A Global Stochastic Modeling Framework to Simulate and Visualize Epidemics

Epidemics have caused major human and monetary losses through the course of human civilization. It is very important that epidemiologists and public health personnel are prepared to handle an impending infectious disease outbreak. the ever-changing demographics, evolving infrastructural resources of geographic regions, emerging and re-emerging diseases, compel the use of simulation to predict disease dynamics. By the means of simulation, public health personnel and epidemiologists can predict the disease dynamics, population groups at risk and their geographic locations beforehand, so that they are prepared to respond in case of an epidemic outbreak. As a consequence of the large numbers of individuals and inter-personal interactions involved in simulating infectious disease spread in a region such as a county, sizeable amounts of data may be produced that have to be analyzed. Methods to visualize this data would be effective in facilitating people from diverse disciplines understand and analyze the simulation. This thesis proposes a framework to simulate and visualize the spread of an infectious disease in a population of a region such as a county. As real-world populations have a non-homogeneous demographic and spatial distribution, this framework models the spread of an infectious disease based on population of and geographic distance between census blocks; social behavioral parameters for demographic groups. the population is stratified into demographic groups in individual census blocks using census data. Infection spread is modeled by means of local and global contacts generated between groups of population in census blocks. the strength and likelihood of the contacts are based on population, geographic distance and social behavioral parameters of the groups involved. the disease dynamics are represented on a geographic map of the region using a heat map representation, where the intensity of infection is mapped to a color scale. This framework provides a tool for public health personnel and epidemiologists to run what-if analyses on disease spread in specific populations and plan for epidemic response. By the means of demographic stratification of population and incorporation of geographic distance and social behavioral parameters into the modeling of the outbreak, this framework takes into account non-homogeneity in demographic mix and spatial distribution of the population. Generation of contacts per population group instead of individuals contributes to lowering computational overhead. Heat map representation of the intensity of infection provides an intuitive way to visualize the disease dynamics

MODELING INFECTIOUS DISEASES USING GLOBAL STOCHASTIC CELLULAR AUTOMATA

Susceptibles-infectives-removals (SIR) and its derivatives are the classic mathematical models for the study of infectious diseases in epidemiology. In order to model and simulate epidemics of an infectious disease, we use cellular automata (CA). The simplifying assumptions of SIR and naive CA limit their applicability to the real world characteristics. A global stochastic cellular automata paradigm (GSCA) is proposed, which incorporates geographic and demographic based interactions. The interaction measure between the cells is a function of population density and Euclidean distance, and has been extended to include geographic, demographic and migratory constraints. The progression of diseases using traditional CA and classic SIR are analyzed, and similar behavior to the SIR model is exhibited by GSCA, using the geographic information systems (GIS) gravity model for interactions. The limitations of the SIR and naive CA models of homogeneous population with uniform mixing are addressed by the GSCA model. The GSCA model is oriented to heterogeneous population, and can incorporate interactions based on geography, demography, environment and migration patterns. The progression of diseases can be modeled at higher levels of fidelity using the GSCA model, and facilitates optimal deployment of public health resources for prevention, control and surveillance of infectious diseases. </jats:p

The Influence of Social Network Graph Structure on Disease Dynamics in a Simulated Environment

The fight against epidemics/pandemics is one of man versus nature. Technological advances have not only improved existing methods for monitoring and controlling disease outbreaks, but have also provided new means for investigation, such as through modeling and simulation. This dissertation explores the relationship between social structure and disease dynamics. Social structures are modeled as graphs, and outbreaks are simulated based on a well-recognized standard, the susceptible-infectious-removed (SIR) paradigm. Two independent, but related, studies are presented. The first involves measuring the severity of outbreaks as social network parameters are altered. The second study investigates the efficacy of various vaccination policies based on social structure. Three disease-related centrality measures are introduced, contact, transmission, and spread centrality, which are related to previously established centrality measures degree, betweenness, and closeness, respectively. The results of experiments presented in this dissertation indicate that reducing the neighborhood size along with outside-of-neighborhood contacts diminishes the severity of disease outbreaks. Vaccination strategies can effectively reduce these parameters. Additionally, vaccination policies that target individuals with high centrality are generally shown to be slightly more effective than a random vaccination policy. These results combined with past and future studies will assist public health officials in their effort to minimize the effects of inevitable disease epidemics/pandemics

Agent-based modeling for environmental management. Case study: virus dynamics affecting Norwegian fish farming in fjords

