2206785
What Have Gene Libraries Done for AIS?
Artificial Immune Systems (AIS) have been shown to be useful, practical and realisable approaches to real-world problems. Most AIS implementations are based around a canonical algorithm such as clonotypic learning, which we may think of as individual, lifetime learning. Yet a species also learns. Gene libraries are often thought of as a biological mechanism for generating combinatorial diversity of antibodies. However, they also bias the antibody creation process, so that they can be viewed as a way of guiding the lifetime learning mechanisms. Over time, the gene libraries in a species will evolve to an appropriate bias for the expected environment (based on species memory). Thus gene libraries are a form of meta-learning which could be useful for AIS. Yet they are hardly ever used. In this paper we consider some of the possible benefits and implications of incorporating the evolution of gene libraries into AIS practice. We examine some of the issues that must be considered if the implementation is to be successful and beneficial.
16182080
Self adaptation of mutation rates in a steady state genetic algorithm
This paper investigates the use of genetically encoded mutation rates within a "steady state" genetic algorithm in order to provide a self-adapting mutation mechanism for incremental evolution. One of the outcomes of this work will be a reduction in the number of parameters required to be set by the operator, thus facilitating the transfer of evolutionary computing techniques into an industrial setting. The NK family of landscapes is used to provide a variety of different problems with known statistical features in order to examine the effects of changing various parameters on the performance of the search. A number of policies are considered for the replacement of members of the population with newly created individuals and recombination of material between parents, and a number of methods of encoding for mutation rate are investigated. Empirical comparisons (using the "best-of current-population" metric) over a range of test problems show that a genetic algorithm incorporating the best "flavour" of the adaptive mutation operator outperformed the same algorithm when using any one of a variety of "standard" fixed mutation rates suggested by other authors.
17502763
Alignment Of Protein Structures With A Memetic Evolutionary Algorithm
CATEGORY: Real-World Applications 
 
Structural comparison of proteins is a core problem in modern biomedical research. Identifying structural similarities is essential for the assessment of the relationship between structure and function in proteins, and structural comparison techniques play a key role in applications like rational drug design. In this paper we consider a technique for protein structure comparison known as the maximum contact map overlap problem. In this problem, the similarity between two protein structures is computed by aligning the proteins to maximize the number of shared contacts in their corresponding contact maps. 
 
We present a new approach to this problem that uses a Multimeme evolutionary algorithm. The best solution found by our algorithm provides a lower bound on the value of the optimal structural alignment between the proteins. We have evaluated the Multimeme algorithm on a range of benchmark problems and compared with previous heuristics. We apply a linear programming method, which provides an upper bound, to assess the accuracy of our solutions. Our experiments show that the Multimeme evolutionary algorithm represents a significant improvement on the current state of the art in metaheuristics for this problem.
17447930
Incorporation of adaptive mutation based on subjective evaluation in an interactive evolution strategy
A rapidly emerging model in the field of adaptive computing is the symbiosis of human expertise with evolutionary algorithms for user controlled and directed search. The two aspects in any EA are the selection of individuals to reproduce based on some measure of their quality or fitness and the application of variation operators to produce new solutions. In the context of interactive evolution, these aspects are compounded by the need for rapid convergence to prevent user fatigue and to provide the user some control over the generation of new solutions. Elsewhere, in the work of the authors (2004), we have examined different policies for best incorporating the user into the evaluation and selection process. In this paper, we explore the hypothesis that user assigned fitness represents a source of information that can be used to control the variation process: effectively to broaden the search if none of the current solutions is promising, or focus the search and improve convergence speed in the vicinity of a good solution. The main aims of this study, therefore, are to analyse the advantages of using a user directed adaptive mutation strategy over fixed mutation step sizes in terms of time to converge and robustness of the resulting solution. We present results showing a qualitatively different type of search process can be obtained by using the user assigned fitness to control the nature of the mutation process. There is also a synergy between user-based selection and fitness-based mutation control which out performs either system on its own.
3062981
Recombination strategy adaptation via evolution of gene linkage
Analyses recombination strategies resulting from evolving gene linkage on a variety of fitness landscapes with known properties. The evolution of "blocks" of linked genes within a gene-pool makes it possible for the recombination strategy to vary in both the amount of genetic material exchanged during the formation of a new individual and in the number of parents contributing genetic material. The strategies evolved are examined in the light of the known properties of the landscapes. The results obtained explain the previously recorded good performance of the algorithm as a self-adaptive mechanism for function optimisation, as the amount and type of recombination is able to adapt to suit the landscape being searched, unlike conventional "fixed" operators.
796697
A tutorial for competent memetic algorithms: model, taxonomy, and design issues
The combination of evolutionary algorithms with local search was named "memetic algorithms" (MAs) (Moscato, 1989). These methods are inspired by models of natural systems that combine the evolutionary adaptation of a population with individual learning within the lifetimes of its members. Additionally, MAs are inspired by Richard Dawkin's concept of a meme, which represents a unit of cultural evolution that can exhibit local refinement (Dawkins, 1976). In the case of MA's, "memes" refer to the strategies (e.g., local refinement, perturbation, or constructive methods, etc.) that are employed to improve individuals. In this paper, we review some works on the application of MAs to well-known combinatorial optimization problems, and place them in a framework defined by a general syntactic model. This model provides us with a classification scheme based on a computable index D, which facilitates algorithmic comparisons and suggests areas for future research. Also, by having an abstract model for this class of metaheuristics, it is possible to explore their design space and better understand their behavior from a theoretical standpoint. We illustrate the theoretical and practical relevance of this model and taxonomy for MAs in the context of a discussion of important design issues that must be addressed to produce effective and efficient MAs.
