Artificial Immune Systems - Models, algorithms and applications

Copyright © 2010 Academic Research Publishing Agency.This article has been made available through the Brunel Open Access Publishing Fund.Artificial Immune Systems (AIS) are computational paradigms that belong to the computational intelligence family and are inspired by the biological immune system. During the past decade, they have attracted a lot of interest from researchers aiming to develop immune-based models and techniques to solve complex computational or engineering problems. This work presents a survey of existing AIS models and algorithms with a focus on the last five years.This article is available through the Brunel Open Access Publishing Fun

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Aisimam - An Artificial immune system based intelligent multiangent model

The goal of this thesis is to develop a biological model for multiagent systems. This thesis explores artificial immune systems, a novel evolutionary paradigm based on the immunological principles. Artificial Immune systems (AIS) are found to be powerful to solve complex computational tasks. The main focus of the thesis is to develop a generic mathematical model that uses the principles of the human immune system in multiagent systems (MAS). The components and properties of the human immune system are studied. On understanding the concepts of A/5, a literature survey of multiagent systems is performed to understand and compare the multiagent concepts and AIS concepts. An analogy between the immune system parameters and the agent theory was derived. Then, an intelligent multiagent model named AISIMAM is derived. It exploits several properties and features of the immune system in multiagent systems. In other words, the intelligence of the immune systems to kill the antigen and the characteristics of the agents are combined in the model. The model is expressed in terms of mathematical expressions. The model is applied to a specific application namely the mine detection and defusion. The simulations are done in MATLAB that runs on a PC. The experimental results of AISIMAM applied to the mine detection problem are discussed. The results are successful and shows that AISIMAM could be an alternative solution to agent based problems. Artificial Immune System is also applied to a pattern recognition problem. The problem experimented is a color image classification problem useful in a real time industrial application. The images are those of wooden components that need to be classified according to the color and type of wood. To solve the classification task, a simple negative selection and genetic algorithm based A/5 algorithm was developed and simulated. The results are compared with the radial basis function approach applied to the same set of input images

Neurofly 2008 abstracts : the 12th European Drosophila neurobiology conference 6-10 September 2008 Wuerzburg, Germany

This volume consists of a collection of conference abstracts

Emergent networks in immune system shape space

The development of a computational model is reported which facilitates the study of emergent principles of human immune system effector T cell clonotype repertoire and its distribution and differentiation. In particular, the question of systemic self-organisation is addressed. The model represents an extension to earlier immune system shape space formalism, such that each activated effector T cell clonotype and respective immunogenic viral epitope is represented as a node in a two-dimensional network space, and edges between nodes models the affinity and clearance pressure applied to the antigen presenting cell bearing the target epitope. As the model is repeatedly exposed to infection by heterologous or mutating viruses, a distinct topology of the network shape space emerges which may offer a theoretical explanation of recent biological experimental results in the field of murine (mouse) cytotoxic T cell activation, apoptosis, crossreactivity, and memory - especially with respect to repeated reinfection. In the past, most discrete computational models of immune response to vira l infections have used separate real space or shape space formalisms. In this work, however, we have developed a model based on a combination of the two, with the objective of demonstrating how emergent behaviour and principles of self organisation may arise from a many-particle microscopic system. This is achieved by using a stochastic model of the lymphatic system as stimulus to a networ

Immune System Based Control and Intelligent Agent Design for Power System Applications

The National Academy of Engineering has selected the US Electric Power Grid as the supreme engineering achievement of the 20th century. Yet, this same grid is struggling to keep up with the increasing demand for electricity, its quality and cost. A growing recognition of the need to modernize the grid to meet future challenges has found articulation in the vision of a Smart Grid in using new control strategies that are intelligent, distributed, and adaptive. The objective of this work is to develop smart control systems inspired from the biological Human Immune System to better manage the power grid at the both generation and distribution levels. The work is divided into three main sections. In the first section, we addressed the problem of Automatic Generation Control design. The Clonal Selection theory is successfully applied as an optimization technique to obtain decentralized control gains that minimize a performance index based on Area Control Errors. Then the Immune Network theory is used to design adaptive controllers in order to diminish the excess maneuvering of the units and help the control areas comply with the North American Electric Reliability Corporation\u27s standards set to insure good quality of service and equitable mutual assistance by the interconnected energy balancing areas. The second section of this work addresses the design and deployment of Multi Agent Systems on both terrestrial and shipboard power systems self-healing using a novel approach based on the Immune Multi-Agent System (IMAS). The Immune System is viewed as a highly organized and distributed Multi-Cell System that strives to heal the body by working together and communicating to get rid of the pathogens. In this work both simulation and hardware design and deployment of the MAS are addressed. The third section of this work consists in developing a small scale smart circuit by modifying and upgrading the existing Analog Power Simulator to demonstrate the effectiveness of the developed technologies. We showed how to develop smart Agents hardware along with a wireless communication platform and the electronic switches. After putting together the different designed pieces, the resulting Multi Agent System is integrated into the Power Simulator Hardware. The multi Agent System developed is tested for fault isolation, reconfiguration, and restoration problems by simulating a permanent three phase fault on one of the feeder lines. The experimental results show that the Multi Agent System hardware developed performed effectively and in a timely manner which confirms that this technology is very promising and a very good candidate for Smart Grid control applications

An Artificial Immune System Strategy for Robust Chemical Spectra Classification via Distributed Heterogeneous Sensors

The timely detection and classification of chemical and biological agents in a wartime environment is a critical component of force protection in hostile areas. Moreover, the possibility of toxic agent use in heavily populated civilian areas has risen dramatically in recent months. This thesis effort proposes a strategy for identifying such agents vis distributed sensors in an Artificial Immune System (AIS) network. The system may be used to complement electronic nose ( E-nose ) research being conducted in part by the Air Force Research Laboratory Sensors Directorate. In addition, the proposed strategy may facilitate fulfillment of a recent mandate by the President of the United States to the Office of Homeland Defense for the provision of a system that protects civilian populations from chemical and biological agents. The proposed system is composed of networked sensors and nodes, communicating via wireless or wired connections. Measurements are continually taken via dispersed, redundant, and heterogeneous sensors strategically placed in high threat areas. These sensors continually measure and classify air or liquid samples, alerting personnel when toxic agents are detected. Detection is based upon the Biological Immune System (BIS) model of antigens and antibodies, and alerts are generated when a measured sample is determined to be a valid toxic agent (antigen). Agent signatures (antibodies) are continually distributed throughout the system to adapt to changes in the environment or to new antigens. Antibody features are determined via data mining techniques in order to improve system performance and classification capabilities. Genetic algorithms (GAs) are critical part of the process, namely in antibody generation and feature subset selection calculations. Demonstrated results validate the utility of the proposed distributed AIS model for robust chemical spectra recognition