed for case study. Lymphoma (verified ratio 88%) was adopted to assess the prediction robustness of MERWMDA based on HMDD v1.0 database. We anticipated that MERWMDA could offer valuable candidates for in vitro biomedical experiments in future.
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Affiliation(s)
- Ya-Wei Niu
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Hua Liu
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Guang-Hui Wang
- School of Mathematics, Shandong University, Jinan 250100, China.
| | - Gui-Ying Yan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
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18
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Ferrer-i-Cancho R, Vitevitch MS. The origins of Zipf's meaning-frequency law. J Assoc Inf Sci Technol 2018. [DOI: 10.1002/asi.24057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ramon Ferrer-i-Cancho
- Complexity and Quantitative Linguistics Lab. LARCA Research Group, Departament de Ciències de la Computació; Universitat Politècnica de Catalunya, Campus Nord, Edifici Omega, Jordi Girona Salgado 1-3; 08034 Barcelona Catalonia Spain
| | - Michael S. Vitevitch
- Spoken Language Laboratory, Department of Psychology; University of Kansas, 1415 Jayhawk Blvd.; Lawrence KS 66045 USA
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19
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Asllani M, Carletti T, Di Patti F, Fanelli D, Piazza F. Hopping in the Crowd to Unveil Network Topology. PHYSICAL REVIEW LETTERS 2018; 120:158301. [PMID: 29756854 DOI: 10.1103/physrevlett.120.158301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Indexed: 05/14/2023]
Abstract
We introduce a nonlinear operator to model diffusion on a complex undirected network under crowded conditions. We show that the asymptotic distribution of diffusing agents is a nonlinear function of the nodes' degree and saturates to a constant value for sufficiently large connectivities, at variance with standard diffusion in the absence of excluded-volume effects. Building on this observation, we define and solve an inverse problem, aimed at reconstructing the a priori unknown connectivity distribution. The method gathers all the necessary information by repeating a limited number of independent measurements of the asymptotic density at a single node, which can be chosen randomly. The technique is successfully tested against both synthetic and real data and is also shown to estimate with great accuracy the total number of nodes.
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Affiliation(s)
- Malbor Asllani
- naXys, Namur Institute for Complex Systems, University of Namur, rempart de la Vierge 8, B 5000 Namur, Belgium
| | - Timoteo Carletti
- naXys, Namur Institute for Complex Systems, University of Namur, rempart de la Vierge 8, B 5000 Namur, Belgium
| | - Francesca Di Patti
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Via Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy
| | - Duccio Fanelli
- Dipartimento di Fisica e Astronomia, Università di Firenze, INFN and CSDC, Via Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy
| | - Francesco Piazza
- University of Orléans and Centre de Biophysique Moléculaire (CBM), CNRS UPR 4301, Rue C. Sadron, 45071 Orléans, France
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20
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Nicosia V, Skardal PS, Arenas A, Latora V. Collective Phenomena Emerging from the Interactions between Dynamical Processes in Multiplex Networks. PHYSICAL REVIEW LETTERS 2017; 118:138302. [PMID: 28409987 DOI: 10.1103/physrevlett.118.138302] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Indexed: 05/28/2023]
Abstract
We introduce a framework to intertwine dynamical processes of different nature, each with its own distinct network topology, using a multilayer network approach. As an example of collective phenomena emerging from the interactions of multiple dynamical processes, we study a model where neural dynamics and nutrient transport are bidirectionally coupled in such a way that the allocation of the transport process at one layer depends on the degree of synchronization at the other layer, and vice versa. We show numerically, and we prove analytically, that the multilayer coupling induces a spontaneous explosive synchronization and a heterogeneous distribution of allocations, otherwise not present in the two systems considered separately. Our framework can find application to other cases where two or more dynamical processes such as synchronization, opinion formation, information diffusion, or disease spreading, are interacting with each other.
