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Protein-protein interactions play a pivotal role in modern molecular biology. Identifying the protein-protein interaction sites is great scientific and practical interest for predicting protein-protein interactions. In this study, we proposed a Gaussian Evolutionary Method (GEM) to optimize 18 features, including ten atomic solvent and eight protein 2nd structure features, for predicting protein-protein interaction sites. The training set consists of 104 unbound proteins selected from PDB and the predicted successful rate is 65.4% (68/104) proteins in the training dataset. These 18 parameters were then applied to a test set with 50 unbound proteins. Based on the threshold obtained from the training set, our method is able to predict the binding sites for 98% (49/50) proteins and yield 46% successful prediction and 42.3% average specificity. Here, a binding-site prediction is considered successful if 50% predicted area is indeed located in protein-protein interface (i.e. the specificity is more than 0.5). We believe that the optimized parameters of our method are useful for analyzing protein-protein interfaces and for interfaces prediction methods and protein-protein docking methods. [ABSTRACT FROM AUTHOR]

The annotation of transcription binding sites in new sequenced genomes is an important and challenging problem. We have previously shown how a regression model that linearly relates gene expression levels to the matching scores of nucleotide patterns allows us to identify DNA-binding sites from a collection of co-regulated genes and their nearby non-coding DNA sequences. Our methodology uses Bayesian models and stochastic search techniques to select transcription factor binding site candidates. Here we show that this methodology allows us to identify binding sites in nearby species. We present examples of annotation crossing from Schizosaccharomyces pombe to Schizosaccharomyces japonicus. We found that the eng1 motif is also regulating a set of 9 genes in S. japonicus. Our framework may have an effective interest in conveying information in the annotation process of a new species. Finally we discuss a number of statistical and biological issues related to the identification of binding sites through covariates of genes expression and sequences. [ABSTRACT FROM AUTHOR]

The Bio-basis Function Neural Network (BBFNN) is a novel neural architecture for peptide classification that makes use of amino acid mutation matrices and a similarity function to model protein peptide data without encoding. This study presents an Evolutionary Bio-basis network (EBBN), an extension to the BBFNN that uses a self adapting Evolution Strategy to optimise a problem specific substitution matrix for much improved model performance. The EBBN is assessed against BBFNN and multi layer perceptron (MLP) models using three datasets covering cleavage sites, epitope sites, and glycoprotein linkage sites. The method exhibits statistically significant improvements in performance for two of these sets. [ABSTRACT FROM AUTHOR]

"Quorum sensing" has been described as "the most consequential molecular microbiology story of the last decade" [1][2]. The purpose of this paper is to study the mechanism of quorum sensing, in order to obtain a deeper understanding of how and when this mechanism works. Our study focuses on the use of an Individual-based Modeling (IbM) method to simulate this phenomenon of "cell-to-cell communication" incorporated in bacterial foraging behavior, in both intracellular and population scales. The simulation results show that this IbM approach can reflect the bacterial behaviors and population evolution in time-varying environments, and provide plausible answers to the emerging question regarding to the significance of this phenomenon of bacterial foraging behaviors. [ABSTRACT FROM AUTHOR]

The ability to measure the transcriptional response after a stimulus has drawn much attention to the underlying gene regulatory networks. Here, we evaluate the application of methods to reconstruct gene regulatory networks by applying them to the SOS response of E. coli, the budding yeast cell cycle and in silico models. For each network we define an a priori validation network, where each interaction is justified by at least one publication. In addition to the existing methods, we propose a SVD based method (NSS). Overall, most reconstruction methods perform well on in silico data sets, both in terms of topological reconstruction and predictability. For biological data sets the application of reconstruction methods is suitable to predict the expression of genes, whereas the topological reconstruction is only satisfactory with steady-state measurements. Surprisingly, the performance measured on in silico data does not correspond with the performance measured on biological data. [ABSTRACT FROM AUTHOR]

In human mesenchymal stem cells the envelope surrounding the nucleus, as visualized by the nuclear lamina, has a round and flat shape. The lamina structure is considerably deformed after activation of cell death (apoptosis). The spatial organization of the lamina is the initial structural change found after activation of the apoptotic pathway, therefore can be used as a marker to identify cells activated for apoptosis. Here we investigated whether the spatial changes in lamina spatial organization can be recognized by machine learning algorithms to classify normal and apoptotic cells. Classical machine learning algorithms were applied to classification of 3D image sections of nuclear lamina proteins, taken from normal and apoptotic cells. We found that the Evolutionary-optimized Support Vector Machine (SVM) algorithm succeeded in the classification of normal and apoptotic cells in a highly satisfying result. This is the first time that cells are classified based on lamina spatial organization using the machine learning approach. We suggest that this approach can be used for diagnostic applications to classify normal and apoptotic cells. [ABSTRACT FROM AUTHOR]

