Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation, and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.Comment: Submitted to 'Systems Medicine' as a book chapte

Agent-based simulation of electricity markets: a literature review

Liberalisation, climate policy and promotion of renewable energy are challenges to players of the electricity sector in many countries. Policy makers have to consider issues like market power, bounded rationality of players and the appearance of fluctuating energy sources in order to provide adequate legislation. Furthermore the interactions between markets and environmental policy instruments become an issue of increasing importance. A promising approach for the scientific analysis of these developments is the field of agent-based simulation. The goal of this article is to provide an overview of the current work applying this methodology to the analysis of electricity markets. --

Coordinated Transit Response Planning and Operations Support Tools for Mitigating Impacts of All-Hazard Emergency Events

This report summarizes current computer simulation capabilities and the availability of near-real-time data sources allowing for a novel approach of analyzing and determining optimized responses during disruptions of complex multi-agency transit system. The authors integrated a number of technologies and data sources to detect disruptive transit system performance issues, analyze the impact on overall system-wide performance, and statistically apply the likely traveler choices and responses. The analysis of unaffected transit resources and the provision of temporary resources are then analyzed and optimized to minimize overall impact of the initiating event

Control designs and reinforcement learning-based management for software defined networks

In this thesis, we focus our investigations around the novel software defined net- working (SDN) paradigm. The central goal of SDN is to smoothly introduce centralised control capabilities to the otherwise distributed computer networks. This is achieved by abstracting and concentrating network control functionalities in a logically centralised control unit, which is referred to as the SDN controller. To further balance between centralised control, scalability and reliability considerations, distributed SDN is introduced to enable the coexistence of multiple physical SDN controllers. For distributed SDN, networking elements are grouped together to form various domains, with each domain managed by an SDN controller. In such a distributed SDN setting, SDN controllers of all domains synchronise with each other to maintain logically centralised network views, which is referred to as controller synchronisation. Centred on the problem of SDN controller synchronisation, this thesis specifically aims at addressing two aspects of the subject as follows. First, we model and analyse the performance enhancements brought by controller synchronisation in distributed SDN from a theoretical perspective. Second, we design intelligent controller synchronisation policies by leveraging existing and creating new Reinforcement Learning (RL) and Deep Learning (DL)-based approaches. In order to understand the performance gains of SDN controller synchronisation from a fundamental and analytical perspective, we propose a two-layer network model based on graphs to capture various characteristics of distributed SDN net- works. Then, we develop two families of analytical methods to investigate the performance of distributed SDN in relationship to network structure and the level of SDN controller synchronisation. The significance of our analytical results is that they can be used to quantify the contribution of controller synchronisation level, in improving the network performance under different network parameters. Therefore, they serve as fundamental guidelines for future SDN performance analyses and protocol designs. For the designs of SDN controller synchronisation policies, most existing works focus on the engineering-centred system design aspect of the problem for ensuring anomaly-free synchronisation. Instead, we emphasise on the performance improvements with respect to (w.r.t.) various networking tasks for designing controller synchronisation policies. Specifically, we investigate various scenarios with diverse control objectives, which range from routing related performance metric to other more sophisticated optimisation goals involving communication and computation resources in networks. We also take into consideration factors such as the scalability and robustness of the policies developed. For this goal, we employ machine learning techniques to assist our policy designs. In particular, we model the SDN controller synchronisation policy as serial decision-making processes and resort to RL-based techniques for developing the synchronisation policy. To this end, we leverage a combination of various RL and DL methods, which are tailored for handling the specific characteristics and requirements in different scenarios. Evaluation results show that our designed policies consistently outperform some already in-use controller synchronisation policies, in certain cases by considerable margins. While exploring existing RL algorithms for solving our problems, we identify some critical issues embedded within these algorithms, such as the enormity of the state-action space, which can cause inefficiency in learning. As such, we propose a novel RL algorithm to address these issues, which is named state action separable reinforcement learning (sasRL). Therefore, the sasRL approach constitutes another major contribution of this thesis in the field of RL research.Open Acces

