The availability of data from many different sources and fields of science has made it possible to map out an increasing number of networks of contacts and interactions. However, quantifying how reliable these data are remains an open problem. From Biology to Sociology and Economy, the identification of false and missing positives has become a problem that calls for a solution. In this work we extend one of newest, best performing models -due to Guimera and Sales-Pardo in 2009- to directed networks. The new methodology is able to identify missing and spurious directed interactions, which renders it particularly useful to analyze data reliability in systems like trophic webs, gene regulatory networks, communication patterns and social systems. We also show, using real-world networks, how the method can be employed to help searching for new interactions in an efficient way.
To identify communities in directed networks, we propose a generalized form of modularity in directed networks by introducing a new quantity LinkRank, which can be considered as the PageRank of links. This generalization is consistent with the original modularity in undirected networks and the modularity optimization methods developed for undirected networks can be directly applied to directed networks by optimizing our new modularity. Also, a model network, which can be used as a benchmark network in further community studies, is proposed to verify our method. Our method is supposed to find c…
A search technique locating network modules, i.e., internally densely connected groups of nodes in directed networks is introduced by extending the Clique Percolation Method originally proposed for undirected networks. After giving a suitable definition for directed modules we investigate their percolation transition in the Erdos-Renyi graph both analytically and numerically. We also analyse four real-world directed networks, including Google's own webpages, an email network, a word association graph and the transcriptional regulatory network of the yeast Saccharomyces cerevisiae. The obtained…
A goal in network science is the geometrical characterization of complex networks. In this direction, we (arXiv:1603.00386; J. Stat. Mech. (2016) P063206) have recently introduced the Forman's discretization of Ricci curvature to the realm of undirected networks. Investigation of Forman curvature in diverse model and real-world undirected networks revealed that this measure captures several aspects of the organization of complex undirected networks. However, many important real-world networks are inherently directed in nature, and the Forman curvature for undirected networks is unsuitable for …
We study the dynamics of diffusion processes acting on directed multiplex networks, i.e., coupled multilayer networks where at least one layer consists of a directed graph. We reveal that directed multiplex networks may exhibit a faster diffusion at an intermediate degree of coupling than when the two layers are fully coupled. We use three simple multiplex examples and a real-world topology to illustrate the characteristics of the directed dynamics that give rise to a regime in which an optimal coupling exists. Given the ubiquity of both directed and multilayer networks in nature, our results …
We explore depth measures for flow hierarchy in directed networks. We define two measures -- rooted depth and relative depth, and discuss differences between them. We investigate how the two measures behave in random Erdos-Renyi graphs of different sizes and densities and explain obtained results.
We study the Greek and Roman mythology using the network theory. We construct a directed network by using a dictionary of Greek and Roman mythology in which the nodes represent the entries listed in the dictionary and we make directional links from an entry to other entries that appear in its explanatory part. We find that this network is clearly not a random network but a directed scale-free network. Also measuring the various quantities which characterize the mythology network, we analyze the Greek and Roman mythology and compare it to other real networks.
We study the prisoner's dilemma model with a noisy imitation evolutionary dynamics on directed out-homogeneous and uncorrelated directed random networks. An heterogeneous pair mean-field approximation is presented showing good agreement with Monte Carlo simulations in the limit of weak selection (high noise) where we obtain analytical predictions for the critical temptations. We discuss the phase diagram as a function of temptation, intensity of noise and coordination number of the networks and we consider both the model with and without self-interaction. We compare our results with available …
Modularity is one of the most prominent properties of real-world complex networks. Here, we address the issue of module identification in two important classes of networks: bipartite networks and directed unipartite networks. Nodes in bipartite networks are divided into two non-overlapping sets, and the links must have one end node from each set. Directed unipartite networks only have one type of nodes, but links have an origin and an end. We show that directed unipartite networks can be conviniently represented as bipartite networks for module identification purposes. We report a novel approa…
The trophic levels of nodes in directed networks can reveal their functional properties. Moreover, the trophic coherence of a network, defined in terms of trophic levels, is related to properties such as cycle structure, stability and percolation. The standard definition of trophic levels, however, borrowed from ecology, suffers from drawbacks such as requiring source nodes, which limit its applicability. Here we propose a simple new definition of trophic level that can be computed on any directed network. We demonstrate how the method can identify node function in examples including ecosystem…
We describe the complex global structure of giant components in directed multiplex networks which generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of $m$ different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices, such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, $m=2$, we define a stro…
First principle network models are crucial to make sense of the intricate topology of real complex networks. While modeling efforts have been quite successful in undirected networks, generative models for networks with asymmetric interactions are still not well developed and are unable to reproduce several basic topological properties. This is particularly disconcerting considering that real directed networks are the norm rather than the exception in many natural and human-made complex systems. In this paper, we fill this gap and show how the network geometry paradigm can be elegantly extended…
We propose some kinetic models of wealth exchange and investigate their behavior on directed networks though numerical simulations. We observe that network topology and directedness yields a variety of interesting features in these models. The nature of asset distribution in such directed networks show varied results, the degree of asset inequality increased with the degree of disorder in the graphs.