Directed search methods and probabilistic approaches have been used as two alternative ways for computational protein design. This paper presents a hybrid methodology that combines features from both approaches. Three estimation of distribution algorithms are applied to the solution of a protein design problem by minimization of contact potentials. The combination of probabilistic models able to represent probabilistic dependencies with the use of information about residues interactions in the protein contact graph is shown to improve the efficiency of search for the problems evaluated. [ABSTRACT FROM AUTHOR]

Although important contributions have been made in recent years within the field of bioprocess model development and validation, in many cases the utility of even relatively good models for process optimization with current state-of-the-art algorithms (mostly offline approaches) is quite low. The main cause for this is that open-loop fermentations do not compensate for the differences observed between model predictions and real variables, whose consequences can lead to quite undesirable consequences. In this work, the performance of two different algorithms belonging to the main groups of Evolutionary Algorithms (EA) and Differential Evolution (DE) is compared in the task of online optimisation of fed-batch fermentation processes. The proposed approach enables to obtain results close to the ones predicted initially by the mathematical models of the process, deals well with the noise in state variables and exhibits properties of graceful degradation. When comparing the optimization algorithms, the DE seems the best alternative, but its superiority seems to decrease when noisier settings are considered. [ABSTRACT FROM AUTHOR]

A common way to characterise important and conserved signals in nucleotide sequences, such as transcription factor binding sites, is via the use of so-called consensus sequences or consensus patterns. A well-known example is the so-called "TATA-box" commonly found in eukaryotic core promoters. Such patterns are valuablein that they offer an insight into basic molecular biology processes, and can support reasoning regarding the understanding, design and control of these processes. However it is rare for such patterns to be accurate; instead they represent a very approximate characterisation of the signal under study. At the opposite extreme, we may instead characterise such a signal via a neural network, or a high-order Markov model, and so on. These have better sensitivity and specificity, but are unreadable, and consequently unhelpful for conveying an understanding of the underlying molecular biology processes that could support insight or reasoning. We describe a simple pattern language, called crisp hypermotifs (CHMs), that leads to highly readable patterns that can support understanding and reasoning, yet achieve greater sensitivity and specificity than the commonly used approaches to crisply characterise a signal. We use evolutionary computation to discover high-performance CHMs from data, and we argue that CHMs be used in place of classical consensus motifs, and justify that by presenting examples derived from a large dataset of mammalian core promoters. We provide CHM alternatives to the well-known core promoter TATA-box and Initiator patterns that have better sensitivity and specificity than their classical counterparts. [ABSTRACT FROM AUTHOR]

Many heuristics used for finding biclusters in microarray data use the mean squared residue as a way of evaluating the quality of biclusters. This has led to the discovery of interesting biclusters. Recently it has been proven that the mean squared residue may fail to identify some interesting biclusters. This motivates us to introduce a new measure, called Virtual Error, for assessing the quality of biclusters in microarray data. In order to test the validity of the proposed measure, we include it within an evolutionary algorithm. Experimental results show that the use of this novel measure is effective for finding interesting biclusters, which could not have been discovered with the use of the mean squared residue. [ABSTRACT FROM AUTHOR]

Inverse protein folding or protein design stands for searching a particular amino acids sequence whose native structure or folding matches a pre specified target. The problem of finding the corresponding folded structure of a particular sequence is, per se, a hard computational problem. We use a genetic algorithm for searching the space of potential sequences, and the fitness of each individual is measured with the output of a second GA performing a minimization process in the space of structures. Using an off-lattice protein-like 2D model, we show how the implemented techniques are able to obtain a variety of sequences attaining the target structures proposed. [ABSTRACT FROM AUTHOR]