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Affiliation(s)
- Vincenzo Nicosia
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | | | - Alex Arenas
- Department d'Enginyeria Informática i Matemátiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Vito Latora
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
- Dipartimento di Fisica ed Astronomia, Università di Catania and INFN, I-95123 Catania, Italy
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21
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Weng T, Small M, Zhang J, Hui P. Lévy Walk Navigation in Complex Networks: A Distinct Relation between Optimal Transport Exponent and Network Dimension. Sci Rep 2015; 5:17309. [PMID: 26601780 PMCID: PMC4658568 DOI: 10.1038/srep17309] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/28/2015] [Indexed: 11/13/2022] Open
Abstract
We investigate, for the first time, navigation on networks with a Lévy
walk strategy such that the step probability scales as
pij ~ dij–α,
where dij is the Manhattan distance between nodes i
and j, and α is the transport exponent. We find that the
optimal transport exponent αopt of such a
diffusion process is determined by the fractal dimension df
of the underlying network. Specially, we theoretically derive the relation
αopt = df + 2
for synthetic networks and we demonstrate that this holds for a number of real-world
networks. Interestingly, the relationship we derive is different from previous
results for Kleinberg navigation without or with a cost constraint, where the
optimal conditions are
α = df
and
α = df + 1,
respectively. Our results uncover another general mechanism for how network
dimension can precisely govern the efficient diffusion behavior on diverse
networks.
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Affiliation(s)
- Tongfeng Weng
- HKUST-DT System and Media Laboratory, Hong Kong University of Science and Technology, HongKong
| | - Michael Small
- The University of Western Australia, Crawley, WA 6009, Australia
| | - Jie Zhang
- Centre for Computational Systems Biology, Fudan University, China
| | - Pan Hui
- HKUST-DT System and Media Laboratory, Hong Kong University of Science and Technology, HongKong
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22
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Sayama H, Sinatra R. Social diffusion and global drift on networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:032809. [PMID: 25871159 DOI: 10.1103/physreve.91.032809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 06/04/2023]
Abstract
We study a mathematical model of social diffusion on a symmetric weighted network where individual nodes' states gradually assimilate to local social norms made by their neighbors' average states. Unlike physical diffusion, this process is not state conservational and thus the global state of the network (i.e., sum of node states) will drift. The asymptotic average node state will be the average of initial node states weighted by their strengths. Here we show that, while the global state is not conserved in this process, the inner product of strength and state vectors is conserved instead, and perfect positive correlation between node states and local averages of their self-neighbor strength ratios always results in upward (or at least neutral) global drift. We also show that the strength assortativity negatively affects the speed of homogenization. Based on these findings, we propose an adaptive link weight adjustment method to achieve the highest upward global drift by increasing the strength-state correlation. The effectiveness of the method was confirmed through numerical simulations and implications for real-world social applications are discussed.
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Affiliation(s)
- Hiroki Sayama
- Collective Dynamics of Complex Systems Research Group, Binghamton University, Binghamton, New York 13902, USA
- Center for Complex Network Research and Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Roberta Sinatra
- Center for Complex Network Research and Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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23
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Memory in network flows and its effects on spreading dynamics and community detection. Nat Commun 2014; 5:4630. [PMID: 25109694 DOI: 10.1038/ncomms5630] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/09/2014] [Indexed: 01/06/2023] Open
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24
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Peng X, Zhang Z. Maximal entropy random walk improves efficiency of trapping in dendrimers. J Chem Phys 2014; 140:234104. [DOI: 10.1063/1.4883335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Lin Y, Zhang Z. Mean first-passage time for maximal-entropy random walks in complex networks. Sci Rep 2014; 4:5365. [PMID: 24947015 PMCID: PMC4064359 DOI: 10.1038/srep05365] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/27/2014] [Indexed: 11/09/2022] Open
Abstract
We perform an in-depth study for mean first-passage time (MFPT)--a primary quantity for random walks with numerous applications--of maximal-entropy random walks (MERW) performed in complex networks. For MERW in a general network, we derive an explicit expression of MFPT in terms of the eigenvalues and eigenvectors of the adjacency matrix associated with the network. For MERW in uncorrelated networks, we also provide a theoretical formula of MFPT at the mean-field level, based on which we further evaluate the dominant scalings of MFPT to different targets for MERW in uncorrelated scale-free networks, and compare the results with those corresponding to traditional unbiased random walks (TURW). We show that the MFPT to a hub node is much lower for MERW than for TURW. However, when the destination is a node with the least degree or a uniformly chosen node, the MFPT is higher for MERW than for TURW. Since MFPT to a uniformly chosen node measures real efficiency of search in networks, our work provides insight into general searching process in complex networks.