We study the SIR ("susceptible, infected, removed/recovered") model on directed graphs with heterogeneous transmission probabilities within the message-passing approximation. We characterize the percolation transition, predict cluster size distributions and suggest vaccination strategies. All predictions are compared to numerical simulations on real networks. The percolation threshold which we predict is a rigorous lower bound to the threshold on real networks. For large, locally tree-like networks, our predictions agree very well with the numerical data.
Previous work on undirected small-world networks established the paradigm that locally structured networks tend to have high density of short loops. On the other hand, many realistic networks are directed. Here we investigate the local organization of directed networks and find, surprisingly, that real networks often have very few short loops as compared to random models. We develop a theory and derive conditions for determining if a given network has more or less loops than its randomized counterpart. These findings carry broad implications for structural and dynamical processes sustained by …
The spread of a disease, a computer virus or information is discussed in a directed complex network. We are concerned with a steady state of the spread for the SIR and SIS dynamic models. In a scale-free directed network it is shown that the threshold of its outbreak in both models approaches zero under a high correlation between nodal indegrees and outdegrees.
We present exact analytical results for the distribution of shortest path lengths (DSPL) in a directed network model that grows by node duplication. Such models are useful in the study of the structure and growth dynamics of gene regulatory networks and scientific citation networks. Starting from an initial seed network, at each time step a random node, referred to as a mother node, is selected for duplication. Its daughter node is added to the network and duplicates each outgoing link of the mother node with probability $p$. In addition, the daughter node forms a directed link to the mother n…
Network is a simple but powerful representation of real-world complex systems. Network community analysis has become an invaluable tool to explore and reveal the internal organization of nodes. However, only a few methods were directly designed for community-detection in directed networks. In this article, we introduce the concept of local community structure in directed networks and provide a generic criterion to describe a local community with two properties. We further propose a stochastic optimization algorithm to rapidly detect a local community, which allows for uncovering the directiona…
The configuration model was originally defined for undirected networks and has recently been extended to directed networks. Many empirical networks are however neither undirected nor completely directed, but instead usually partially directed meaning that certain edges are directed and others are undirected. In the paper we define a configuration model for such networks where nodes have in-, out-, and undirected degrees that may be dependent. We prove conditions under which the resulting degree distributions converge to the intended degree distributions. The new model is shown to better approx…
Directed networks such as gene regulation networks and neural networks are connected by arcs (directed links). The nodes in a directed network are often strongly interwound by a huge number of directed cycles, which lead to complex information-processing dynamics in the network and make it highly challenging to infer the intrinsic direction of information flow. In this theoretical paper, based on the principle of minimum-feedback, we explore the node hierarchy of directed networks and distinguish feedforward and feedback arcs. Nearly optimal node hierarchy solutions, which minimize the number …
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, has been recently generalized to weighted, undirected networks. Here we extend the CC to the case of (binary and weighted) directed networks and we compute its expected value for random graphs. We distinguish between CCs that count all directed triangles in the graph (independently of the direction of their edges) and CCs that only consider particular types of…
Coarse graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve the same statistical properties as well as the dynamic behaviors as the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse graining in directed networks lacks of consideration. In this paper, we proposed a Topology-aware Coarse Graining (TCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto …
Based only on the information gathered in a snapshot of a directed network, we present a formal way of checking if the proposed model is correct for the empirical growing network under study. In particular, we show how to estimate the attractiveness, and present an application of the model presented in [arxiv:0704.1847] to the scientific publications network from the ISI dataset.