The Human Immunodeficiency Virus (HIV) encodes an enzyme, called HIV protease, which is responsible for the generation of infectious viral particles by cleaving the virus polypeptides. Many efforts have been devoted to perform accurate predictions on the HIV-protease cleavability of peptides, in order to design efficient inhibitor drugs. Over the last decade, linear and nonlinear supervised learning methods have been extensively used to discriminate between protease-cleavable and non cleavable peptides. In this paper we consider four different proteins encoding schemes and we apply a discrete variant of linear support vector machines to predict their HIV protease-cleavable status. Empirical results indicate the effectiveness of the proposed method, that is able to classify with the highest accuracy the cleavable and non cleavable peptides contained in two publicly available benchmark datasets. Moreover, the optimal classification rules generated are characterized by a strong generalization capability, as shown by their accuracy in predicting the HIV protease cleavable status of peptides in out-of-sample datasets. [ABSTRACT FROM AUTHOR]

Knowledge of protein-protein interaction sites is vital to determine proteins' function and involvement in different pathways. Support Vector Machines (SVM) have been proposed over the recent years to predict protein-protein interface residues, primarily based on single amino acid sequence inputs. We investigate the features of amino acids that can be best used with SVM for predicting residues at protein-protein interfaces. The optimal feature set was derived from investigation into features such as amino acid composition, hydrophobic characters of amino acids, secondary structure propensity of amino acids, accessible surface areas, and evolutionary information generated by PSI-BLAST profiles. Using a backward elimination procedure, amino acid composition, accessible surface areas, and evolutionary information generated by PSI-BLAST profiles gave the best performance. The present approach achieved overall prediction accuracy of 74.2% for 77 individulal proteins collected from the Protein Data Bank, which is better than the previously reported accuracies. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) form a large functional family of small noncoding RNAs and play an important role as posttranscriptional regulators, by repressing the translation of mRNAs. Recently, the processing mechanism of miRNAs has been reported to involve Drosha/DGCR8 complex and Dicer, however, the exact mechanism and molecular principle are still unknown. We thus have tried to understand the related phenomena in terms of the tertiary structure of pre-miRNA. Unfortunately, the tertiary structure of RNA double helix has not been studied sufficiently compared to that of DNA double helix. The tertiary structure of pre-miRNA double helix is determined by 15 types of dinucleotide step (d-step) parameters for three classes of angles, i.e., twist, roll, and tilt. In this study, we estimate the 45 d-step parameters (15 types by 3 classes) using an evolutionary algorithm, under several assumptions inferred from the literature. Considering the trade-off among the four objective functions in our study, we deployed a multi-objective evolutionary algorithm, NSGA-II, to the search for a nondominant set of parameters. The performance of our method was evaluated on a separate test dataset. Our study provides a novel approach to understanding the processing mechanism of pre-miRNAs with respect to their tertiary structure and would be helpful for developing a comprehensible prediction method for pre-miRNA and mature miRNA structures. [ABSTRACT FROM AUTHOR]

An important goal of human genetics is the identification of DNA sequence variations that are predictive of who is at risk for various common diseases. The focus of the present study is on the challenge of detecting and characterizing nonlinear attribute interactions or dependencies in the context of a genome-wide genetic study. The first question we address is whether the ReliefF algorithm is suitable for attribute selection in this domain. The second question we address is whether we can improve ReliefF for selecting important genetic attributes. Using simulated genetic datasets, we show that ReliefF is significantly better than a naïve chi-square test of independence for selecting two interacting attributes out of 103 candidates. In addition, we show that ReliefF can be improved in this domain by systematically removing the worst attributes and re-estimating ReliefF weights. Our simulation studies demonstrate that this new Tuned ReliefF (TuRF) algorithm is significantly better than ReliefF. [ABSTRACT FROM AUTHOR]

The effective reverse engineering of biochemical networks is one of the great challenges of systems biology. The contribution of this paper is two-fold: 1) We introduce a new method for reverse engineering genetic regulatory networks from gene expression data; 2) We demonstrate how nonlinear gene networks can be inferred from steady-state data alone. The reverse engineering method is based on an evolutionary algorithm that employs a novel representation called Analog Genetic Encoding (AGE), which is inspired from the natural encoding of genetic regulatory networks. AGE can be used with biologically plausible, nonlinear gene models where analytical approaches or local gradient based optimisation methods often fail. Recently there has been increasing interest in reverse engineering linear gene networks from steady-state data. Here we demonstrate how more accurate nonlinear dynamical models can also be inferred from steady-state data alone. [ABSTRACT FROM AUTHOR]

