Resolution of ranking hierarchies in directed networks

Identifying hierarchies and rankings of nodes in directed graphs is fundamental in many applications such as social network analysis, biology, economics, and finance. A recently proposed method identifies the hierarchy by finding the ordered partition of nodes which minimises a score function, termed agony. This function penalises the links violating the hierarchy in a way depending on the strength of the violation. To investigate the resolution of ranking hierarchies we introduce an ensemble of random graphs, the Ranked Stochastic Block Model. We find that agony may fail to identify hierarchies when the structure is not strong enough and the size of the classes is small with respect to the whole network. We analytically characterise the resolution threshold and we show that an iterated version of agony can partly overcome this resolution limit.Comment: 27 pages, 9 figure

Dynamic hierarchies in temporal directed networks

The outcome of interactions in many real-world systems can be often explained by a hierarchy between the participants. Discovering hierarchy from a given directed network can be formulated as follows: partition vertices into levels such that, ideally, there are only forward edges, that is, edges from upper levels to lower levels. In practice, the ideal case is impossible, so instead we minimize some penalty function on the backward edges. One practical option for such a penalty is agony, where the penalty depends on the severity of the violation. In this paper we extend the definition of agony to temporal networks. In this setup we are given a directed network with time stamped edges, and we allow the rank assignment to vary over time. We propose 2 strategies for controlling the variation of individual ranks. In our first variant, we penalize the fluctuation of the rankings over time by adding a penalty directly to the optimization function. In our second variant we allow the rank change at most once. We show that the first variant can be solved exactly in polynomial time while the second variant is NP-hard, and in fact inapproximable. However, we develop an iterative method, where we first fix the change point and optimize the ranks, and then fix the ranks and optimize the change points, and reiterate until convergence. We show empirically that the algorithms are reasonably fast in practice, and that the obtained rankings are sensible

Detecting Evolving Patterns of Self-Organizing Networks by Flow Hierarchy Measurement

Hierarchies occur widely in evolving self-organizing ecological, biological, technological and social networks, but detecting and comparing hierarchies is difficult. Here we present a metric and technique to quantitatively assess the extent to which self-organizing directed networks exhibit a flow hierarchy. Flow hierarchy is a commonly observed but theoretically overlooked form of hierarchy in networks. We show that the ecological, neurobiological, economic and information processing networks are generally more hierarchical than their comparable random networks. We further discovered that hierarchy degree has increased over the course of the evolution of Linux kernels, confirming an early hypothesis by Herbert Simon on the emergence of hierarchy in evolutionary processes. Taken together, our results suggest that hierarchy is a central organizing feature of real-world evolving networks, and the measurement of hierarchy opens the way to understand the structural regimes and evolutionary patterns of self-organizing networks. Our measurement technique makes it possible to objectively compare hierarchies of different networks and of different evolutionary stages of a single network, and compare evolving patterns of different networks. It can be applied to various complex systems, which can be represented as directed networks

Global network structure of dominance hierarchy of ant workers

Dominance hierarchy among animals is widespread in various species and believed to serve to regulate resource allocation within an animal group. Unlike small groups, however, detection and quantification of linear hierarchy in large groups of animals are a difficult task. Here, we analyse aggression-based dominance hierarchies formed by worker ants in Diacamma sp. as large directed networks. We show that the observed dominance networks are perfect or approximate directed acyclic graphs, which are consistent with perfect linear hierarchy. The observed networks are also sparse and random but significantly different from networks generated through thinning of the perfect linear tournament (i.e., all individuals are linearly ranked and dominance relationship exists between every pair of individuals). These results pertain to global structure of the networks, which contrasts with the previous studies inspecting frequencies of different types of triads. In addition, the distribution of the out-degree (i.e., number of workers that the focal worker attacks), not in-degree (i.e., number of workers that attack the focal worker), of each observed network is right-skewed. Those having excessively large out-degrees are located near the top, but not the top, of the hierarchy. We also discuss evolutionary implications of the discovered properties of dominance networks.Comment: 5 figures, 2 tables, 4 supplementary figures, 2 supplementary table