We study random graph models for directed acyclic graphs, an important class of networks that includes citation networks, food webs, and feed-forward neural networks among others. We propose two specific models, roughly analogous to the fixed edge number and fixed edge probability variants of traditional undirected random graphs. We calculate a number of properties of these models, including particularly the probability of connection between a given pair of vertices, and compare the results with real-world acyclic network data finding that theory and measurements agree surprisingly well -- far…
With recent advances in high-throughput cell biology the amount of cellular biological data has grown drastically. Such data is often modeled as graphs (also called networks) and studying them can lead to new insights into molecule-level organization. A possible way to understand their structure is by analysing the smaller components that constitute them, namely network motifs and graphlets. Graphlets are particularly well suited to compare networks and to assess their level of similarity but are almost always used as small undirected graphs of up to five nodes, thus limiting their applicabili…
We reveal a hierarchical, multilayer organization of finite components -- i.e., tendrils and tubes -- around the giant connected components in directed networks and propose efficient algorithms allowing one to uncover the entire organization of key real-world directed networks, such as the World Wide Web, the neural network of \emph{Caenorhabditis elegans}, and others. With increasing damage, the giant components decrease in size while the number and size of tendril layers increase, enhancing the susceptibility of the networks to damage.
The study of triangles in graphs is a standard tool in network analysis, leading to measures such as the \emph{transitivity}, i.e., the fraction of paths of length $2$ that participate in triangles. Real-world networks are often directed, and it can be difficult to "measure" this network structure meaningfully. We propose a collection of \emph{directed closure values} for measuring triangles in directed graphs in a way that is analogous to transitivity in an undirected graph. Our study of these values reveals much information about directed triadic closure. For instance, we immediately see tha…
We investigate the evolutionary dynamics in directed and/or weighted networks. We study the fixation probability of a mutant in finite populations in stochastic voter-type dynamics for several update rules. The fixation probability is defined as the probability of a newly introduced mutant in a wild-type population taking over the entire population. In contrast to the case of undirected and unweighted networks, the fixation probability of a mutant in directed networks is characterized not only by the degree of the node that the mutant initially invades but by the global structure of networks. …
In the compromise model of continuous opinions proposed by Deffuant et al, the states of two agents in a network can start to converge if they are neighbors and if their opinions are sufficiently close to each other, below a given threshold of tolerance $ε$. In directed networks, if agent i is a neighbor of agent j, j need not be a neighbor of i. In Watts-Strogatz networks we performed simulations to find the averaged number of final opinions $<F>$ and their distribution as a function of $ε$ and of the network structural disorder. In directed networks $<F>$ exhibits a rich structure, being lar…
In this paper, a directed network model for world-wide web is presented. The out-degree of the added nodes are supposed to be scale-free and its mean value is $m$. This model exhibits small-world effect, which means the corresponding networks are of very short average distance and highly large clustering coefficient. More interesting, the in-degree distribution obeys the power-law form with the exponent $γ=2+1/m$, depending on the average out-degree. This finding is supported by the empirical data, which has not been emphasized by the previous studies on directed networks.
This work presents exact expressions for size distributions of weak/multilayer connected components in two generalisations of the configuration model: networks with directed edges and multiplex networks with arbitrary number of layers. The expressions are computable in a polynomial time, and, under some restrictions, are tractable from the asymptotic theory point of view. If first partial moments of the degree distribution are finite, the size distribution for two-layer connected components in multiplex networks exhibits exponent $-\frac{3}{2}$ in the critical regime, whereas the size distribu…
Uncovering factors underlying the network formation is a long-standing challenge for data mining and network analysis. In particular, the microscopic organizing principles of directed networks are less understood than those of undirected networks. This article proposes a hypothesis named potential theory, which assumes that every directed link corresponds to a decrease of a unit potential and subgraphs with definable potential values for all nodes are preferred. Combining the potential theory with the clustering and homophily mechanisms, it is deduced that the Bi-fan structure consisting of 4 …
When we represent real-world systems as networks, the directions of links often convey valuable information. Finding module structures that respect link directions is one of the most important tasks for analyzing directed networks. Although many notions of a directed module have been proposed, no consensus has been reached. This lack of consensus results partly because there might exist distinct types of modules in a single directed network, whereas most previous studies focused on an independent criterion for modules. To address this issue, we propose a generic notion of the so-called truss s…
Detecting significant community structure in networks with incomplete observations is challenging because the evidence for specific solutions fades away with missing data. For example, recent research shows that flow-based community detection methods can highlight spurious communities in sparse undirected and unweighted networks with missing links. Current Bayesian approaches developed to overcome this problem do not work for incomplete observations in weighted and directed networks that describe network flows. To address this gap, we extend the idea behind the Bayesian estimate of the map equ…
