Assessing the significance of knockout cascades in metabolic networks

Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of individual or sets of nodes, followed by the assessment of the inflicted damage. For complex metabolic networks, it has been suggested that evolutionary pressure may favor robustness against reaction removal. However, the removal of a reaction and its impact on the network may as well be interpreted as selective regulation of pathway activities, suggesting a tradeoff between the efficiency of regulation and vulnerability. Here, we employ a cascading failure algorithm to simulate the removal of single and pairs of reactions from the metabolic networks of two organisms, and estimate the significance of the results using two different null models: degree preserving and mass-balanced randomization. Our analysis suggests that evolutionary pressure promotes larger cascades of non-viable reactions, and thus favors the ability of efficient metabolic regulation at the expense of robustness

How to Compare the Scientific Contributions between Research Groups

We present a method to analyse the scientific contributions between research groups. Given multiple research groups, we construct their journal/proceeding graphs and then compute the similarity/gap between them using network analysis. This analysis can be used for measuring similarity/gap of the topics/qualities between research groups' scientific contributions. We demonstrate the practicality of our method by comparing the scientific contributions by Korean researchers with those by the global researchers for information security in 2006 - 2008. The empirical analysis shows that the current security research in South Korea has been isolated from the global research trend

Network harness: bundles of routes in public transport networks

Public transport routes sharing the same grid of streets and tracks are often found to proceed in parallel along shorter or longer sequences of stations. Similar phenomena are observed in other networks built with space consuming links such as cables, vessels, pipes, neurons, etc. In the case of public transport networks (PTNs) this behavior may be easily worked out on the basis of sequences of stations serviced by each route. To quantify this behavior we use the recently introduced notion of network harness. It is described by the harness distribution P(r,s): the number of sequences of s consecutive stations that are serviced by r parallel routes. For certain PTNs that we have analyzed we observe that the harness distribution may be described by power laws. These power laws observed indicate a certain level of organization and planning which may be driven by the need to minimize the costs of infrastructure and secondly by the fact that points of interest tend to be clustered in certain locations of a city. This effect may be seen as a result of the strong interdependence of the evolutions of both the city and its PTN. To further investigate the significance of the empirical results we have studied one- and two-dimensional models of randomly placed routes modeled by different types of walks. While in one dimension an analytic treatment was successful, the two dimensional case was studied by simulations showing that the empirical results for real PTNs deviate significantly from those expected for randomly placed routes.Comment: 12 pages, 24 figures, paper presented at the Conference ``Statistical Physics: Modern Trends and Applications'' (23-25 June 2009, Lviv, Ukaine) dedicated to the 100th anniversary of Mykola Bogolyubov (1909-1992

Tunable and Growing Network Generation Model with Community Structures

Recent years have seen a growing interest in the modeling and simulation of social networks to understand several social phenomena. Two important classes of networks, small world and scale free networks have gained a lot of research interest. Another important characteristic of social networks is the presence of community structures. Many social processes such as information diffusion and disease epidemics depend on the presence of community structures making it an important property for network generation models to be incorporated. In this paper, we present a tunable and growing network generation model with small world and scale free properties as well as the presence of community structures. The major contribution of this model is that the communities thus created satisfy three important structural properties: connectivity within each community follows power-law, communities have high clustering coefficient and hierarchical community structures are present in the networks generated using the proposed model. Furthermore, the model is highly robust and capable of producing networks with a number of different topological characteristics varying clustering coefficient and inter-cluster edges. Our simulation results show that the model produces small world and scale free networks along with the presence of communities depicting real world societies and social networks.Comment: Social Computing and Its Applications, SCA 13, Karlsruhe : Germany (2013

Eigenvector-based identification of bipartite subgraphs

We report our experiments in identifying large bipartite subgraphs of simple connected graphs which are based on the sign pattern of eigenvectors belonging to the extremal eigenvalues of different graph matrices: adjacency, signless Laplacian, Laplacian, and normalized Laplacian matrix. We compare the performance of these methods to a local switching algorithm based on the Erdos bound that each graph contains a bipartite subgraph with at least half of its edges. Experiments with one scale-free and three random graph models, which cover a wide range of real-world networks, show that the methods based on the eigenvectors of the normalized Laplacian and the adjacency matrix yield slightly better, but comparable results to the local switching algorithm. We also formulate two edge bipartivity indices based on the former eigenvectors, and observe that the method of iterative removal of edges with maximum bipartivity index until one obtains a bipartite subgraph, yields comparable results to the local switching algorithm, and significantly better results than an analogous method that employs the edge bipartivity index of Estrada and Gomez-Gardenes.Comment: 20 pages, 8 figure

Stay Awhile and Listen: User Interactions in a Crowdsourced Platform Offering Emotional Support

Internet and online-based social systems are rising as the dominant mode of communication in society. However, the public or semi-private environment under which most online communications operate under do not make them suitable channels for speaking with others about personal or emotional problems. This has led to the emergence of online platforms for emotional support offering free, anonymous, and confidential conversations with live listeners. Yet very little is known about the way these platforms are utilized, and if their features and design foster strong user engagement. This paper explores the utilization and the interaction features of hundreds of thousands of users on 7 Cups of Tea, a leading online platform offering online emotional support. It dissects the level of activity of hundreds of thousands of users, the patterns by which they engage in conversation with each other, and uses machine learning methods to find factors promoting engagement. The study may be the first to measure activities and interactions in a large-scale online social system that fosters peer-to-peer emotional support

Evolving Clustered Random Networks

We propose a Markov chain simulation method to generate simple connected random graphs with a specified degree sequence and level of clustering. The networks generated by our algorithm are random in all other respects and can thus serve as generic models for studying the impacts of degree distributions and clustering on dynamical processes as well as null models for detecting other structural properties in empirical networks

Contagions in Random Networks with Overlapping Communities

We consider a threshold epidemic model on a clustered random graph with overlapping communities. In other words, our epidemic model is such that an individual becomes infected as soon as the proportion of her infected neighbors exceeds the threshold q of the epidemic. In our random graph model, each individual can belong to several communities. The distributions for the community sizes and the number of communities an individual belongs to are arbitrary. We consider the case where the epidemic starts from a single individual, and we prove a phase transition (when the parameter q of the model varies) for the appearance of a cascade, i.e. when the epidemic can be propagated to an infinite part of the population. More precisely, we show that our epidemic is entirely described by a multi-type (and alternating) branching process, and then we apply Sevastyanov's theorem about the phase transition of multi-type Galton-Watson branching processes. In addition, we compute the entries of the matrix whose largest eigenvalue gives the phase transition.Comment: Minor modifications for the second version: added comments (end of Section 3.2, beginning of Section 5.3); moved remark (end of Section 3.1, beginning of Section 4.1); corrected typos; changed titl