Mitigate SIR epidemic spreading via contact blocking in temporal networks

Progress has been made in how to suppress epidemic spreading on temporal networks via blocking all contacts of targeted nodes or node pairs. In this work, we develop contact blocking strategies that remove a fraction of contacts from a temporal (time evolving) human contact network to mitigate the spread of a Susceptible-Infected-Recovered epidemic. We define the probability that a contact c(i, j, t) is removed as a function of a given centrality metric of the corresponding link l(i, j) in the aggregated network and the time t of the contact. The aggregated network captures the number of contacts between each node pair. A set of 12 link centrality metrics have been proposed and each centrality metric leads to a unique contact removal strategy. These strategies together with a baseline strategy (random removal) are evaluated in empirical contact networks via the average prevalence, the peak prevalence and the time to reach the peak prevalence. We find that the epidemic spreading can be mitigated the best when contacts between node pairs that have fewer contacts and early contacts are more likely to be removed. A strategy tends to perform better when the average number contacts removed from each node pair varies less. The aggregated pruned network resulted from the best contact removal strategy tends to have a large largest eigenvalue, a large modularity and probably a small largest connected component size.

Calculation of centralities in protein kinase A

Topological analysis of amino acid networks is a common method that can help to understand the roles of individual residues. The most popular approach for network construction is to create a connection between residues if they interact. These interactions are usually weighted by absolute values of correlation coefficients or mutual information. Here we argue that connections in such networks have to reflect levels of cohesion within the protein instead of a simple fact of interaction between residues. If this is correct, an indiscriminate combination of correlation and anti-correlation, as well as the all-inclusive nature of the mutual information metrics, should be detrimental for the analysis. To test our hypothesis, we studied amino acid networks of the protein kinase A created by Local Spatial Pattern alignment, a method that can detect conserved patterns formed by Cα-Cβ vectors. Our results showed that, in comparison with the traditional methods, this approach is more efficient in detecting functionally important residues. Out of four studied centrality metrics, Closeness centrality was the least efficient measure of residue importance. Eigenvector centrality proved to be ineffective as the spectral gap values of the networks were very low due to the bilobal structure of the kinase. We recommend using joint graphs of Betweenness centrality and Degree centrality to visualize different aspects of amino acid roles.

Analysing the Impact of Pedestrian Network Centrality on Segment-Level Pedestrian Density

Studies have shown that street network centrality measures are capable of explaining a significant proportion of pedestrian activity. These studies typically employ street centreline networks that differ significantly from the networks that pedestrians use to traverse the built environment. Presently, centrality approaches are rarely applied to dedicated pedestrian network (DPNs). This creates uncertainty regarding their ability to explain pedestrian activity when derived from DPNs. This study addresses that gap by investigating the extent to which centrality metrics derived from DPNs can explain observed pedestrian densities, both alone and when controlling for other built environment variables in metro station environments in Asia. In total, four DPNs were created centred on metro stations in Bangkok, Manila, Osaka, and Taipei chosen to represent different urban typologies. Multivariate results show that centrality metrics alone explain a mere 6–24% of observed pedestrian densities when calculated on DPNs. When all factors are considered, the contribution of centrality remained consistent in most study sites but is somewhat reduced with land-use variables and proximity to rail transit revealed as the strongest predictors of pedestrian density. Pedestrian design factors were also frequently associated with pedestrian density. Finally, stronger associations between centrality and pedestrian densities were observed in the denser, more complex pedestrian environments. These findings provide insight into the performance of centrality measures applied to DPNs expanding pedestrian network research in this area.

Temporal Degree-Degree and Closeness-Closeness: A New Centrality Metrics for Social Network Analysis

In the area of network analysis, centrality metrics play an important role in defining the “most important” actors in a social network. However, nowadays, most types of networks are dynamic, meaning their topology changes over time. The connection weights and the strengths of social links between nodes are an important concept in a social network. The new centrality measures are proposed for weighted networks, which relies on a time-ordered weighted graph model, generalized temporal degree and closeness centrality. Furthermore, two measures—Temporal Degree-Degree and Temporal Closeness-Closeness—are employed to better understand the significance of nodes in weighted dynamic networks. Our study is caried out according to real dynamic weighted networks dataset of a university-based karate club. Through extensive experiments and discussions of the proposed metrics, our analysis proves that there is an effectiveness on the impact of each node throughout social networks.

Centrality of drug targets in protein networks

Background In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitness’ based on its node characteristics within annotated protein functional networks to complement contingent therapeutic hypotheses. Results We observed that targets of approved, selective small molecule drugs exhibit high node centrality within protein networks relative to a broader set of investigational targets spanning various development stages. Targets of approved drugs also exhibit higher centrality than other proteins within their respective functional class. These findings expand on previous reports of drug targets’ network centrality by suggesting some centrality metrics such as low topological coefficient as inherent characteristics of a ‘good’ target, relative to other exploratory targets and regardless of its functional class. These centrality metrics could thus be indicators of an individual protein’s ‘fitness’ as potential drug target. Correlations between protein nodes’ network centrality and number of associated publications underscored the possibility of knowledge bias as an inherent limitation to such predictions. Conclusions Despite some entanglement with knowledge bias, like structure-oriented ‘druggability’ assessments of new protein targets, centrality metrics could assist early pharmaceutical discovery teams in evaluating potential targets with limited experimental proof of concept and help allocate resources for an effective drug discovery pipeline.

Benchmark for Discriminating Power of Edge Centrality Metrics

Edge centrality has found wide applications in various aspects. Many edge centrality metrics have been proposed, but the crucial issue that how good the discriminating power of a metric is, with respect to other measures, is still open. In this paper, we address the question about the benchmark of the discriminating power of edge centrality metrics. We first use the automorphism concept to define equivalent edges, based on which we introduce a benchmark for the discriminating power of edge centrality measures and develop a fast approach to compare the discriminating power of different measures. According to the benchmark, for a desirable measure, equivalent edges have identical metric scores, while inequivalent edges possess different scores. However, we show that even in a toy graph, inequivalent edges cannot be discriminated by three existing edge centrality metrics. We then present a novel edge centrality metric called forest centrality (FC). Extensive experiments on real-world networks and model networks indicate that FC has better discriminating power than three existing edge centrality metrics.

A network approach to rank countries chasing sustainable development

In 2015, the United Nations established the Agenda 2030 for sustainable development, addressing the major challenges the world faces and introducing the 17 Sustainable Development Goals (SDGs). How are countries performing in their challenge toward sustainable development? We address this question by treating countries and Goals as a complex bipartite network. While network science has been used to unveil the interconnections among the Goals, it has been poorly exploited to rank countries for their achievements. In this work, we show that the network representation of the countries-SDGs relations as a bipartite system allows one to recover aggregate scores of countries’ capacity to cope with SDGs as the solutions of a network’s centrality exercise. While the Goals are all equally important by definition, interesting differences self-emerge when non-standard centrality metrics, borrowed from economic complexity, are adopted. Innovation and Climate Action stand as contrasting Goals to be accomplished, with countries facing the well-known trade-offs between economic and environmental issues even in addressing the Agenda. In conclusion, the complexity of countries’ paths toward sustainable development cannot be fully understood by resorting to a single, multipurpose ranking indicator, while multi-variable analyses shed new light on the present and future of sustainable development.