Systems biology is the ever-growing field of integrating molecular knowledge about biological organisms into an understanding at the systems level. For this endeavour, automatic network reconstruction tools are urgently needed. In the present contribution, we show how the applicability of evolutionary algorithms to systems biology can be improved by a domain-specific representation and algorithmic extensions, especially a separation of network structure evolution from evolution of kinetic parameters. In a case study, our presented tool is applied to a model of the mitotic spindle checkpoint in the human cell cycle. [ABSTRACT FROM AUTHOR]

A path diagram relates observed, pairwise, variable correlations to a functional structure which describes the hypothesized causal relations between the variables. Here we combine path diagrams, heuristics and evolutionary search into a system which seeks to improve existing gene regulatory models. Our evaluation shows that once a correct model has been identified it receives a lower prediction error compared to incorrect models, indicating the overall feasibility of this approach. However, with smaller samples the observed correlations gradually become more misleading, and the evolutionary search increasingly converges on suboptimal models. Future work will incorporate publicly available sources of experimentally verified biological facts to computationally suggest model modifications which might improve the model's fitness. [ABSTRACT FROM AUTHOR]

In some areas of bioinformatics (like protein folding or sequence alignment) the full alphabet of amino acid symbols is not necessary. Often, better results are received with simplified alphabets. In general, simplified alphabets are as universal as possible. In this paper we show that this concept may not be optimal. We present a genetic algorithm for alphabet simplifying and we use it in a method based on global sequence alignment. We demonstrate that our algorithm is much faster and produces better results than the previously presented genetic algorithm. We also compare alphabets constructed on the base of universal substitution matrices like BLOSUM with our alphabets built through sequence alignment and propose a new coefficient describing the value of alphabets in the sequence alignment context. Finally we show that our simplified alphabets give better results in a sequence classification (using k-NN classifier), than most previously presented simplified alphabets and better than full 20-letter alphabet. [ABSTRACT FROM AUTHOR]

Understanding the self-regulatory mechanisms controlling the spatial and temporal structure of multicellular organisms represents one of the major challenges in molecular biology. In the context of plants, shoot apical meristems (SAMs), which are populations of dividing, undifferentiated cells that generate organs at the tips of stems and branches throughout the life of a plant, are of particular interest and currently studied intensively. Here, one key goal is to identify the genetic regulatory network organizing the structure of a SAM and generating the corresponding spatial gene expression patterns. This paper addresses one step in the design of SAM models based on ordinary differential equations (ODEs): parameter estimation for spatial pattern formation. We assume that the topology of the genetic regulatory network is given, while the parameters of an ODE system need to be determined such that a particular stable pattern over the SAM cell population emerges. To this end, we propose an evolutionary algorithm-based approach and investigate different ways to improve the efficiency of the search process. Preliminary results are presented for the Brusselator, a well-known reaction-diffusion system. [ABSTRACT FROM AUTHOR]

Classification of microarray data requires the selection of subsets of relevant genes in order to achieve good classification performance. This article presents a genetic embedded approach that performs the selection task for a SVM classifier. The main feature of the proposed approach concerns the highly specialized crossover and mutation operators that take into account gene ranking information provided by the SVM classifier. The effectiveness of our approach is assessed using three well-known benchmark data sets from the literature, showing highly competitive results. [ABSTRACT FROM AUTHOR]

Biomedical research has been revolutionized by high-throughput techniques and the enormous amount of biological data they are able to generate. The interest shown over network models and systems biology is rapidly raising. Genetic networks arise as an essential task to mine these data since they explain the function of genes in terms of how they influence other genes. Many modeling approaches have been proposed for building genetic networks up. However, it is not clear what the advantages and disadvantages of each model are. There are several ways to discriminate network building models, being one of the most important whether the data being mined presents a static or dynamic fashion. In this work we compare static and dynamic models over a problem related to the inflammation and the host response to injury. We show how both models provide complementary information and cross-validate the obtained results. [ABSTRACT FROM AUTHOR]