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Affiliation(s)
- Yuan Lin
- School of Computer Science, Fudan University, Shanghai 200433, China
- Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Zhongzhi Zhang
- School of Computer Science, Fudan University, Shanghai 200433, China
- Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China
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26
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Abstract
Assessing the navigability of interconnected networks (transporting information, people, or goods) under eventual random failures is of utmost importance to design and protect critical infrastructures. Random walks are a good proxy to determine this navigability, specifically the coverage time of random walks, which is a measure of the dynamical functionality of the network. Here, we introduce the theoretical tools required to describe random walks in interconnected networks accounting for structure and dynamics inherent to real systems. We develop an analytical approach for the covering time of random walks in interconnected networks and compare it with extensive Monte Carlo simulations. Generally speaking, interconnected networks are more resilient to random failures than their individual layers per se, and we are able to quantify this effect. As an application--which we illustrate by considering the public transport of London--we show how the efficiency in exploring the multiplex critically depends on layers' topology, interconnection strengths, and walk strategy. Our findings are corroborated by data-driven simulations, where the empirical distribution of check-ins and checks-out is considered and passengers travel along fastest paths in a network affected by real disruptions. These findings are fundamental for further development of searching and navigability strategies in real interconnected systems.
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27
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Hoßfeld T, Burger V, Hinrichsen H, Hirth M, Tran-Gia P. On the computation of entropy production in stationary social networks. SOCIAL NETWORK ANALYSIS AND MINING 2014. [DOI: 10.1007/s13278-014-0190-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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29
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Bonaventura M, Nicosia V, Latora V. Characteristic times of biased random walks on complex networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:012803. [PMID: 24580277 DOI: 10.1103/physreve.89.012803] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 06/03/2023]
Abstract
We consider degree-biased random walkers whose probability to move from a node to one of its neighbors of degree k is proportional to k(α), where α is a tuning parameter. We study both numerically and analytically three types of characteristic times, namely (i) the time the walker needs to come back to the starting node, (ii) the time it takes to visit a given node for the first time, and (iii) the time it takes to visit all the nodes of the network. We consider a large data set of real-world networks and we show that the value of α which minimizes the three characteristic times differs from the value α(min)=-1 analytically found for uncorrelated networks in the mean-field approximation. In addition to this, we found that assortative networks have preferentially a value of α(min) in the range [-1,-0.5], while disassortative networks have α(min) in the range [-0.5,0]. We derive an analytical relation between the degree correlation exponent ν and the optimal bias value α(min), which works well for real-world assortative networks. When only local information is available, degree-biased random walks can guarantee smaller characteristic times than the classical unbiased random walks by means of an appropriate tuning of the motion bias.
