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In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…

Populations and Evolution · Quantitative Biology 2025-11-17 Niels Holtgrefe , Katharina T. Huber , Leo van Iersel , Mark Jones , Vincent Moulton

The function of a real network depends not only on the reliability of its own components, but is affected also by the simultaneous operation of other real networks coupled with it. Robustness of systems composed of interdependent network…

Physics and Society · Physics 2015-07-10 Filippo Radicchi

In many real network systems, nodes usually cooperate with each other and form groups, in order to enhance their robustness to risks. This motivates us to study a new type of percolation, group percolation, in interdependent networks under…

Physics and Society · Physics 2018-03-21 Zexun Wang , Dong Zhou , Yanqing Hu

We study the effects of nonreciprocity and network structure on percolation. To this end, we investigate nonreciprocal random networks - directed networks for which the probability of a link occurring from node i to node j differs from the…

Statistical Mechanics · Physics 2025-10-07 Chanania Steinbock

In complex networks a common task is to identify the most important or "central" nodes. There are several definitions, often called centrality measures, which often lead to different results. Here we study extensively correlations between…

Physics and Society · Physics 2009-11-13 Magnus Jungsbluth , Bernd Burghardt , Alexander K. Hartmann

In recent years, there have been intense research efforts to develop efficient methods for probabilistic inference in probabilistic influence diagrams or belief networks. Many people have concluded that the best methods are those based on…

Artificial Intelligence · Computer Science 2013-04-05 Ross D. Shachter , Stig K. Andersen , Kim-Leng Poh

Using parallels with the quantum scattering theory, developed for processes in nuclear and mesoscopic physics and quantum chaos, we construct a reduced Google matrix $G_R$ which describes the properties and interactions of a certain subset…

Physics and Society · Physics 2016-02-09 K. M. Frahm , D. L. Shepelyansky

Many empirical networks display an inherent tendency to cluster, i.e. to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs,…

Physics and Society · Physics 2009-11-13 Giorgio Fagiolo

During the last two decades, we easilly see that the World Wide Web's link structure is modeled as the directed graph. In this paper, we will model the World Wide Web's link structure as the directed hypergraph. Moreover, we will develop…

Social and Information Networks · Computer Science 2022-09-07 Loc Tran , Tho Quan , An Mai

We introduce a new class of auto-encoders for directed graphs, motivated by a direct extension of the Weisfeiler-Leman algorithm to pairs of node labels. The proposed model learns pairs of interpretable latent representations for the nodes…

Machine Learning · Computer Science 2022-02-28 Georgios Kollias , Vasileios Kalantzis , Tsuyoshi Idé , Aurélie Lozano , Naoki Abe

Efficient techniques to navigate networks with local information are fundamental to sample large-scale online social systems and to retrieve resources in peer-to-peer systems. Biased random walks, i.e. walks whose motion is biased on…

Physics and Society · Physics 2016-06-29 Federico Battiston , Vincenzo Nicosia , Vito Latora

Many complex networks in nature have directed links, a property that affects the network's navigability and large-scale topology. Here we study the percolation properties of such directed scale-free networks with correlated in- and…

Disordered Systems and Neural Networks · Physics 2009-11-07 N. Schwartz , R. Cohen , D. ben-Avraham , A. -L. Barabasi , S. Havlin

We investigate the heterogeneity of outcomes of repeated instances of percolation experiments in complex networks using a message passing approach to evaluate heterogeneous, node dependent probabilities of belonging to the giant or…

Statistical Mechanics · Physics 2020-09-15 Reimer Kuehn , Jort van Mourik

Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and…

Biological Physics · Physics 2010-10-05 Robin Palotai , Peter Csermely

In this paper new results on personalized PageRank are shown. We consider directed graphs that may contain dangling nodes. The main result presented gives an analytical characterization of all the possible values of the personalized…

Discrete Mathematics · Computer Science 2012-07-13 Esther Garcia , Francisco Pedroche , Miguel Romance

Great part of the interest in complex networks has been motivated by the presence of structured, frequently non-uniform, connectivity. Because diverse connectivity patterns tend to result in distinct network dynamics, and also because they…

Disordered Systems and Neural Networks · Physics 2009-11-13 Paulino R. Villas Boas , Francisco A. Rodrigues , Gonzalo Travieso , Luciano da F. Costa

The robustness of complex networks against node failure and malicious attack has been of interest for decades, while most of the research has focused on random attack or hub-targeted attack. In many real-world scenarios, however, attacks…

Physics and Society · Physics 2015-06-23 Shuai Shao , Xuqing Huang , H Eugene Stanley , Shlomo Havlin

The arrangement of network nodes in hyperbolic spaces has become a widely studied problem, motivated by numerous results suggesting the existence of hidden metric spaces behind the structure of complex networks. Although several methods…

Physics and Society · Physics 2023-02-06 Bianka Kovács , Gergely Palla

We present Regularized Linear Embedding (RLE), a novel method that projects a collection of linked documents (e.g. citation network) into a pretrained word embedding space. In addition to the textual content, we leverage a matrix of…

Information Retrieval · Computer Science 2020-01-17 Antoine Gourru , Adrien Guille , Julien Velcin , Julien Jacques

Grouping the nodes of a graph into clusters is a standard technique for studying networks. We study a problem where we are given a directed network and are asked to partition the graph into a sequence of coherent groups. We assume that…

Social and Information Networks · Computer Science 2025-12-08 Iiro Kumpulainen , Nikolaj Tatti