A critical challenge of the postgenomic era is to understand how genes are differentially regulated in and between genetic networks. The fact that such co-regulated genes may be differentially regulated suggests that subtle differences in the shared cis-acting regulatory elements are likely significant, however it is unknown which of these features increase or reduce expression of genes. In principle, this expression can be measured by microarray experiments, though they incorporate systematic errors, and moreover produce a limited classification (e.g. up/down regulated genes). In this work, we present an unsupervised machine learning method to tackle the complexities governing gene expression, which considers gene expression data as one feature among many. It analyzes features concurrently, recognizes dynamic relations and generates profiles, which are groups of promoterssharing common features. The method makes use of multiobjective techniques to evaluate the performance of profiles, and has a multimodal approach to produce alternative descriptions of same expression target. We apply this method to probe the regulatory networks governed by the PhoP/PhoQ two-component system in the enteric bacteria Escherichia coli and Salmonella enterica. Our analysis uncovered profiles that were experimentally validated, suggesting correlations between promoter regulatory features and gene expression kinetics measured by green fluorescent protein (GFP) assays. [ABSTRACT FROM AUTHOR]

Protein translocation, the transport of newly synthesized proteins out of the cell, is a fundamental mechanism of life. We are interested in understanding how cells recognize the proteins that are to be exported and how the necessary information is encoded in the so called "Signal Sequences". In this paper, we address these problems by building a physico-chemical model of signal sequence recognition, using experimental data. This model was built using decision trees. In a first phase the classifier were built from a set of features derived from the current knowledge about signal sequences. It was then expanded by feature generation with genetic algorithms. The resulting predictors are efficient, achieving an accuracy of more than 99% with our wild-type proteins set. Furthermore the generated features can give us a biological insight about the export mechanism. Our tool is freely available through a web interface. [ABSTRACT FROM AUTHOR]

We propose a feature selection method for multiclass classification. The proposed method selects features in backward elimination and computes feature ranking scores at each step from analysis of weight vectors of multiple two-class linear Support Vector Machine classifiers from one-versus-one or one-versus-all decomposition of a multi-class classification problem. We evaluated the proposed method on three gene expression datasets for multiclass cancer classification. For comparison, one filtering feature selection method was included in the numerical study. The study demonstrates the effectiveness of the proposed method in selecting a compact set of genes to ensure a good classification accuracy. [ABSTRACT FROM AUTHOR]

In liquid chromatography-mass spectrometry (LC-MS) based expression proteomics, samples from different groups are analyzed comparatively in order to detect differences that can possibly be caused by the disease under study (potential biomarker detection). To this end, advanced computational techniques are needed. Peak alignment and detection are two key steps in the analysis process of LC-MS datasets. In this paper we propose an algorithm for LC-MS peak detection and alignment. The goal of the algorithm is to group together peaks generated by the same peptide but detected in different samples. It employs clustering with a new weighted similarity measure and automatic selection of the number of clusters. Moreover, it supports parallelization by acting on blocks. Finally, it allows incorporation of available domain knowledge for constraining and refining the search for aligned peaks. Application of the algorithm to a LC-MS dataset generated by a spike-in experiment substantiates the effectiveness of the proposed technique. [ABSTRACT FROM AUTHOR]

Analysis of medical datasets has some specific requirements not always fulfilled by standard Machine Learning methods. In particular, heterogeneous and missing data must be tolerated, the results should be easily interpretable. Moreover, with genetic data, often the combination of two or more attributes leads to non-linear effects not detectable for each attribute on its own. We present a new ML algorithm, HCS, taking inspiration from learning classifier systems, decision trees and statistical hypothesis testing. We show the results of applying this algorithm to a well-known benchmark dataset, and to HNSCC, a dataset studying the connection between smoke and genetic patterns to the development of oral cancer. [ABSTRACT FROM AUTHOR]

Computational methods allowing reliable pharmacokinetics predictions for newly synthesized compounds are critically relevant for drug discovery and development. Here we present an empirical study focusing on various versions of Genetic Programming and other well known Machine Learning techniques to predict Median Oral Lethal Dose (LD50) and Plasma Protein Binding (%PPB) levels. Since these two parameters respectively characterize the harmful effects and the distribution into human body of a drug, their accurate prediction is essential for the selection of effective molecules. The obtained results confirm that Genetic Programming is a promising technique for predicting pharmacokinetics parameters, both from the point of view of the accurateness and of the generalization ability. [ABSTRACT FROM AUTHOR]