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Affiliation(s)
- Moreno Bonaventura
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom and School of Business and Management, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Vincenzo Nicosia
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Vito Latora
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom and Dipartimento di Fisica e Astronomia, Università di Catania and INFN, 95123 Catania, Italy
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30
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Lin Y, Zhang Z. Random walks in weighted networks with a perfect trap: an application of Laplacian spectra. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062140. [PMID: 23848660 DOI: 10.1103/physreve.87.062140] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Indexed: 06/02/2023]
Abstract
Trapping processes constitute a primary problem of random walks, which characterize various other dynamical processes taking place on networks. Most previous works focused on the case of binary networks, while there is much less related research about weighted networks. In this paper, we propose a general framework for the trapping problem on a weighted network with a perfect trap fixed at an arbitrary node. By utilizing the spectral graph theory, we provide an exact formula for mean first-passage time (MFPT) from one node to another, based on which we deduce an explicit expression for average trapping time (ATT) in terms of the eigenvalues and eigenvectors of the Laplacian matrix associated with the weighted graph, where ATT is the average of MFPTs to the trap over all source nodes. We then further derive a sharp lower bound for the ATT in terms of only the local information of the trap node, which can be obtained in some graphs. Moreover, we deduce the ATT when the trap is distributed uniformly in the whole network. Our results show that network weights play a significant role in the trapping process. To apply our framework, we use the obtained formulas to study random walks on two specific networks: trapping in weighted uncorrelated networks with a deep trap, the weights of which are characterized by a parameter, and Lévy random walks in a connected binary network with a trap distributed uniformly, which can be looked on as random walks on a weighted network. For weighted uncorrelated networks we show that the ATT to any target node depends on the weight parameter, that is, the ATT to any node can change drastically by modifying the parameter, a phenomenon that is in contrast to that for trapping in binary networks. For Lévy random walks in any connected network, by using their equivalence to random walks on a weighted complete network, we obtain the optimal exponent characterizing Lévy random walks, which have the minimal average of ATTs taken over all target nodes.
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Affiliation(s)
- Yuan Lin
- School of Computer Science, Fudan University, Shanghai 200433, China
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31
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Noise enhances information transfer in hierarchical networks. Sci Rep 2013; 3:1223. [PMID: 23390574 PMCID: PMC3565226 DOI: 10.1038/srep01223] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 01/11/2013] [Indexed: 11/21/2022] Open
Abstract
We study the influence of noise on information transmission in the form of packages shipped between nodes of hierarchical networks. Numerical simulations are performed for artificial tree networks, scale-free Ravasz-Barabási networks as well for a real network formed by email addresses of former Enron employees. Two types of noise are considered. One is related to packet dynamics and is responsible for a random part of packets paths. The second one originates from random changes in initial network topology. We find that the information transfer can be enhanced by the noise. The system possesses optimal performance when both kinds of noise are tuned to specific values, this corresponds to the Stochastic Resonance phenomenon. There is a non-trivial synergy present for both noisy components. We found also that hierarchical networks built of nodes of various degrees are more efficient in information transfer than trees with a fixed branching factor.
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32
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Ochab JK. Maximal-entropy random walk unifies centrality measures. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:066109. [PMID: 23368006 DOI: 10.1103/physreve.86.066109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Indexed: 06/01/2023]
Abstract
This paper compares a number of centrality measures and several (dis-)similarity matrices with which they can be defined. These matrices, which are used among others in community detection methods, represent quantities connected to enumeration of paths on a graph and to random walks. Relationships between some of these matrices are derived in the paper. These relationships are inherited by the centrality measures. They include measures based on the principal eigenvector of the adjacency matrix, path enumeration, as well as on the stationary state, stochastic matrix, or mean first-passage times of a random walk. As the random walk defining the centrality measure can be arbitrarily chosen, we pay particular attention to the maximal-entropy random walk, which serves as a very distinct alternative to the ordinary (diffusive) random walk used in network analysis. The various importance measures, defined both with the use of ordinary random walk and the maximal-entropy random walk, are compared numerically on a set of benchmark graphs with varying mixing parameter and are grouped with the use of the agglomerative clustering technique. It is shown that centrality measures defined with the two different random walks cluster into two separate groups. In particular, the group of centrality measures defined by the maximal-entropy random walk does not cluster with any other measures on change of graphs' parameters, and members of this group produce mutually closer results than members of the group defined by the ordinary random walk.