Beyond core-periphery relationship in the EC cooperation

During the current process of EU enlargement, regions are confronted with a need to revise their relative position within the newly formed socio-economic, spatial and cultural spaces. As existing equilibria are severely affected, the type and direction of developmental trends of member states (and regions) are increasingly questioned. Concerns are being raised about the risks that the annealing process would trigger a number of undesirable processes, i.e. loss of comparative advantages, regions lagging behind, accentuation of socio-economic gaps, social unbalances resulting from migration flows of poor population. These might hamper the path of European integration and eventually result in a reinforcement of the more accessible well developed areas and a loss of more peripheral and relatively underdeveloped ones. In this context, cooperation amongst the member states, and in particular, their local governments, may play a significant role to both overcome those risks and favouring the EU integration process. Information on cooperation (and integration) for the European countries is extensive and provides detailed accounts of the initiatives which have been undertaken since the establishment of EU programs in the early sixties. Although the variety of cooperation (integration) programs which have been launched as the EU unification progressed are well documented, existing studies have rarely questioned the kind of evolution ( i.e. type and extent of the changes underlying the various initiatives) those programs underwent. The aim of this paper is to undertake a preliminary step in this analysis. A claim is made that: a. on the one hand, the widening of the scopes of cooperation programs and increasing number of eligible actors involved are significantly reinforcing the potentials of cooperation in favouring the integration process not only among the member countries but also different kind of areas (i.e. between metropolitan and peripheral cities); b. on the other hand, there is a need to refine the current approaches to cooperation and develop a conceptual framework which serves as a basis for both formulating the various initiatives and defining effective benchmarks for their evaluation. The paper is organized in three main sections. The first addresses some methodological questions about the definition of what should be understood as a cooperation situation. An effort is made to identify a conceptual framework which might be relevant for dealing with cooperative actions in a institutionalised setting. This is then used in the second section to provide an account of the evolution of the EU programs on cooperation. Finally, in the last section attention is turned to the strengths (i.e. greater attention to the spatial dimension of cooperation programs, more equalitarian relationships amongst the participants) and weaknesses (i.e. lack of a shared model of cooperative actions) of the current approaches to cooperation. An effort is made to emphasize a few relevant questions which can be challenging in the current EU policies and thinking.

Multi-layered model of individual HIV infection progression and mechanisms of phenotypical expression

Cite as: Perrin, Dimitri (2008) Multi-layered model of individual HIV infection progression and mechanisms of phenotypical expression. PhD thesis, Dublin City University

Airport Passenger Processing Technology: A Biometric Airport Journey

A passengers’ traveling journey throughout the airport is anything but simple. A passenger goes through numerous hoops and hurdles before safely boarding the aircraft. Many airports today are implementing isolated solutions for passenger processing. Some of these technologies include automated self-service kiosks and bag tag, self-service bag drop-off, along with automated self-service gates for boarding and border control. These solutions can be integrated with biometric systems to enhance passenger handling. This thesis analyzes the current passenger processing technology implemented at airports around the world and their associated challenges that passengers face. A new passenger processing technology called a biometric single token identification (ID) is presented as a solution to help alleviate current issues. By using a medium-sized international airport as a case study, the results show that a single token ID is beneficial to the time it takes to process a passenger. Furthermore, it demonstrates that implementation of a single token ID with self-service technology can provide enhanced passenger travel experience, improving operational process efficiency, all while ensuring safety and security

Modeling The Spatiotemporal Dynamics Of Cells In The Lung

Multiple research problems related to the lung involve a need to take into account the spatiotemporal dynamics of the underlying component cells. Two such problems involve better understanding the nature of the allergic inflammatory response to explore what might cause chronic inflammatory diseases such as asthma, and determining the rules underlying stem cells used to engraft decellularized lung scaffolds in the hopes of growing new lungs for transplantation. For both problems, we model the systems computationally using agent-based modeling, a tool that enables us to capture these spatiotemporal dynamics by modeling any biological system as a collection of agents (cells) interacting with each other and within their environment. This allows to test the most important pieces of biological systems together rather than in isolation, and thus rapidly derive biological insights from resulting complex behavior that could not have been predicted beforehand, which we can then use to guide wet lab experimentation. For the allergic response, we hypothesized that stimulation of the allergic response with antigen results in a response with formal similarity to a muscle twitch or an action potential, with an inflammatory phase followed by a resolution phase that returns the system to baseline. We prepared an agent-based model (ABM) of the allergic inflammatory response and determined that antigen stimulation indeed results in a twitch-like response. To determine what might cause chronic inflammatory diseases where the twitch presumably cannot resolve back to baseline, we then tested multiple potential defects to the model. We observed that while most of these potential changes lessen the magnitude of the response but do not affect its overall behavior, extending the lifespan of activated pro-inflammatory cells such as neutrophils and eosinophil results in a prolonged inflammatory response that does not resolve to baseline. Finally, we performed a series of experiments involving continual antigen stimulation in mice, determining that there is evidence in the cytokine, cellular and physiologic (mechanical) response consistent with our hypothesis of a finite twitch and an associated refractory period. For stem cells, we made a 3-D ABM of a decellularized scaffold section seeded with a generic stem cell type. We then programmed in different sets of rules that could conceivably underlie the cell\u27s behavior, and observed the change in engraftment patterns in the scaffold over selected timepoints. We compared the change in those patterns against the change in experimental scaffold images seeded with C10 epithelial cells and mesenchymal stem cells, two cell types whose behaviors are not well understood, in order to determine which rulesets more closely match each cell type. Our model indicates that C10s are more likely to survive on regions of higher substrate while MSCs are more likely to proliferate on regions of higher substrate