Background: Norwegian fish-farming industry is an important industry, rapidly growing, and facing significant challenges such as the spread of pathogens1, trade-off between locations, fish production and health. There is a need for research, i.e. the development of theories (models), methods, techniques and tools for analysis, prediction and management, i.e. strategy development, policy design and decision making, to facilitate a sustainable industry. Loss due to the disease outbreaks in the aquaculture systems pose a large risk to a sustainable fish industry system, and pose a risk to the coastal and fjord ecosystem systems as a whole. Norwegian marine aquaculture systems are located in open areas (i.e. fjords) where they overlap and interact with other systems (e.g. transport, wild life, tourist, etc.). For instance, shedding viruses from aquaculture sites affect the wild fish in the whole fjord system. Fish disease spread and pathogen transmission in such complex systems, is process that it is difficult to predict, analyze, and control. There are several time-variant factors such as fish density, environmental conditions and other biological factors that affect the spread process. In this thesis, we developed methods to examine these factors on fish disease spread in fish populations and on pathogen spread in the time-space domain. Then we develop methods to control and manage the aquaculture system by finding optimal system settings in order to have a minimum infection risk and a high production capacity. Aim: The overall objective of the thesis is to develop agent-based models, methods and tools to facilitate the management of aquaculture production in Norwegian fjords by predicting the pathogen dynamics, distribution, and transmission in marine aquaculture systems. Specifically, the objectives are to assess agent-based modeling as an approach to understanding fish disease spread processes, to develop agent-based models that help us predict, analyze and understand disease dynamics in the context of various scenarios, and to develop a framework to optimize the location and the load of the aquaculture systems so as to minimize the infection risk in a growing fish industry. Methods: We use agent-based method to build models to simulate disease dynamics in fish populations and to simulate pathogen transmission between several aquaculture sites in a Norwegian fjord. Also, we use particle swarm optimization algorithm to identify agent-based models’ parameters so as to optimize the dynamics of the system model. In this context, we present a framework for using a particle swarm optimization algorithm to identify the parameter values of the agent-based model of aquaculture system that are expected to yield the optimal fish densities and farm locations that avoid the risk of spreading disease. The use of particle swarm optimization algorithm helps in identifying optimal agent-based models’ input parameters depending on the feedback from the agentbased models’ outputs. Results: As the thesis is built on three main studies, the results of the thesis work can be divided into three components. In the first study, we developed many agent-based models to simulate fish disease spread in stand-alone fish populations. We test the models in different scenarios by varying the agents (i.e. fish and pathogens) parameters, environment parameters (i.e. seawater temperature and currents), and interactions (interaction between agents-agents, and agents-environment) parameters. We use sensitivity analysis method to test different key input parameters such as fish density, fish swimming behavior, seawater temperature, and sea currents to show their effects on the disease spread process. Exploring the sensitivity of fish disease dynamics to these key parameters helps in combatting fish disease spread. In the second study, we build infection risk maps in a space-time domain, by developing agent-based models to identify the pathogen transmission patterns. The agent-based method helps us advance our understanding of pathogen transmission and builds risk maps to help us reduce the spread of infectious fish diseases. By using this method, we may study the spatial and dynamic aspects of the spread of infections and address the stochastic nature of the infection process. In the third study, we developed a framework for the optimization of the aquaculture systems. The framework uses particle swarm optimization algorithm to optimize agent-based models’ parameters so as to optimize the objective function. The framework was tested by developing a model to find optimal fish densities and farm locations in marine aquaculture system in a Norwegian fjord. Results show so that the rapid convergence of the presented particle swarm optimization algorithm to the optimal solution, - the algorithm requires a maximum of 18 iterations to find the best solution which can increase the fish density to three times while keeping the risk of infection at an accepted level. Conclusion: There are many contributions of this research work. First, we assessed the agent-based modeling as a method to simulate and analyze fish disease spread dynamics as a foundation for managing aquaculture systems. Results from this study demonstrate how effective the use of agentbased method is in the simulation of infectious diseases. By using this method, we are able to study spatial aspects of the spread of fish diseases and address the stochastic nature of infections process. Agent-based models are flexible, and they can include many external factors that affect fish disease dynamics such as interactions with wild fish and ship traffic. Agent-based models successfully help us to overcome the problem associated with lack of data in fish disease transmission and contribute to our understanding of different cause-effects relationships in the dynamics of fish diseases. Secondly, we developed methods to build infection risk maps in a space-time domain conditioned upon the identification of the pathogen transmission patterns in such a space-time domain, so as to help prevent and, if needed, combat infectious fish diseases by informing the management of the fish industry in Norway. Finally, we developed a method by which we may optimize the fish densities and farm locations of aquaculture systems so as to ensure a sustainable fish industry with a minimum risk of infection and a high production capacity. This PhD study offers new research-based approaches, models and tools for analysis, predictions and management that can be used to facilitate a sustainable development of the marine aquaculture industry with a maximal economic outcome and a minimal environmental impact