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Affiliation(s)
- J K Ochab
- Marian Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, PL-30-059 Kraków, Poland.
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33
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Antonioni A, Tomassini M. Degree correlations in random geometric graphs. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:037101. [PMID: 23031054 DOI: 10.1103/physreve.86.037101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 08/21/2012] [Indexed: 06/01/2023]
Abstract
Spatially embedded networks are important in several disciplines. The prototypical spatial network we assume is the Random Geometric Graph, of which many properties are known. Here we present new results for the two-point degree correlation function in terms of the clustering coefficient of the graphs for two-dimensional space in particular, with extensions to arbitrary finite dimensions.
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Affiliation(s)
- A Antonioni
- Information Systems Department, Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland.
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34
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Capitán JA, Borge-Holthoefer J, Gómez S, Martinez-Romo J, Araujo L, Cuesta JA, Arenas A. Local-based semantic navigation on a networked representation of information. PLoS One 2012; 7:e43694. [PMID: 22937081 PMCID: PMC3427177 DOI: 10.1371/journal.pone.0043694] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/23/2012] [Indexed: 11/18/2022] Open
Abstract
The size and complexity of actual networked systems hinders the access to a global knowledge of their structure. This fact pushes the problem of navigation to suboptimal solutions, one of them being the extraction of a coherent map of the topology on which navigation takes place. In this paper, we present a Markov chain based algorithm to tag networked terms according only to their topological features. The resulting tagging is used to compute similarity between terms, providing a map of the networked information. This map supports local-based navigation techniques driven by similarity. We compare the efficiency of the resulting paths according to their length compared to that of the shortest path. Additionally we claim that the path steps towards the destination are semantically coherent. To illustrate the algorithm performance we provide some results from the Simple English Wikipedia, which amounts to several thousand of pages. The simplest greedy strategy yields over an 80% of average success rate. Furthermore, the resulting content-coherent paths most often have a cost between one- and threefold compared to shortest-path lengths.
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Affiliation(s)
- José A Capitán
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, Tarragona, Spain.
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35
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Perotti JI, Billoni OV. Smart random walkers: the cost of knowing the path. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:011120. [PMID: 23005381 DOI: 10.1103/physreve.86.011120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 05/30/2012] [Indexed: 06/01/2023]
Abstract
In this work we study the problem of targeting signals in networks using entropy information measurements to quantify the cost of targeting. We introduce a penalization rule that imposes a restriction on the long paths and therefore focuses the signal to the target. By this scheme we go continuously from fully random walkers to walkers biased to the target. We found that the optimal degree of penalization is mainly determined by the topology of the network. By analyzing several examples, we have found that a small amount of penalization reduces considerably the typical walk length, and from this we conclude that a network can be efficiently navigated with restricted information.
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Affiliation(s)
- Juan I Perotti
- Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba and Instituto de Física Enrique Gaviola, IFEG-CONICET, Ciudad Universitaria, 5000 Córdoba, Argentina.
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36
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Kishore V, Santhanam MS, Amritkar RE. Extreme events and event size fluctuations in biased random walks on networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:056120. [PMID: 23004834 DOI: 10.1103/physreve.85.056120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Indexed: 06/01/2023]
Abstract
Random walk on discrete lattice models is important to understand various types of transport processes. The extreme events, defined as exceedences of the flux of walkers above a prescribed threshold, have been studied recently in the context of complex networks. This was motivated by the occurrence of rare events such as traffic jams, floods, and power blackouts which take place on networks. In this work, we study extreme events in a generalized random walk model in which the walk is preferentially biased by the network topology. The walkers preferentially choose to hop toward the hubs or small degree nodes. In this setting, we show that extremely large fluctuations in event sizes are possible on small degree nodes when the walkers are biased toward the hubs. In particular, we obtain the distribution of event sizes on the network. Further, the probability for the occurrence of extreme events on any node in the network depends on its "generalized strength," a measure of the ability of a node to attract walkers. The generalized strength is a function of the degree of the node and that of its nearest neighbors. We obtain analytical and simulation results for the probability of occurrence of extreme events on the nodes of a network using a generalized random walk model. The result reveals that the nodes with a larger value of generalized strength, on average, display lower probability for the occurrence of extreme events compared to the nodes with lower values of generalized strength.