An extension to Hopfield's model of associative memory is studied in the present work. In particular, this paper is focused in giving solutions to the two main problems present in the model: the apparition of spurious patterns in the learning phase (implying the well-known and undesirable effect of storing the opposite pattern) and the problem of its reduced capacity (the probability of error in the retrieving phase increases as the number of stored patterns grows). In this work, a method to avoid spurious patterns is presented and studied, and an explanation to the previously mentioned effect is given. Another novel technique to increase the capacity of a network is proposed here, based on the idea of using several reference points when storing patterns. It is studied in depth, and an explicit formula for the capacity of the network is provided. This formula shows the linear dependence of the capacity of the new model on the number of reference points, implying the increase of the capacity in this model. [ABSTRACT FROM AUTHOR]

We describe a new software tool, called Spieldose (in English, musical box), suited to the automatic music composition task. Our system is based on the paradigm of Interactive Genetic Algorithms (abbreviated as Interactive GA) where the parent selection stage in a typical GA is made by the user according to his/her subjective criteria. The tool permits to integrate the interaction between the system and the potential users when they create their melodies. One important contribution of this work is the proposal of specific musical genetic operators (different types of crossover, mutation and improvement operators) which ensure that the generated melodies are in concordance with Music Theory and they are also nice to listening. Moreover, our software tool can be customized to a particular musical style by including the specific musical knowledge domain in the system. For validation purposes, we used Spieldose to compose different pieces corresponding to the classicism. [ABSTRACT FROM AUTHOR]

Cardiac auscultation still remains today as the basic technique to easily achieve a cardiac valvular diagnosis. Nowadays, auscultation can be powered with automated computer-aided analysis systems to provide objective, accurate, documented and cost-effective diagnosis. This is particulary useful when such systems offer remote diagnosis capabilities. ASEPTIC is a telediagnosis system for cardiac sounds that allows the analysis of remote phonocardiographic signals. The pattern recognition stage of ASEPTIC is presented in this paper. It is based in feature selection from the cardiac events, and classification using a multilayer perceptron artificial neural network trained with Levenberg-Marquardt algorithm for fast convergence. Three categories of records have been considered: normal, with holosystolic murmur, and with midsystolic murmur. Experimental results show high correct classification rates for the three categories: 100%, 92.69%, and 97.57%, respectively. [ABSTRACT FROM AUTHOR]

In this paper we propose a method for building possibilistic temporal constraint networks that better summarizes the huge set of mined timed-stamped sequences from a temporal data mining process. It belongs to the well-known second-order data mining problem, where the vast amount of simple sequences or patterns needs to be summarized further. It is a very important topic because the huge number of temporal associations extracted in the temporal data mining step makes the knowledge discovery process practically unmanageable for human experts. The method is based on the Theory of Evidence of Shafer as a mathematical tool for obtaining the fuzzy measures involved in the temporal network. This work also presents briefly a practical example describing an application of this proposal in the Intensive Care domain. [ABSTRACT FROM AUTHOR]

Temporal abstraction methods produce high level descriptions of a parameter evolution from collections of temporal data. As the level of abstraction of the data is increased, it becomes easier to use them in a reasoning process based on high-level explicit knowledge. Furthermore, the volume of data to be treated is reduced and, subsequently, the reasoning becomes more efficient. Besides, there exist domains, such as medicine, in which there is some imprecision when describing the temporal location of data, especially when they are based on subjective observations. In this work, we describe how the use of fuzzy temporal constraint networks enables temporal imprecision to be considered in temporal abstraction. [ABSTRACT FROM AUTHOR]

Conductive plastics have become an alternative to traditional metallic cabinets to shield boxes from electromagnetic interferences. The wide range of available conductivities with these materials can satisfy any particular design. A design with an outer metallic layer and an inner layer of conductive dielectric can obtain advantages from both materials. In this paper the design by means of genetic algorithms of electronic systems cabinets made of new plastic materials to reduce electromagnetic radiated interferences in enclosures with an aperture is described. This optimization procedure requires the use of electromagnetic simulators with a high computational cost. A 2D simulation tool is used in this work for evaluating 3D structures, reducing drastically the computation time. The relationship between obtained solutions and skin depth parameter is evaluated to help in design procedures. A commercial 3D full wave electromagnetic tool has been used to validate the obtained results. [ABSTRACT FROM AUTHOR]

In this paper we present a software tool for the automatic design of collective behaviors in animated feature films. The most successful existing commercial solutions used in animation studios require an explicit knowledge by the designer of the AI or other techniques and involve the hand design of many parameters. Our main motivation consists in developing a design tool that permits creating the behaviors of the characters from a high level perspective, using general concepts related to the final desired objectives, and to judge these behaviors from a visual point of view, thus abstracting the designer from the computational techniques in the system core. In this case, a bioinspired approach has been followed consisting in the incremental generation of controllers for simulated agents using evolution. An example of flocking activity is created with the system. [ABSTRACT FROM AUTHOR]

