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

Metaheuristic design of feedforward neural networks: a review of two decades of research

Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

A Hierarchal Planning Framework for AUV Mission Management in a Spatio-Temporal Varying Ocean

The purpose of this paper is to provide a hierarchical dynamic mission planning framework for a single autonomous underwater vehicle (AUV) to accomplish task-assign process in a limited time interval while operating in an uncertain undersea environment, where spatio-temporal variability of the operating field is taken into account. To this end, a high level reactive mission planner and a low level motion planning system are constructed. The high level system is responsible for task priority assignment and guiding the vehicle toward a target of interest considering on-time termination of the mission. The lower layer is in charge of generating optimal trajectories based on sequence of tasks and dynamicity of operating terrain. The mission planner is able to reactively re-arrange the tasks based on mission/terrain updates while the low level planner is capable of coping unexpected changes of the terrain by correcting the old path and re-generating a new trajectory. As a result, the vehicle is able to undertake the maximum number of tasks with certain degree of maneuverability having situational awareness of the operating field. The computational engine of the mentioned framework is based on the biogeography based optimization (BBO) algorithm that is capable of providing efficient solutions. To evaluate the performance of the proposed framework, firstly, a realistic model of undersea environment is provided based on realistic map data, and then several scenarios, treated as real experiments, are designed through the simulation study. Additionally, to show the robustness and reliability of the framework, Monte-Carlo simulation is carried out and statistical analysis is performed. The results of simulations indicate the significant potential of the two-level hierarchical mission planning system in mission success and its applicability for real-time implementation

A memetic particle swarm optimisation algorithm for dynamic multi-modal optimisation problems

Copyright @ 2011 Taylor & Francis.Many real-world optimisation problems are both dynamic and multi-modal, which require an optimisation algorithm not only to find as many optima under a specific environment as possible, but also to track their moving trajectory over dynamic environments. To address this requirement, this article investigates a memetic computing approach based on particle swarm optimisation for dynamic multi-modal optimisation problems (DMMOPs). Within the framework of the proposed algorithm, a new speciation method is employed to locate and track multiple peaks and an adaptive local search method is also hybridised to accelerate the exploitation of species generated by the speciation method. In addition, a memory-based re-initialisation scheme is introduced into the proposed algorithm in order to further enhance its performance in dynamic multi-modal environments. Based on the moving peaks benchmark problems, experiments are carried out to investigate the performance of the proposed algorithm in comparison with several state-of-the-art algorithms taken from the literature. The experimental results show the efficiency of the proposed algorithm for DMMOPs.This work was supported by the Key Program of National Natural Science Foundation (NNSF) of China under Grant no. 70931001, the Funds for Creative Research Groups of China under Grant no. 71021061, the National Natural Science Foundation (NNSF) of China under Grant 71001018, Grant no. 61004121 and Grant no. 70801012 and the Fundamental Research Funds for the Central Universities Grant no. N090404020, the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant no. EP/E060722/01 and Grant EP/E060722/02, and the Hong Kong Polytechnic University under Grant G-YH60

EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences.

The availability of genome-wide epigenomic datasets enables in-depth studies of epigenetic modifications and their relationships with chromatin structures and gene expression. Various alignment tools have been developed to align nucleotide or protein sequences in order to identify structurally similar regions. However, there are currently no alignment methods specifically designed for comparing multi-track epigenomic signals and detecting common patterns that may explain functional or evolutionary similarities. We propose a new local alignment algorithm, EpiAlign, designed to compare chromatin state sequences learned from multi-track epigenomic signals and to identify locally aligned chromatin regions. EpiAlign is a dynamic programming algorithm that novelly incorporates varying lengths and frequencies of chromatin states. We demonstrate the efficacy of EpiAlign through extensive simulations and studies on the real data from the NIH Roadmap Epigenomics project. EpiAlign is able to extract recurrent chromatin state patterns along a single epigenome, and many of these patterns carry cell-type-specific characteristics. EpiAlign can also detect common chromatin state patterns across multiple epigenomes, and it will serve as a useful tool to group and distinguish epigenomic samples based on genome-wide or local chromatin state patterns

Linear, Deterministic, and Order-Invariant Initialization Methods for the K-Means Clustering Algorithm

Over the past five decades, k-means has become the clustering algorithm of choice in many application domains primarily due to its simplicity, time/space efficiency, and invariance to the ordering of the data points. Unfortunately, the algorithm's sensitivity to the initial selection of the cluster centers remains to be its most serious drawback. Numerous initialization methods have been proposed to address this drawback. Many of these methods, however, have time complexity superlinear in the number of data points, which makes them impractical for large data sets. On the other hand, linear methods are often random and/or sensitive to the ordering of the data points. These methods are generally unreliable in that the quality of their results is unpredictable. Therefore, it is common practice to perform multiple runs of such methods and take the output of the run that produces the best results. Such a practice, however, greatly increases the computational requirements of the otherwise highly efficient k-means algorithm. In this chapter, we investigate the empirical performance of six linear, deterministic (non-random), and order-invariant k-means initialization methods on a large and diverse collection of data sets from the UCI Machine Learning Repository. The results demonstrate that two relatively unknown hierarchical initialization methods due to Su and Dy outperform the remaining four methods with respect to two objective effectiveness criteria. In addition, a recent method due to Erisoglu et al. performs surprisingly poorly.Comment: 21 pages, 2 figures, 5 tables, Partitional Clustering Algorithms (Springer, 2014). arXiv admin note: substantial text overlap with arXiv:1304.7465, arXiv:1209.196

A Multi-Agent Architecture for the Design of Hierarchical Interval Type-2 Beta Fuzzy System

This paper presents a new methodology for building and evolving hierarchical fuzzy systems. For the system design, a tree-based encoding method is adopted to hierarchically link low dimensional fuzzy systems. Such tree structural representation has by nature a flexible design offering more adjustable and modifiable structures. The proposed hierarchical structure employs a type-2 beta fuzzy system to cope with the faced uncertainties, and the resulting system is called the Hierarchical Interval Type-2 Beta Fuzzy System (HT2BFS). For the system optimization, two main tasks of structure learning and parameter tuning are applied. The structure learning phase aims to evolve and learn the structures of a population of HT2BFS in a multiobjective context taking into account the optimization of both the accuracy and the interpretability metrics. The parameter tuning phase is applied to refine and adjust the parameters of the system. To accomplish these two tasks in the most optimal and faster way, we further employ a multi-agent architecture to provide both a distributed and a cooperative management of the optimization tasks. Agents are divided into two different types based on their functions: a structure agent and a parameter agent. The main function of the structure agent is to perform a multi-objective evolutionary structure learning step by means of the Multi-Objective Immune Programming algorithm (MOIP). The parameter agents have the function of managing different hierarchical structures simultaneously to refine their parameters by means of the Hybrid Harmony Search algorithm (HHS). In this architecture, agents use cooperation and communication concepts to create high-performance HT2BFSs. The performance of the proposed system is evaluated by several comparisons with various state of art approaches on noise-free and noisy time series prediction data sets and regression problems. The results clearly demonstrate a great improvement in the accuracy rate, the convergence speed and the number of used rules as compared with other existing approaches