Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm

The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class–II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming and cost intensive. Therefore, computational methods have been found helpful in classifying these peptides as binders or non-binders. We have applied negative selection algorithm, an artificial immune system approach to predict MHC class–II binders and non-binders. For the evaluation of the NSA algorithm, five fold cross validation has been used and six MHC class–II alleles have been taken. The average area under ROC curve for HLA-DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1501, DRB1*1301 have been found to be 0.75, 0.77, 0.71, 0.72, and 0.69, and 0.84 respectively indicating good predictive performance for the small training set

The design of an evolutionary algorithm for artificial immune system based failure detector generation and optimization

The development of an evolutionary algorithm and accompanying software for the generation and optimization of artificial immune system-based failure detectors is presented in this thesis. These detectors use the Artificial Immune System-based negative selection strategy. The utility is a part of an integrated set of methodologies for the detection, identification, and evaluation of a wide variety of aircraft sub-system abnormal conditions. The evolutionary algorithm and accompanying software discussed in this document is concerned with the creation, optimization, and testing of failure detectors based on the negative selection strategy. A preliminary phase consists of processing data from flight tests for self definition including normalization, duplicate removal, and clustering. A first phase of the evolutionary algorithm produces, through an iterative process, a set of detectors that do not overlap with the self and achieve a prescribed level of coverage of the non-self. A second phase consists of a classic evolutionary algorithm that attempts to optimize the number of detectors, overlapping between detectors, and coverage of the non-self while maintaining no overlapping with the self. For this second phase, the initial population is composed of sets of detectors, called individuals, obtained in the first phase. Specific genetic operators have been defined to accommodate different detector shapes, such as hyper-rectangles, hyper-spheres, hyper-ellipsoids and hyper-rotational-ellipsoids. The output of this evolutionary algorithm consists of an optimized set of detectors which is intended for later use as a part of a detection, identification, and evaluation scheme for aircraft sub-system failure.;An interactive design environment has been developed in MATLAB that relies on an advanced user-friendly graphical interface and on a substantial library of alternative algorithms to allow maximum flexibility and effectiveness in the design of detector sets for artificial immune system-based abnormal condition detection. This user interface is designed for use with Windows and MATLAB 7.6.0, although measures have been taken to maintain compatibility with MATLAB version 7.0.4 and higher, with limited interface compatibility. This interface may also be used with UNIX versions of MATLAB, version 7.0.4 or higher.;The results obtained show the feasibility of optimizing the various shapes in 2, 3, and 6 dimensions. Hyper-spheres are generally faster than the other three shapes, though they do not necessarily exhibit the best detection results. Hyper-ellipsoids and hyper-rotational-ellipsoids generally show somewhat better detection performance than hyper-spheres, but at a higher calculation cost. Calculation time for optimization of hyper-rectangles seems to be highly susceptible to dimensionality, taking increasingly long in higher dimensions. In addition, hyper-rectangles tend to need a higher number of detectors to achieve adequate coverage of the solution space, though they exhibit very little overlapping among detectors. However, hyper-rectangles are consistently and considerably quicker to calculate detection for than the other shapes, which may make them a promising candidate for online detection schemes

Immune network algorithm in monthly streamflow prediction at Johor river

This study proposes an alternative method in generating future stream flow data with single-point river stage. Prediction of stream flow data is important in water resources engineering for planning and design purposes in order to estimate long term forecasting. This paper utilizes Artificial Immune System (AIS) in modelling the stream flow of one stations of Johor River. AIS has the abilities of self-organizing, memory, recognition, adaptive and ability of learning inspired from the immune system. Immune Network Algorithm is part of the three main algorithm in AIS. The model of Immune Network Algorithm used in this study is aiNet. The training process in aiNet is partly inspired by clonal selection principle and the other part uses antibody interactions for removing redundancy and finding data patterns. Like any other traditional statistical and stochastic techniques, results from this study, exhibit that, Immune Network Algorithm is capable of producing future stream flow data at monthly duration with various advantages

Optimum Design of Shell and Tube Heat Exchanger Using Artificial Immune System Approach

This paper presents the economic optimization of shell and tube heat exchangers design approach through an artificial immune system algorithm for minimizing the cost. Since complex geometric parameters, with thermodynamic and fluid dynamic factors, consume more time and offer a minimum possibility for an optimum result in the case of conventional design, the design process becomes difficult. The proposed algorithm provides the designer with an optimum solution in less amount of time by analyzing three different case studies.  Three design variables such as shell internal diameter, tube outer diameter and baffle spacing from the different design parameters are taken into account for this optimization. The results are weighed against those obtained by various researchers

Artificial immune systems based committee machine for classification application

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.A new adaptive learning Artificial Immune System (AIS) based committee machine is developed in this thesis. The new proposed approach efficiently tackles the general problem of clustering high-dimensional data. In addition, it helps on deriving useful decision and results related to other application domains such classification and prediction. Artificial Immune System (AIS) is a branch of computational intelligence field inspired by the biological immune system, and has gained increasing interest among researchers in the development of immune-based models and techniques to solve diverse complex computational or engineering problems. This work presents some applications of AIS techniques to health problems, and a thorough survey of existing AIS models and algorithms. The main focus of this research is devoted to building an ensemble model integrating different AIS techniques (i.e. Artificial Immune Networks, Clonal Selection, and Negative Selection) for classification applications to achieve better classification results. A new AIS-based ensemble architecture with adaptive learning features is proposed by integrating different learning and adaptation techniques to overcome individual limitations and to achieve synergetic effects through the combination of these techniques. Various techniques related to the design and enhancements of the new adaptive learning architecture are studied, including a neuro-fuzzy based detector and an optimizer using particle swarm optimization method to achieve enhanced classification performance. An evaluation study was conducted to show the performance of the new proposed adaptive learning ensemble and to compare it to alternative combining techniques. Several experiments are presented using different medical datasets for the classification problem and findings and outcomes are discussed. The new adaptive learning architecture improves the accuracy of the ensemble. Moreover, there is an improvement over the existing aggregation techniques. The outcomes, assumptions and limitations of the proposed methods with its implications for further research in this area draw this research to its conclusion

