An Evolutionary Perspective of Virus Propagation

This paper presents an evolutionary algorithm that simulates simplified scenarios of the diffusion of an infectious disease within a given population. The proposed evolutionary epidemic diffusion (EED) computational model has a limited number of variables and parameters, but is still able to simulate a variety of configurations that have a good adherence to real-world cases. The use of two space distances and the calculation of spatial 2-dimensional entropy are also examined. Several simulations demonstrate the feasibility of the EED for testing distinct social, logistic and economy risks. The performance of the system dynamics is assessed by several variables and indices. The global information is efficiently condensed and visualized by means of multidimensional scaling.info:eu-repo/semantics/publishedVersio

Dynamic Core Community Detection and Information Diffusion Processes on Networks

Interest in network science has been increasingly shared among various research communities due to its broad range of applications. Many real world systems can be abstracted as networks, a group of nodes connected by pairwise edges, and examples include friendship networks, metabolic networks, and world wide web among others. Two of the main research areas in network science that have received a lot of focus are community detection and information diffusion. As for community detection, many well developed algorithms are available for such purposes in static networks, for example, spectral partitioning and modularity function based optimization algorithms. As real world data becomes richer, community detection in temporal networks becomes more and more desirable and algorithms such as tensor decomposition and generalized modularity function optimization are developed. One scenario not well investigated is when the core community structure persists over long periods of time with possible noisy perturbations and changes only over periods of small time intervals. The contribution of this thesis in this area is to propose a new algorithm based on low rank component recovery of adjacency matrices so as to identify the phase transition time points and improve the accuracy of core community structure recovery. As for information diffusion, traditionally it was studied using either threshold models or independent interaction models as an epidemic process. But information diffusion mechanism is different from epidemic process such as disease transmission because of the reluctance to tell stale news and to address this issue other models such as DK model was proposed taking into consideration of the reluctance of spreaders to diffuse the information as time goes by. However, this does not capture some cases such as the losing interest of information receivers as in viral marketing. The contribution of this thesis in this area is we proposed two new models coined susceptible-informed-immunized (SIM) model and exponentially time decaying susceptible-informed (SIT) model to successfully capture the intrinsic time value of information from both the spreader and receiver points of view. Rigorous analysis of the dynamics of the two models were performed based mainly on mean field theory. The third contribution of this thesis is on the information diffusion optimization. Controlling information diffusion has been widely studied because of its important applications in areas such as social census, disease control and marketing. Traditionally the problem is formulated as identifying the set of k seed nodes, informed initially, so as to maximize the diffusion size. Heuristic algorithms have been developed to find approximate solutions for this NP-hard problem, and measures such as k-shell, node degree and centrality have been used to facilitate the searching for optimal solutions. The contribution of this thesis in this field is to design a more realistic objective function and apply binary particle swarm optimization algorithm for this combinatorial optimization problem. Instead of fixating the seed nodes size and maximize the diffusion size, we maximize the profit defined as the revenue, which is simply the diffusion size, minus the cost of setting those seed nodes, which is designed as a function of degrees of the seed nodes or a measure that is similar to the centrality of nodes. Because of the powerful algorithm, we were able to study complex scenarios such as information diffusion optimization on multilayer networks.PHDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/145937/1/wbao_1.pd

Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Tackling complexity in biological systems: Multi-scale approaches to tuberculosis infection

Tuberculosis is an ancient disease responsible for more than a million deaths per year worldwide, whose complex infection cycle involves dynamical processes that take place at different spatial and temporal scales, from single pathogenic cells to entire hosts' populations. In this thesis we study TB disease at different levels of description from the perspective of complex systems sciences. On the one hand, we use complex networks theory for the analysis of cell interactomes of the causative agent of the disease: the bacillus Mycobacterium tuberculosis. Here, we analyze the gene regulatory network of the bacterium, as well as its network of protein interactions and the way in which it is transformed as a consequence of gene expression adaptation to disparate environments. On the other hand, at the level of human societies, we develop new models for the description of TB spreading on complex populations. First, we develop mathematical models aimed at addressing, from a conceptual perspective, the interplay between complexity of hosts' populations and certain dynamical traits characteristic of TB spreading, like long latency periods and syndemic associations with other diseases. On the other hand, we develop a novel data-driven model for TB spreading with the objective of providing faithful impact evaluations for novel TB vaccines of different types

Artificial Immune Systems: Principle, Algorithms and Applications

The present thesis aims to make an in-depth study of adaptive identification, digital channel equalization, functional link artificial neural network (FLANN) and Artificial Immune Systems (AIS).Two learning algorithms CPSO and IPSO are also developed in this thesis. These new algorithms are employed to train the weights of a low complexity FLANN structure by way of minimizing the squared error cost function of the hybrid model. These new models are applied for adaptive identification of complex nonlinear dynamic plants and equalization of nonlinear digital channel. Investigation has been made for identification of complex Hammerstein models. To validate the performance of these new models simulation study is carried out using benchmark complex plants and nonlinear channels. The results of simulation are compared with those obtained with FLANN-GA, FLANN-PSO and MLP-BP based hybrid approaches. Improved identification and equalization performance of the proposed method have been observed in all cases