Multiobjective optimization problems have become an important issue at many engineering problems. A tradeoff between several design criteria is required and important efforts are made for the development of Multiobjective Optimization Techniques and, in particular, Evolutionary Multiobjective Optimization. Usually these algorithms produce a set of optimum solutions in Pareto sense, there is not a unique solution. The designer (Decision Maker) has to finally select one solution for each particular problem, then he has to select from a set of Pareto solutions, the most adequate solution according to his preferences. It is widely accepted that visualization tools are valuable tools to provide the Decision Maker (DM) with a meaningful way to analyze Pareto set and then to help to select an adequate solution. This work describes a new graphical way to represent high dimensional and large sets of Pareto solutions, allowing an easier analysis, and helping the DM to select an adequate solution. [ABSTRACT FROM AUTHOR]

One of the most important feature of the Neural Gas is its ability to preserve the topology in the projection of highly dimensional input spaces to lower dimensions vector quantizations. For this reason, the Neural Gas has proven to be a valuable tool in data mining applications. In this paper an incremental ensemble method for the combination of various Neural Gas models is proposed. Several models are trained with bootstrap samples of the data, the "codebooks" with similar Voronoi polygons are merged in one fused node and neighborhood relations are established by linking similar fused nodes. The aim of combining the Neural Gas is to improve the quality and robustness of the topological representation of the single model. We have called this model Fusion-NG. Computational experiments show that the Fusion-NG model effectively preserves the topology of the input space and improves the representation of the single Neural Gas model. Furthermore, the Fusion-NG explicitly shows the neighborhood relations of it prototypes. We report the performance results using synthetic and real datasets, the latter obtained from a benchmark site. [ABSTRACT FROM AUTHOR]

In this paper, we confront a variant of the cutting-stock problem with multiple objectives. The starting point is a solution calculated by a heuristic algorithm, termed SHRP, that aims to optimize the two main objectives, i.e. the number of cuts and the number of different patterns. Here, we propose a multi-objective genetic algorithm to optimize other secondary objectives such as changeovers, completion times of orders pondered by priorities and open stacks. We report experimental results showing that the multi-objective genetic algorithm is able to improve the solutions obtained by SHRP on the secondary objectives. [ABSTRACT FROM AUTHOR]

In this paper we propose a hybrid method, combining heuristics and local search, to solve flow shop scheduling problems under uncertainty. This method is compared with a genetic algorithm from the literature, enhanced with three new multi-objective functions. Both single objective and multi-objective approaches are taken for two optimisation goals: minimisation of completion time and fulfilment of due date constraints. We present results for newly generated examples that illustrate the effectiveness of each method. [ABSTRACT FROM AUTHOR]

We consider the fuzzy job shop problem, a job shop scheduling problem with uncertain task durations and flexible due dates, with different objective functions and a GA as solving method. We propose a method to generate benchmark problems with variable uncertainty and analyse the performance of the objective functions in terms of the objective values and the sensitivity to variations in the uncertainty. [ABSTRACT FROM AUTHOR]

Auscultation of the heart is a medical technique that still today is used to provide a fast diagnosis about the heart condition. Compression of the heart sounds (or phonocardiogram) is very convenient to reduce bandwidth in telediagnosis systems that aid the physician in the evaluation of the cardiovascular state. The compression algorithm used depends on several parameters, which can take a diversity of values. Genetic algorithms have been used to obtain the optimal set of values for the compression parameters that optimize the performance of the compression for a test set of cardiac recordings. The optimized results were obtained very quickly, and optimal values agreed for (almost) all the test records. [ABSTRACT FROM AUTHOR]

The article presents an integrated resolution of the joint production and maintenance scheduling problem in hybrid flowshop. Two resolution methods are used on the basis of a new coding to represent a joint production and maintenance scheduling: Taboo search where we proposed an algorithm for the generation of a joint initial solution and neighbourhood, and GA where we proposed new joint operators for crossover and mutation. Computational experiments are conducted on a large set of instances and the resulting genetic algorithm gives the best results so far. [ABSTRACT FROM AUTHOR]

