Leandro Nunes de Castro

Recent Developments In Biologically Inspired Computing

Recent Developments in Biologically Inspired Computing is necessary reading for undergraduate and graduate students, and researchers interested in knowing the most recent advances in problem-solving techniques inspired by nature. This book covers the most relevant areas in computational intelligence, including evolutionary algorithms, artificial neural networks, artificial immune systems and swarm systems. It also brings together novel and philosophical trends in the exciting fields of artificial life and robotics. This book has the advantage of covering a large number of computational approaches, presenting the state-of-the-art before entering into the details of specific extensions and new developments. Pseudocodes, flow charts and examples of applications are provided of the new approaches presented.

Evolving clusters in gene-expression data

Clustering is a useful exploratory tool for gene-expression data. Although successful applications of clustering techniques have been reported in the literature, there is no method of choice in the gene-expression analysis community. Moreover, there are only a few works that deal with the problem of automatically estimating the number of clusters in bioinformatics datasets. Most clustering methods require the number k of clusters to be either specified in advance or selected a posteriori from a set of clustering solutions over a range of k. In both cases, the user has to select the number of clusters. This paper proposes improvements to a clustering genetic algorithm that is capable of automatically discovering an optimal number of clusters and its corresponding optimal partition based upon numeric criteria. The proposed improvements are mainly designed to enhance the efficiency of the original clustering genetic algorithm, resulting in two new clustering genetic algorithms and an evolutionary algorithm for clustering (EAC). The original clustering genetic algorithm and its modified versions are evaluated in several runs using six gene-expression datasets in which the right clusters are known a priori. The results illustrate that all the proposed algorithms perform well in gene-expression data, although statistical comparisons in terms of the computational efficiency of each algorithm point out that EAC outperforms the others. Statistical evidence also shows that EAC is able to outperform a traditional method based on multiple runs of k-means over a range of k.

An artificial immune network for multimodal function optimization on dynamic environments

Multimodal optimization algorithms inspired by the immune system are generally characterized by a dynamic control of the population size and by diversity maintenance along the search. One of the most popular proposals is denoted opt-aiNet (artificial immune network for optimization) and is extended here to deal with time-varying fitness functions. Additional procedures are designed to improve the overall performance and the robustness of the immune-inspired approach, giving rise to a version for dynamic optimization, denoted dopt-aiNet. Firstly, challenging benchmark problems in static multimodal optimization are considered to validate the new proposal. No parameter adjustment is necessary to adapt the algorithm according to the peculiarities of each problem. In the sequence, dynamic environments are considered, and usual evaluation indices are adopted to assess the performance of dopt-aiNet and compare with alternative solution procedures available in the literature.

An Overview of Artificial Immune Systems

The immune system is highly distributed, highly adaptive, self-organising in nature, maintains a memory of past encounters and has the ability to continually learn about new encounters. From a computational point of view, the immune system has much to offer by way of inspiration to computer scientists and engineers alike. As computational problems become more complex, increasingly, people are seeking out novel approaches to these problems, often turning to nature for inspiration. A great deal of attention is now being paid to the vertebrae immune system as a potential source of inspiration, where it is thought that different insights and alternative solutions can be gleaned, over and above other biologically inspired methods. Given this rise in attention to the immune system, it seems appropriate to explore this area in some detail. This survey explores the salient features of the immune system that are inspiring computer scientists and engineers to build Artificial Immune Systems (AIS). An extensive survey of applications is presented, ranging from network security to optimisation and machine learning. However, this is not complete, as no survey ever is, but it is hoped this will go some way to illustrate the potential of this exciting and novel area of research.

Artificial homeostatic system: a novel approach

Many researchers are developing frameworks inspired by natural, especially biological, systems to solve complex real-world problems. This work extends previous work in the field of biologically inspired computing, proposing an artificial endocrine system for autonomous robot navigation. Having intrinsic self-organizing behaviour, the novel artificial endocrine system can be applied to a wide range of problems, particularly those that involve decision making under changing environmental conditions, such as autonomous robot navigation. This work draws on “embodied cognitive science”, including the study of intelligence, adaptivity, homeostasis, and the dynamic aspects of cognition, in order to help lay down fundamental principles and techniques for a novel approach to more biologically plausible artificial homeostatic systems. Results from using the artificial endocrine system to control a simulated robot are presented.

Adaptive radius immune algorithm for data clustering

Many algorithms perform data clustering by compressing the original data into a more compact and interpretable representation, which can be more easily inspected for the presence of clusters. This, however, can be a risky alternative, because the simplified representation may contain distortions mainly related to the density information present in the data, which can considerably act on the clustering results. In order to treat this deficiency, this paper proposes an Adaptive Radius Immune Algorithm (ARIA), which is capable of maximally preserving the density information after compression by implementing an antibody adaptive suppression radius that varies inversely with the local density in the space. ARIA is tested with both artificial and real world problems obtaining a better performance than the aiNet algorithm and showing that preserving the density information leads to refined clustering results.

An immunological filter for spam

Spam messages are continually filling email boxes of practically every Web user. To deal with this growing problem, the development of high-performance filters to block those unsolicited messages is strongly required. An Antibody Network, more precisely SRABNET (Supervised Real-Valued Antibody Network), is proposed as an alternative filter to detect spam. The model of the antibody network is generated automatically from the training dataset and evaluated on unseen messages. We validate this approach using a public corpus, called PU1, which has a large collection of encrypted personal e-mail messages containing legitimate messages and spam. Finally, we compared the performance with the well known naive Bayes filter using some performances indexes that will be presented.

Improving the Efficiency of a Clustering Genetic Algorithm

Finding optimal clusterings is a difficult task. Most clustering methods require the number of clusters to be specified in advance, and hierarchical methods typically produce a set of clusterings. In both cases, the user has to select the number of clusters. This paper proposes improvements for a clustering genetic algorithm that is capable of finding an optimal number of clusters and their partitions automatically, based upon numeric criteria. The proposed improvements were designed to enhance the efficiency of a clustering genetic algorithm. The modified algorithms are evaluated in several simulations.

A Cluster-Based Feature Selection Approach

This paper proposes a filter-based method for feature selection. The filter is based on the partitioning of the feature space into clusters of similar features. The number of clusters and, consequently, the cardinality of the subset of selected features, is automatically estimated from the data. Empirical results illustrate the performance of the proposed algorithm, which in general has obtained competitive results in terms of classification accuracy when compared to a state of the art algorithm for feature selection, but with more modest computing time requirements.

Bioinformatics Data Analysis Using an Artificial Immune Network

This work describes a new proposal for gene expression data clustering based on a combination of an immune network, named aiNet, and the minimal spanning tree (MST). The aiNet is an AIS inspired by the immune network theory. Its main role is to perform data compression and to identify portions of the input space representative of a given data set. The output of aiNet is a set of antibodies that represent the data set in a simplified way. The MST is then built on this network, and clusters are determined by using a new method for detecting the inconsistent edges of the tree. An important advantage of this technique over the classical approaches, like hierarchical clustering, is that there is no need of previous knowledge about the number of clusters and their distributions. The hybrid algorithm was first applied to a benchmark data set to demonstrate its validity, and its results were compared with those produced by other approaches from the literature. Using the full yeast S. cerevisiae gene expression data set, it was possible to detect a strong interconnection of the genes, hindering the perception of inconsistencies that may lead to the separation of data into clusters.