Word Activation Forces Map Word Networks

Words associate with each other in a manner of intricate clusters^1-3^. Yet the brain capably encodes the complex relations into workable networks^4-7^ such that the onset of a word in the brain automatically and selectively activates its associates, facilitating language understanding and generation^8-10^. One believes that the activation strength from one word to another forges and accounts for the latent structures of the word networks. This implies that mapping the word networks from brains to computers^11,12^, which is necessary for various purposes^1,2,13-15^, may be achieved through modeling the activation strengths. However, although a lot of investigations on word activation effects have been carried out^8-10,16-20^, modeling the activation strengths remains open. Consequently, huge labor is required to do the mappings^11,12^. Here we show that our found word activation forces, statistically defined by a formula in the same form of the universal gravitation, capture essential information on the word networks, leading to a superior approach to the mappings. The approach compatibly encodes syntactical and semantic information into sparse coding directed networks, comprehensively highlights the features of individual words. We find that based on the directed networks, sensible word clusters and hierarchies can be efficiently discovered. Our striking results strongly suggest that the word activation forces might reveal the encoding of word networks in the brain

Directed Network Laplacians and Random Graph Models

We consider spectral methods that uncover hidden structures in directed networks. We develop a general framework that allows us to associate methods based on optimization formulations with maximum likelihood problems on random graphs. 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 new classes of directed random graph models. Using this random graph setting, we are able to compare the two algorithms on a given network and quantify which structure is more likely to be present. We illustrate the approach on synthetic and real networks, and discuss practical implementation issues

Directed Scattering for Knowledge Graph-based Cellular Signaling Analysis

Directed graphs are a natural model for many phenomena, in particular scientific knowledge graphs such as molecular interaction or chemical reaction networks that define cellular signaling relationships. In these situations, source nodes typically have distinct biophysical properties from sinks. Due to their ordered and unidirectional relationships, many such networks also have hierarchical and multiscale structure. However, the majority of methods performing node- and edge-level tasks in machine learning do not take these properties into account, and thus have not been leveraged effectively for scientific tasks such as cellular signaling network inference. We propose a new framework called Directed Scattering Autoencoder (DSAE) which uses a directed version of a geometric scattering transform, combined with the non-linear dimensionality reduction properties of an autoencoder and the geometric properties of the hyperbolic space to learn latent hierarchies. We show this method outperforms numerous others on tasks such as embedding directed graphs and learning cellular signaling networks.Comment: 5 pages, 3 figure

Hierarchy measure for complex networks

Nature, technology and society are full of complexity arising from the intricate web of the interactions among the units of the related systems (e.g., proteins, computers, people). Consequently, one of the most successful recent approaches to capturing the fundamental features of the structure and dynamics of complex systems has been the investigation of the networks associated with the above units (nodes) together with their relations (edges). Most complex systems have an inherently hierarchical organization and, correspondingly, the networks behind them also exhibit hierarchical features. Indeed, several papers have been devoted to describing this essential aspect of networks, however, without resulting in a widely accepted, converging concept concerning the quantitative characterization of the level of their hierarchy. Here we develop an approach and propose a quantity (measure) which is simple enough to be widely applicable, reveals a number of universal features of the organization of real-world networks and, as we demonstrate, is capable of capturing the essential features of the structure and the degree of hierarchy in a complex network. The measure we introduce is based on a generalization of the m-reach centrality, which we first extend to directed/partially directed graphs. Then, we define the global reaching centrality (GRC), which is the difference between the maximum and the average value of the generalized reach centralities over the network. We investigate the behavior of the GRC considering both a synthetic model with an adjustable level of hierarchy and real networks. Results for real networks show that our hierarchy measure is related to the controllability of the given system. We also propose a visualization procedure for large complex networks that can be used to obtain an overall qualitative picture about the nature of their hierarchical structure.Comment: 29 pages, 9 figures, 4 table