A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models

An Internet-Oriented Multilayer Network Model Characterization and Robustness Analysis Method

The Internet creates multidimensional and complex relationships in terms of the composition, application and mapping of social users. Most of the previous related research has focused on the single-layer topology of physical device networks but ignored the study of service access relationships and the social structure of users on the Internet. Here, we propose a composite framework to understand how the interaction between the physical devices network, business application network, and user role network affects the robustness of the entire Internet. In this paper, a multilayer network consisting of a physical device layer, business application layer and user role layer is constructed by collecting experimental network data. We characterize the disturbance process of the entire multilayer network when a physical entity device fails by designing nodal disturbance to investigate the interactions that exist between the different network layers. Meanwhile, we analyze the characteristics of the Internet-oriented multilayer network structure and propose a heuristic multilayer network topology generation algorithm based on the initial routing topology and networking pattern, which simulates the evolution process of multilayer network topology. To further analyze the robustness of this multilayer network model, we combined a total of six target node ranking indicators including random strategy, degree centrality, betweenness centrality, closeness centrality, clustering coefficient and network constraint coefficient, performed node deletion simulations in the experimental network, and analyzed the impact of component types and interactions on the robustness of the overall multilayer network based on the maximum component change in the network. These results provide new insights into the operational processes of the Internet from a multi-domain data fusion perspective, reflecting that the coupling relationships that exist between the different interaction layers are closely linked to the robustness of multilayer networks.

Gene Regulatory Identification Based on the Novel Hybrid Time-Delayed Method

Gene regulatory network (GRN) inference with biology data is a difficult and serious issue in the field of system biology. In order to detect the direct associations of GRN more accurately, a novel two-step GRN inference technique based on the time-delayed correlation coefficient (TDCC) and time-delayed complex-valued S-system model (TDCVSS) is proposed. First, a TDCC algorithm is utilized to construct an initial network. Second, a TDCVSS model is utilized to prune the network topology in order to delete false-positive regulatory relationships for each target gene. The complex-valued restricted additive tree and complex-valued differential evolution are proposed to approximate the optimal TDCVSS model. Finally, the overall network could be inferred by integrating the regulations of all target genes. Two real gene expression datasets from E. coli and S. cerevisiae gene networks are utilized to evaluate the performances of our proposed two-step GRN inference algorithm. The results demonstrated that the proposed algorithm could infer GRN more correct than classical methods and time-delayed methods.