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 have already been developed for the hyperbolic embedding of undirected networks, approaches able to deal with directed networks are still in their infancy. Here, we propose a framework based on the dimension reduction of proximity matrices reflecting the network topology, coupled with a general conversion method transforming Euclidean node coordinates into hype…
Many complex networks are described by directed links; in such networks, a link represents, for example, the control of one node over the other node or unidirectional information flows. Some centrality measures are used to determine the relative importance of nodes specifically in directed networks. We analyze such a centrality measure called the influence. The influence represents the importance of nodes in various dynamics such as synchronization, evolutionary dynamics, random walk, and social dynamics. We analytically calculate the influence in various networks, including directed multipart…
We consider spectral methods that uncover hidden structures in directed networks. We establish and exploit connections between node reordering via (a) minimizing an objective function and (b) maximizing the likelihood of a random graph model. We focus on two existing spectral approaches that build and analyse Laplacian-style matrices via the minimization of frustration and trophic incoherence. These algorithms aim to reveal directed periodic and linear hierarchies, respectively. We show that reordering nodes using the two algorithms, or mapping them onto a specified lattice, is associated with…
The Sznajd model is investigated in the directed Erdos--Renyi network with the clusterization coefficient enhanced to 0.3 by the method of Holme and Kim (Phys. Rev. E65 (2002) 026107). Within additional triangles, all six links are present. In this network, some nodes preserve the minority opinion. The time tau of getting equilibrium is found to follow the log-normal distribution and it increases linearly with the system size. Its dependence on the initial opinion distribution is different from the analytical results for fully connected networks.
Epidemics have so far been mostly studied in undirected networks. However, many real-world networks, such as the social network Twitter and the WWW networks, upon which information, emotion or malware spreads, are shown to be directed networks, composed of both unidirectional links and bidirectional links. We define the directionality as the percentage of unidirectional links. The epidemic threshold for the susceptible-infected-susceptible (SIS) epidemic has been proved to be 1/lambda_{1} in directed networks by N-intertwined Mean-field Approximation, where lambda_{1}, also called as spectral …
Network embedding is a fervid topic in current networks science and observes that most real complex systems can be embedded in hidden metrics space and emerge as the geometrical property, where the geometric distance between nodes determines the likelihood of links connected. Among those, hyperbolic space associated with the structural organization of many real complex systems, it has thus received extensive attention. However, the majority of methods and measurements, recently developed, less take these features into consideration for the asymmetry of links. Here, we discuss how to multiplex …
Power law distribution is common in real-world networks including online social networks. Many studies on complex networks focus on the characteristics of vertices, which are always proved to follow the power law. However, few researches have been done on edges in directed networks. In this paper, edge balance ratio is firstly proposed to measure the balance property of edges in directed networks. Based on edge balance ratio, balance profile and positivity are put forward to describe the balance level of the whole network. Then the distribution of edge balance ratio is theoretically analyzed. …
Using Monte Carlo simulations, we study the evolution of contigent cooperation and ethnocentrism in the one-move game. Interactions and reproduction among computational agents are simulated on {\it undirected} and {\it directed} Barabási-Albert (BA) networks. We first replicate the Hammond-Axelrod model of in-group favoritism on a square lattice and then generalize this model on {\it undirected} and {\it directed} BA networks for both asexual and sexual reproduction cases. Our simulations demonstrate that irrespective of the mode of reproduction, ethnocentric strategy becomes common even thoug…
We introduce and analyze a model of a multi-directed Eulerian network, that is a directed and weighted network where a path exists that passes through all the edges of the network once and only once. Networks of this type can be used to describe information networks such as human language or DNA chains. We are able to calculate the strength and degree distribution in this network and find that they both exhibit a power law with an exponent between 2 and 3. We then analyze the behavior of the accelerated version of the model and find that the strength distribution has a double slope power law b…
We introduce a reshuffled approach to empirical analyze signs' organization in real directed signed social networks of Epinions and Slashdots from the global viewpoint. In the reshuffled approach, each negative link has probability $p_{rs}$ to exchange its sign with another positive link chosen randomly. Through calculating the entropies of social status ($S_{in}$ and $S_{out}$) of and mimicking opinion formation of the majority-rule model on each reshuffled signed network, we find that $S_{in}$ and $S_{out}$ reach their own minimum values as well as the magnetization $|m^{*}|$ reaches its max…
In usual scale-free networks of Barabasi-Albert type, a newly added node selects randomly m neighbors from the already existing network nodes, proportionally to the number of links these had before. Then the number N(k) of nodes with k links each decays as 1/k^gamma where gamma=3 is universal, i.e. independent of m. Now we use a limited directedness in the construction of the network, as a result of which the exponent gamma decreases from 3 to 2 for increasing m.