Social Network Simulation and Mining Social Media to Advance Epidemiology

Traditional Public Health decision-support can benefit from the Web and social media revolution. This dissertation presents approaches to mining social media benefiting public health epidemiology. Through discovery and analysis of trends in Influenza related blogs, a correlation to Centers for Disease Control and Prevention (CDC) influenza-like-illness patient reporting at sentinel health-care providers is verified. A second approach considers personal beliefs of vaccination in social media. A vaccine for human papillomavirus (HPV) was approved by the Food and Drug Administration in May 2006. The virus is present in nearly all cervical cancers and implicated in many throat and oral cancers. Results from automatic sentiment classification of HPV vaccination beliefs are presented which will enable more accurate prediction of the vaccine's population-level impact. Two epidemic models are introduced that embody the intimate social networks related to HPV transmission. Ultimately, aggregating these methodologies with epidemic and social network modeling facilitate effective development of strategies for targeted interventions

On The Application Of Computational Modeling To Complex Food Systems Issues

Transdisciplinary food systems research aims to merge insights from multiple fields, often revealing confounding, complex interactions. Computational modeling offers a means to discover patterns and formulate novel solutions to such systems-level problems. The best models serve as hubs—or boundary objects—which ground and unify a collaborative, iterative, and transdisciplinary process of stakeholder engagement. This dissertation demonstrates the application of agent-based modeling, network analytics, and evolutionary computational optimization to the pressing food systems problem areas of livestock epidemiology and global food security. It is comprised of a methodological introduction, an executive summary, three journal-article formatted chapters, and an overarching discussion section. Chapter One employs an agent-based computer model (RUSH-PNBM v.1.1) developed to study the potential impact of the trend toward increased producer specialization on resilience to catastrophic epidemics within livestock production chains. In each run, an infection is introduced and may spread according to probabilities associated with the various modes of contact between hog producer, feed mill, and slaughter plant agents. Experimental data reveal that more-specialized systems are vulnerable to outbreaks at lower spatial densities, have more abrupt percolation transitions, and are characterized by less-predictable outcomes; suggesting that reworking network structures may represent a viable means to increase biosecurity. Chapter Two uses a calibrated, spatially-explicit version of RUSH-PNBM (v.1.2) to model the hog production chains within three U.S. states. Key metrics are calculated after each run, some of which pertain to overall network structures, while others describe each actor’s positionality within the network. A genetic programming algorithm is then employed to search for mathematical relationships between multiple individual indicators that effectively predict each node’s vulnerability. This “meta-metric” approach could be applied to aid livestock epidemiologists in the targeting of biosecurity interventions and may also be useful to study a wide range of complex network phenomena. Chapter Three focuses on food insecurity resulting from the projected gap between global food supply and demand over the coming decades. While no single solution has been identified, scholars suggest that investments into multiple interventions may stack together to solve the problem. However, formulating an effective plan of action requires knowledge about the level of change resulting from a given investment into each wedge, the time before that effect unfolds, the expected baseline change, and the maximum possible level of change. This chapter details an evolutionary-computational algorithm to optimize investment schedules according to the twin goals of maximizing global food security and minimizing cost. Future work will involve parameterizing the model through an expert informant advisory process to develop the existing framework into a practicable food policy decision-support tool

Novel Analytical Modelling-based Simulation of Worm Propagation in Unstructured Peer-to-Peer Networks