This work presents the results on applying a genetic approach for solving the Dial-A-Ride Problem (DARP). The problem consists of assigning and scheduling a set of user transport requests to a fleet of available vehicles in the most efficient way according to a given objective function. The literature offers different heuristics for solving DARP, a well known NP-hard problem, which range from traditional insertion and clustering algorithms to soft computing techniques. On the other hand, the approach through Genetic Algorithms (GA) has been experienced in problems of combinatorial optimization. We present our experience and results of a study to develop and test different GAs in the aim of finding an appropriate encoding and configuration, specifically for the DARP problem with time windows. [ABSTRACT FROM AUTHOR]

The new learning classifier system is described to classify real-valued data. The approach applies the continous-valued context-free grammar based system GCS. In order to handle effectively, the terminal rules have been replaced by the so-called environment probing rules. The rGCS model has been tested on the checkerboard problem. [ABSTRACT FROM AUTHOR]

In this work we use simulated evolution to corroborate the adaptability of the natural genetic code. An adapted genetic algorithm searches for optimal hypothetical codes. The adaptability is measured as the average variation of the hydrophobicity that experiment the encoded amino acids when errors or mutations are presented in the codons of the hypothetical codes. Different types of mutations and base position mutation probabilities are considered in this study. [ABSTRACT FROM AUTHOR]

In this article, a methodology to obtain the Feasible Parameter Set (FPS) and a nominal model in a non-linear robust identification problem is presented. Several norms are taken into account simultaneously to define the FPS which improves the model quality but, as counterpart, it increases the optimization problem complexity. To determine the FPS a multimodal optimization problem with an infinite number of minima, which constitute the FPS, is presented and a special evolutionary algorithm (ε−GA) is used to characterize it. Finally, an application to a thermal process identification, where · ∞  and ·1 norms have been considered simultaneously, is presented to illustrate the technique. [ABSTRACT FROM AUTHOR]

We consider the numerical evolutionary optimization of dynamic molecular alignment by shaped femtosecond laser pulses. We study a simplified model of this quantum control problem, which allows the full physical investigation of the optimal solutions. By using specific variants of Derandomized Evolution Strategies, subject to parameterizations which are known to be superior for this problem, the numerical results reveal different conceptual physics structures for the different optimization procedures. These results are strong both from the algorithmic as well as from the physics perspectives. This shows that Natural Computing techniques can be used to derive new insights into Physics. [ABSTRACT FROM AUTHOR]

The paper describes a methodology for constructing a possible combination of different basis functions (sigmoidal and product) for the hidden layer of a feed forward neural network, where the architecture, weights and node typology are learned based on evolutionary programming. This methodology is tested using simulated Gaussian data set classification problems with different linear correlations between input variables and different variances. It was found that combined basis functions are the more accurate for classification than pure sigmoidal or product-unit models. Combined basis functions present competitive results which are obtained using linear discriminant analysis, the best classification methodology for Gaussian data sets. [ABSTRACT FROM AUTHOR]

This article proposes a context-free grammar to be used in grammar-guided genetic programming systems to automatically design feed-forward neural architectures. This grammar has three important features. The sentences that belong to the grammar are binary strings that directly encode all the valid neural architectures only. This rules out the appearance of illegal points in the search space. Second, the grammar has the property of being ambiguous and semantically redundant. Therefore, there are alternative ways of reaching the optimum. Third, the grammar starts by generating small networks. This way it can efficiently adapt to the complexity of the problem to be solved. From the results, it is clear that these three properties are beneficial to the convergence process of the grammar-guided genetic programming system. [ABSTRACT FROM AUTHOR]

In this work we present a new proposal in order to model the probability distribution in the estimation of distribution algorithms. This approach is based on using dependency networks [1] instead of Bayesian networks or simpler models in which structure is limited. Dependency networks are probabilistic graphical models similar to Bayesian networks, but with a significant difference: they allow directed cycles in the graph. This difference can be an important advantage because of two main reasons. First, in some real problems cyclic relationships appear between variables an this fact cannot be represented in a Bayesian network. Secondly, dependency networks can be built easily due to the fact that there is no need to check the existence of cycles as in a Bayesian network. In this paper we propose to use a general (multivariate) model in order to deal with a richer representation, however, in this initial approach to the problem we also propose to constraint the construction phase in order to use only bivariate statistics. The algorithm is compared with classical approaches with the same complexity order, i.e. bivariate models as chains and trees. [ABSTRACT FROM AUTHOR]