We generate new mathematical tools with which to quantify the macroscopic topological structure of large directed networks. This is achieved via a statistical mechanical analysis of constrained maximum entropy ensembles of directed random graphs with prescribed joint distributions for in- and outdegrees and prescribed degree-degree correlation functions. We calculate exact and explicit formulae for the leading orders in the system size of the Shannon entropies and complexities of these ensembles, and for information-theoretic distances. The results are applied to data on gene regulation networ…
Community detection has been one of the central problems in network studies and directed network is particularly challenging due to asymmetry among its links. In this paper, we found that incorporating the direction of links reveals new perspectives on communities regarding to two different roles, source and terminal, that a node plays in each community. Intriguingly, such communities appear to be connected with unique spectral property of the graph Laplacian of the adjacency matrix and we exploit this connection by using regularized SVD methods. We propose harvesting algorithms, coupled with …
The recursive removal of leaves (dead end vertices) and their neighbors from an undirected network results, when this pruning algorithm stops, in a so-called core of the network. This specific subgraph should be distinguished from $k$-cores, which are principally different subgraphs in networks. If the vertex mean degree of a network is sufficiently large, the core is a giant cluster containing a finite fraction of vertices. We find that generalization of this pruning algorithm to directed networks provides a significantly more complex picture of cores. By implementing a rate equation approach…
We propose a continuum model for the degree distribution of directed networks in free and open-source software. The degree distributions of links in both the in-directed and out-directed dependency networks follow Zipf's law for the intermediate nodes, but the heavily linked nodes and the poorly linked nodes deviate from this trend and exhibit finite-size effects. The finite-size parameters make a quantitative distinction between the in-directed and out-directed networks. For the out-degree distribution, the initial condition for a dynamic evolution corresponds to the limiting count of the mos…
We propose a framework for the visualization of directed networks relying on the eigenfunctions of the magnetic Laplacian, called here Magnetic Eigenmaps. The magnetic Laplacian is a complex deformation of the well-known combinatorial Laplacian. Features such as density of links and directionality patterns are revealed by plotting the phases of the first magnetic eigenvectors. An interpretation of the magnetic eigenvectors is given in connection with the angular synchronization problem. Illustrations of our method are given for both artificial and real networks.
It has often been taken as a working assumption that directed links in information networks are frequently formed by "short-cutting" a two-step path between the source and the destination -- a kind of implicit "link copying" analogous to the process of triadic closure in social networks. Despite the role of this assumption in theoretical models such as preferential attachment, it has received very little direct empirical investigation. Here we develop a formalization and methodology for studying this type of directed closure process, and we provide evidence for its important role in the format…
Critical nodes or "middlemen" have an essential place in both social and economic networks when considering the flow of information and trade. This paper extends the concept of critical nodes to directed networks. We identify strong and weak middlemen. Node contestability is introduced as a form of competition in networks; a duality between uncontested intermediaries and middlemen is established. The brokerage power of middlemen is formally expressed and a general algorithm is constructed to measure the brokerage power of each node from the networks adjacency matrix. Augmentations of the broke…
We derive analytic expressions for the possibility, probability, and expected size of global spreading events starting from a single infected seed for a broad collection of contagion processes acting on random networks with both directed and undirected edges and arbitrary degree-degree correlations. Our work extends previous theoretical developments for the undirected case, and we provide numerical support for our findings by investigating an example class of networks for which we are able to obtain closed-form expressions.
Though commonly found in the real world, directed networks have received relatively less attention from the literature in which concerns their topological and dynamical characteristics. In this work, we develop a magnetic Laplacian-based framework that can be used for studying directed complex networks. More specifically, we introduce a specific heat measurement that can help to characterize the network topology. It is shown that, by using this approach, it is possible to identify the types of several networks, as well as to infer parameters underlying specific network configurations. Then, we…
Respondent driven sampling (RDS) is a method often used to estimate population properties (e.g. sexual risk behavior) in hard-to-reach populations. It combines an effective modified snowball sampling methodology with an estimation procedure that yields unbiased population estimates under the assumption that the sampling process behaves like a random walk on the social network of the population. Current RDS estimation methodology assumes that the social network is undirected, i.e. that all edges are reciprocal. However, empirical social networks in general also have non-reciprocated edges. To a…