Millions of users world-wide are sharing content using Peer-to-Peer (P2P) networks, such as Skype and Bit Torrent. While such new innovations undoubtedly bring benefits, there are nevertheless some associated threats. One of the main hazards is that P2P worms can penetrate the network, even from a single node and then spread rapidly. Understanding the propagation process of such worms has always been a challenge for researchers. Different techniques, such as simulations and analytical models, have been adopted in the literature. While simulations provide results for specific input parameter values, analytical models are rather more general and potentially cover the whole spectrum of given parameter values. Many attempts have been made to model the worm propagation process in P2P networks. However, the reported analytical models to-date have failed to cover the whole spectrum of all relevant parameters and have therefore resulted in high false-positives. This consequently affects the immunization and mitigation strategies that are adopted to cope with an outbreak of worms. The first key contribution of this thesis is the development of a susceptible, exposed, infectious, and Recovered (SEIR) analytical model for the worm propagation process in a P2P network, taking into account different factors such as the configuration diversity of nodes, user behaviour and the infection time-lag. These factors have not been considered in an integrated form previously and have been either ignored or partially addressed in state-of-the-art analytical models. Our proposed SEIR analytical model holistically integrates, for the first time, these key factors in order to capture a more realistic representation of the whole worm propagation process. The second key contribution is the extension of the proposed SEIR model to the mobile M-SEIR model by investigating and incorporating the role of node mobility, the size of the worm and the bandwidth of wireless links in the worm propagation process in mobile P2P networks. The model was designed to be flexible and applicable to both wired and wireless nodes. The third contribution is the exploitation of a promising modelling paradigm, Agent-based Modelling (ABM), in the P2P worm modelling context. Specifically, to exploit the synergies between ABM and P2P, an integrated ABM-Based worm propagation model has been built and trialled in this research for the first time. The introduced model combines the implementation of common, complex P2P protocols, such as Gnutella and GIA, along with the aforementioned analytical models. Moreover, a comparative evaluation between ABM and conventional modelling tools has been carried out, to demonstrate the key benefits of ease of real-time analysis and visualisation. As a fourth contribution, the research was further extended by utilizing the proposed SEIR model to examine and evaluate a real-world data set on one of the most recent worms, namely, the Conficker worm. Verification of the model was achieved using ABM and conventional tools and by then comparing the results on the same data set with those derived from developed benchmark models. Finally, the research concludes that the worm propagation process is to a great extent affected by different factors such as configuration diversity, user-behaviour, the infection time lag and the mobility of nodes. It was found that the infection propagation values derived from state-of-the-art mathematical models are hypothetical and do not actually reflect real-world values. In summary, our comparative research study has shown that infection propagation can be reduced due to the natural immunity against worms that can be provided by a holistic exploitation of the range of factors proposed in this work

Multi-Scale Simulation of Complex Systems: A Perspective of Integrating Knowledge and Data

Complex system simulation has been playing an irreplaceable role in understanding, predicting, and controlling diverse complex systems. In the past few decades, the multi-scale simulation technique has drawn increasing attention for its remarkable ability to overcome the challenges of complex system simulation with unknown mechanisms and expensive computational costs. In this survey, we will systematically review the literature on multi-scale simulation of complex systems from the perspective of knowledge and data. Firstly, we will present background knowledge about simulating complex system simulation and the scales in complex systems. Then, we divide the main objectives of multi-scale modeling and simulation into five categories by considering scenarios with clear scale and scenarios with unclear scale, respectively. After summarizing the general methods for multi-scale simulation based on the clues of knowledge and data, we introduce the adopted methods to achieve different objectives. Finally, we introduce the applications of multi-scale simulation in typical matter systems and social systems

Arquitectura de un sistema integrado para diseño dirigido por modelos en el contexto de internet de las cosas con aplicaciones en medicina

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Informática, Departamento de Arquitectura de Computadores y Automática, leída el 14-10-20222Over the past few years, we have seen how processing and storage architectures become cheaper and more efficient, communication infrastructures become faster and more scalable, and many new ways of interacting with the world around us are being developed. Every day more devices are connected to the network, and the generation of data worldwide is growing exponentially. In this context, the Internet of Things promises to be the new technological revolution, as was the introduction of the network of networks or universal mobile accessibility in tis day...A lo largo de los últimos años hemos visto cómo las arquitecturas de procesamiento y almacenamiento se vuelven más baratas y eficientes, las infraestructuras de comunicación se hacen más rápidas y escalables, y se desarrollan multitud de nuevas formas de interactuar con el mundo que nos rodea. Cada día más dispositivos se conectan a la red, y la generación de datos a nivel mundal está creciendo exponencialmente. En este contexto, el Internet de las cosas promete ser la nueva revolución tecnológica, como en su día lo fue la introducción de la red de redes o la accesibilidad móvil universal...Fac. de InformáticaTRUEunpu