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Ochab JK, Burda Z. Exact solution for statics and dynamics of maximal-entropy random walks on Cayley trees. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021145. [PMID: 22463190 DOI: 10.1103/physreve.85.021145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Indexed: 05/31/2023]
Abstract
We provide analytical solutions for two types of random walk: generic random walk (GRW) and maximal-entropy random walk (MERW) on a Cayley tree with arbitrary branching number, root degree, and number of generations. For MERW, we obtain the stationary state given by the squared elements of the eigenvector associated with the largest eigenvalue λ(0) of the adjacency matrix. We discuss the dynamics, depending on the second largest eigenvalue λ(1), of the probability distribution approaching to the stationary state. We find different scaling of the relaxation time with the system size, which is generically shorter for MERW than for GRW. We also signal that depending on the initial conditions, there are relaxations associated with lower eigenvalues which are induced by symmetries of the tree. In general, we find that there are three regimes of a tree structure resulting in different statics and dynamics of MERW; these correspond to strongly, critically, and weakly branched roots.
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Affiliation(s)
- J K Ochab
- Marian Smoluchowski Institute of Physics and Mark Kac Complex Systems Research Center, Jagiellonian University, Reymonta 4, PL-30-059 Kraków, Poland.
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Zhao K, Halu A, Severini S, Bianconi G. Entropy rate of nonequilibrium growing networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:066113. [PMID: 22304161 DOI: 10.1103/physreve.84.066113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Indexed: 05/31/2023]
Abstract
New entropy measures have been recently introduced for the quantification of the complexity of networks. Most of these entropy measures apply to static networks or to dynamical processes defined on static complex networks. In this paper we define the entropy rate of growing network models. This entropy rate quantifies how many labeled networks are typically generated by the growing network models. We analytically evaluate the difference between the entropy rate of growing tree network models and the entropy of tree networks that have the same asymptotic degree distribution. We find that the growing networks with linear preferential attachment generated by dynamical models are exponentially less than the static networks with the same degree distribution for a large variety of relevant growing network models. We study the entropy rate for growing network models showing structural phase transitions including models with nonlinear preferential attachment. Finally, we bring numerical evidence that the entropy rate above and below the structural phase transitions follows a different scaling with the network size.
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Affiliation(s)
- Kun Zhao
- Department of Physics, Northeastern University, Boston, 02115 Massachusetts, USA
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Lambiotte R, Sinatra R, Delvenne JC, Evans TS, Barahona M, Latora V. Flow graphs: interweaving dynamics and structure. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:017102. [PMID: 21867345 DOI: 10.1103/physreve.84.017102] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Indexed: 05/31/2023]
Abstract
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential because different dynamical processes may be affected very differently by network topology. A full characterization of such systems thus requires a formalization that encompasses both aspects simultaneously, rather than relying only on the topological adjacency matrix. To achieve this, we introduce the concept of flow graphs, namely weighted networks where dynamical flows are embedded into the link weights. Flow graphs provide an integrated representation of the structure and dynamics of the system, which can then be analyzed with standard tools from network theory. Conversely, a structural network feature of our choice can also be used as the basis for the construction of a flow graph that will then encompass a dynamics biased by such a feature. We illustrate the ideas by focusing on the mathematical properties of generic linear processes on complex networks that can be represented as biased random walks and their dual consensus dynamics, and show how our framework improves our understanding of these processes.
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Affiliation(s)
- R Lambiotte
- Department of Mathematics, Imperial College London, London, United Kingdom
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