Bioinspired Principles for Large-Scale Networked Sensor Systems: An Overview

Biology has often been used as a source of inspiration in computer science and engineering. Bioinspired principles have found their way into network node design and research due to the appealing analogies between biological systems and large networks of small sensors. This paper provides an overview of bioinspired principles and methods such as swarm intelligence, natural time synchronization, artificial immune system and intercellular information exchange applicable for sensor network design. Bioinspired principles and methods are discussed in the context of routing, clustering, time synchronization, optimal node deployment, localization and security and privacy

BIOLOGICAL INSPIRED INTRUSION PREVENTION AND SELF-HEALING SYSTEM FOR CRITICAL SERVICES NETWORK

With the explosive development of the critical services network systems and Internet, the need for networks security systems have become even critical with the enlargement of information technology in everyday life. Intrusion Prevention System (IPS) provides an in-line mechanism focus on identifying and blocking malicious network activity in real time. This thesis presents new intrusion prevention and self-healing system (SH) for critical services network security. The design features of the proposed system are inspired by the human immune system, integrated with pattern recognition nonlinear classification algorithm and machine learning. Firstly, the current intrusions preventions systems, biological innate and adaptive immune systems, autonomic computing and self-healing mechanisms are studied and analyzed. The importance of intrusion prevention system recommends that artificial immune systems (AIS) should incorporate abstraction models from innate, adaptive immune system, pattern recognition, machine learning and self-healing mechanisms to present autonomous IPS system with fast and high accurate detection and prevention performance and survivability for critical services network system. Secondly, specification language, system design, mathematical and computational models for IPS and SH system are established, which are based upon nonlinear classification, prevention predictability trust, analysis, self-adaptation and self-healing algorithms. Finally, the validation of the system carried out by simulation tests, measuring, benchmarking and comparative studies. New benchmarking metrics for detection capabilities, prevention predictability trust and self-healing reliability are introduced as contributions for the IPS and SH system measuring and validation. Using the software system, design theories, AIS features, new nonlinear classification algorithm, and self-healing system show how the use of presented systems can ensure safety for critical services networks and heal the damage caused by intrusion. This autonomous system improves the performance of the current intrusion prevention system and carries on system continuity by using self-healing mechanism

Monitoring and Control Framework for Advanced Power Plant Systems Using Artificial Intelligence Techniques

This dissertation presents the design, development, and simulation testing of a monitoring and control framework for dynamic systems using artificial intelligence techniques. A comprehensive monitoring and control system capable of detecting, identifying, evaluating, and accommodating various subsystem failures and upset conditions is presented. The system is developed by synergistically merging concepts inspired from the biological immune system with evolutionary optimization algorithms and adaptive control techniques.;The proposed methodology provides the tools for addressing the complexity and multi-dimensionality of the modern power plants in a comprehensive and integrated manner that classical approaches cannot achieve. Current approaches typically address abnormal condition (AC) detection of isolated subsystems of low complexity, affected by specific AC involving few features with limited identification capability. They do not attempt AC evaluation and mostly rely on control system robustness for accommodation. Addressing the problem of power plant monitoring and control under AC at this level of completeness has not yet been attempted.;Within the proposed framework, a novel algorithm, namely the partition of the universe, was developed for building the artificial immune system self. As compared to the clustering approach, the proposed approach is less computationally intensive and facilitates the use of full-dimensional self for system AC detection, identification, and evaluation. The approach is implemented in conjunction with a modified and improved dendritic cell algorithm. It allows for identifying the failed subsystems without previous training and is extended to address the AC evaluation using a novel approach.;The adaptive control laws are designed to augment the performance and robustness of baseline control laws under normal and abnormal operating conditions. Artificial neural network-based and artificial immune system-based approaches are developed and investigated for an advanced power plant through numerical simulation.;This dissertation also presents the development of an interactive computational environment for the optimization of power plant control system using evolutionary techniques with immunity-inspired enhancements. Several algorithms mimicking mechanisms of the immune system of superior organisms, such as cloning, affinity-based selection, seeding, and vaccination are used. These algorithms are expected to enhance the computational effectiveness, improve convergence, and be more efficient in handling multiple local extrema, through an adequate balance between exploration and exploitation.;The monitoring and control framework formulated in this dissertation applies to a wide range of technical problems. The proposed methodology is demonstrated with promising results using a high validity DynsimRTM model of the acid gas removal unit that is part of the integrated gasification combined cycle power plant available at West Virginia University AVESTAR Center. The obtained results show that the proposed system is an efficient and valuable technique to be applied to a real world application. The implementation of this methodology can potentially have significant impacts on the operational safety of many complex systems