5406998
Security for Virtual Private Intranets
As telecommuting grows, businesses must consider security when extending their network environment to employees' homes. Researchers at the University of Pennsylvania have addressed the problem with smart cards, operating system modifications, and network authentication. We note the distinction between trust and integrity: trust is determined through the verification of components and the dependencies among them, while integrity demonstrates that components haven't been modified. Thus integrity checking in a trustworthy system is about preserving an established trust or trust relationship. Our solution to the challenge of isolating functional roles that may share a single hardware platform is called secure identity based lending (SIBL). SIBL provides multiple personalities by partitioning the hard drive into n+1 partitions, where n is the number of supported personalities. All personalities use the system partition for core operating system components and shared applications. Each of the personalities is also associated with one of the remaining partitions, which are encrypted using a symmetric algorithm.
9844851
Communicating emotion through a haptic link: Design space and methodology
Communication of affect across a distance is not well supported by current technology, despite its importance to interpersonal interaction in modern lifestyles. Touch is a powerful conduit for emotional connectedness, and thus mediating haptic (touch) displays have been proposed to address this deficiency; but suitable evaluative methodology has been elusive. In this paper, we offer a first, structured examination of a design space for haptic support of remote affective communication, by analyzing the space and then comparing haptic models designed to manipulate its key dimensions. In our study, dyads (intimate pairs or strangers) are asked to communicate specified emotions using a purely haptic link that consists of virtual models rendered on simple knobs. These models instantiate both interaction metaphors of varying intimacy, and representations of virtual interpersonal distance. Our integrated objective and subjective observations imply that emotion can indeed be communicated through this medium, and confirm that the factors examined influence emotion communication performance as well as preference, comfort and connectedness. The proposed design space and the study results have implications for future efforts to support affective communication using the haptic modality, and the study approach comprises a first model for systematic evaluation of haptically expressed affect.
17495706
Fault-tolerance in distributed query processing
Fault-tolerance has long been a feature of database systems, with transactions supporting the structuring of applications so as to ensure continuation of updating applications in spite of machine failures. For read-only queries the perceived wisdom has been that support for fault-tolerance is too expensive to be worthwhile. Distributed query processing is coming to be seen as a promising way of implementing applications that combine structured data and analysis operations in dynamic distributed settings such as computational grids. Such a query may be long-running and having to redo the whole query after a failure may cause problems (e.g. if the result may trigger business or safety critical activities). This work describes and evaluates a new scheme for adding fault-tolerance to distributed query processing through a rollback-recovery mechanism. The high level expression of user requests in a physical algebra offers opportunities for tuning the fault-tolerance provision so as to reduce the cost, and give better performance than employment of generic fault-tolerance mechanisms at the lowest level of query processing. This paper outlines how the publicly-available OGSA-DQP computational grid-based distributed query processing system can be modified to include support for fault-tolerance and presents a performance evaluation which includes measurements of the cost of both protocol overheads and rollback-recovery, for a set of example distributed queries.
6106969
Service-Based Distributed Querying on the Grid
Service-based approaches (such as Web Services and the Open Grid Services Architecture) have gained considerable attention recently for supporting distributed application development in e-business and e-science. The emergence of a service-oriented view of hardware and software resources raises the question as to how database management systems and technologies can best be deployed or adapted for use in such an environment. This paper explores one aspect of service-based computing and data management, viz., how to integrate query processing technology with a service-based Grid. The paper describes in detail the design and implementation of a service-based distributed query processor for the Grid. The query processor is service-based in two orthogonal senses: firstly, it supports querying over data storage and analysis resources that are made available as services, and, secondly, its internal architecture factors out as services the functionalities related to the construction of distributed query plans on the one hand, and to their execution over the Grid on the other. The resulting system both provides a declarative approach to service orchestration in the Grid, and demonstrates how query processing can benefit from dynamic access to computational resources on the Grid.
17082505
Designing Biomorphs with an Interactive Genetic Algorithm
We describe an interactive version of the Genetic Algorithm which can be used to evolve Fourier series based \biomorphs." The user plays the role of a binary-valued objective function. The usual Genetic operators of Selection, Mutation, and Crossover are applied normally. We discuss the Interactive Genetic Algorithm's use as a teaching tool and in domains in which measures of utility are di cult or impossible to specify mathematically. We argue that the evolution of biomorphs can be considered an ergonomic design problem, and with the evolution of biomorphs as an example, we argue that a large class of design problems can be cast as \imprecise optimization" and \solved" with Interactive Genetic Algorithms. Thus IGAs can be used for applications that fall somewhere between AI, optimization, and CAD.