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

Data Partition and Communication On Parallel Heuristik Model Based on Clonal Selection Algorithm

Researchers conducted experiments on parallel algorithms, which are inspired by the clonal selection, called Clonal Selection Algorithm (CSA). This algorithm is a population-based heuristic solution. Course-grained parallelism model applied to improve the execution time. Inter-process communication overhead is addressed by adjusting the communication frequencies and size of data communicated. In this research, conducted experiments on six parallel computing models represent all possible partitions and communications. Experiments conducted using data of NP-Problem, Traveling Salesman Problem (TSP). The algorithm is implemented using the model of message passing libraries using MPJExpress. Experiments conducted in a cluster computation environment. Result shows the best parallelism model is achieved by partitioning the initial population data at the beginning of communication and the end of generation. Communication frequency can be up to per 1% of the population size generated. Using four dataset from TSPLib, this reseache shows effect of the communication frequency that increased the best cost, from 44.16% to 87.01% for berlin52.tsp; from 9.61% to 53.43%  for kroA100.tsp, and from 12.22% to 17.18% for tsp225.tsp. With eight processors, using communication frequency will be reduced the execution time e.g 93.07%, 91.60%, 89.60%, 74.74% for burma14.tsp, berlin52.tsp, kroA100.tsp, and tsp225.tsp respectively. We conclude that frequency of communication greatly affects the execution time, and also the best cost. It improved execution time and best cost

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

Accurate Viral Population Assembly From Ultra-Deep Sequencing Data

Motivation: Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors. Results: In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation–maximization algorithm to estimate abundances of the assembled viral variants in the population. Results on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads

Protein multiple sequence alignment by hybrid bio-inspired algorithms

This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the ‘weighted sum of pairs’ as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space

DEVELOPMENT OF SECUREPLUS ANTIVIRUS WITH THE ARTIFICIAL IMMUNE SYSTEMMODEL

This paper is about Malware proliferation in the wide and the development of an Antivirus called Secure Plus. Malware is a generic name for malfunctioned program codes that could wreak destructive impacts on Information Technology critical infrastructures. These malware usually use various techniques to avoid being detected; usually they are encrypted using hybridized cryptographic algorithms. Malware may be detected using antivirus that can scan the database signatures already accumulated and stored by antivirus vendors in some server. These stored databases signatures can then be compared with zero-day malware through comparison with the benign software. The zero-day malware are of sophisticated program codes that can transmute into different transforming patterns; yet retain their portent functionalities attributes and are now of billion categories by deverse clones. This paper after over viewing the literatures on ground (and they are of large numerical numbers), attempts to make its contribution to the design and development of Antivirus that can detect those zero-day or metamorphic malware. This proposed Antivirus being developed is christened Secure Plus that applies the heuristic Artificial Immune System Algorithm for the design and development. The tested experimental outputs are provided as prove of the Secure Plus effectual functionality worthy of application but need further works through to detect malware proactively

10361 Abstracts Collection and Executive Summary -- Theory of Evolutionary Algorithms

From September 5 to 10, the Dagstuhl Seminar 10361 ``Theory of Evolutionary Algorithms \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general

Traveling Salesman Problem

This book is a collection of current research in the application of evolutionary algorithms and other optimal algorithms to solving the TSP problem. It brings together researchers with applications in Artificial Immune Systems, Genetic Algorithms, Neural Networks and Differential Evolution Algorithm. Hybrid systems, like Fuzzy Maps, Chaotic Maps and Parallelized TSP are also presented. Most importantly, this book presents both theoretical as well as practical applications of TSP, which will be a vital tool for researchers and graduate entry students in the field of applied Mathematics, Computing Science and Engineering