A Multiobjective Evolutionary Conceptual Clustering Methodology for Gene Annotation Within Structural Databases: A Case of Study on the Gene Ontology Database

Current tools and techniques devoted to examine the content of large databases are often hampered by their inability to support searches based on criteria that are meaningful to their users. These shortcomings are particularly evident in data banks storing representations of structural data such as biological networks. Conceptual clustering techniques have demonstrated to be appropriate for uncovering relationships between features that characterize objects in structural data. However, typical con ceptual clustering approaches normally recover the most obvious relations, but fail to discover the lessfrequent but more informative underlying data associations. The combination of evolutionary algorithms with multiobjective and multimodal optimization techniques constitutes a suitable tool for solving this problem. We propose a novel conceptual clustering methodology termed evolutionary multiobjective conceptual clustering (EMO-CC), re lying on the NSGA-II multiobjective (MO) genetic algorithm. We apply this methodology to identify conceptual models in struc tural databases generated from gene ontologies. These models can explain and predict phenotypes in the immunoinflammatory response problem, similar to those provided by gene expression or other genetic markers. The analysis of these results reveals that our approach uncovers cohesive clusters, even those comprising a small number of observations explained by several features, which allows describing objects and their interactions from different perspectives and at different levels of detail.Ministerio de Ciencia y Tecnología TIC-2003-00877Ministerio de Ciencia y Tecnología BIO2004-0270EMinisterio de Ciencia y Tecnología TIN2006-1287

Mining a Small Medical Data Set by Integrating the Decision Tree and t-test

[[abstract]]Although several researchers have used statistical methods to prove that aspiration followed by the injection of 95% ethanol left in situ (retention) is an effective treatment for ovarian endometriomas, very few discuss the different conditions that could generate different recovery rates for the patients. Therefore, this study adopts the statistical method and decision tree techniques together to analyze the postoperative status of ovarian endometriosis patients under different conditions. Since our collected data set is small, containing only 212 records, we use all of these data as the training data. Therefore, instead of using a resultant tree to generate rules directly, we use the value of each node as a cut point to generate all possible rules from the tree first. Then, using t-test, we verify the rules to discover some useful description rules after all possible rules from the tree have been generated. Experimental results show that our approach can find some new interesting knowledge about recurrent ovarian endometriomas under different conditions.[[journaltype]]國外[[incitationindex]]EI[[booktype]]紙本[[countrycodes]]FI

Efficient Learning Machines

Computer scienc

Computer-Aided Multi-Objective Optimization in Small Molecule Discovery

Molecular discovery is a multi-objective optimization problem that requires identifying a molecule or set of molecules that balance multiple, often competing, properties. Multi-objective molecular design is commonly addressed by combining properties of interest into a single objective function using scalarization, which imposes assumptions about relative importance and uncovers little about the trade-offs between objectives. In contrast to scalarization, Pareto optimization does not require knowledge of relative importance and reveals the trade-offs between objectives. However, it introduces additional considerations in algorithm design. In this review, we describe pool-based and de novo generative approaches to multi-objective molecular discovery with a focus on Pareto optimization algorithms. We show how pool-based molecular discovery is a relatively direct extension of multi-objective Bayesian optimization and how the plethora of different generative models extend from single-objective to multi-objective optimization in similar ways using non-dominated sorting in the reward function (reinforcement learning) or to select molecules for retraining (distribution learning) or propagation (genetic algorithms). Finally, we discuss some remaining challenges and opportunities in the field, emphasizing the opportunity to adopt Bayesian optimization techniques into multi-objective de novo design

An exploration of evolutionary computation applied to frequency modulation audio synthesis parameter optimisation

With the ever-increasing complexity of sound synthesisers, there is a growing demand for automated parameter estimation and sound space navigation techniques. This thesis explores the potential for evolutionary computation to automatically map known sound qualities onto the parameters of frequency modulation synthesis. Within this exploration are original contributions in the domain of synthesis parameter estimation and, within the developed system, evolutionary computation, in the form of the evolutionary algorithms that drive the underlying optimisation process. Based upon the requirement for the parameter estimation system to deliver multiple search space solutions, existing evolutionary algorithmic architectures are augmented to enable niching, while maintaining the strengths of the original algorithms. Two novel evolutionary algorithms are proposed in which cluster analysis is used to identify and maintain species within the evolving populations. A conventional evolution strategy and cooperative coevolution strategy are defined, with cluster-orientated operators that enable the simultaneous optimisation of multiple search space solutions at distinct optima. A test methodology is developed that enables components of the synthesis matching problem to be identified and isolated, enabling the performance of different optimisation techniques to be compared quantitatively. A system is consequently developed that evolves sound matches using conventional frequency modulation synthesis models, and the effectiveness of different evolutionary algorithms is assessed and compared in application to both static and timevarying sound matching problems. Performance of the system is then evaluated by interview with expert listeners. The thesis is closed with a reflection on the algorithms and systems which have been developed, discussing possibilities for the future of automated synthesis parameter estimation techniques, and how they might be employed

A Soft Computing Based Approach for Multi-Accent Classification in IVR Systems

A speaker's accent is the most important factor affecting the performance of Natural Language Call Routing (NLCR) systems because accents vary widely, even within the same country or community. This variation also occurs when non-native speakers start to learn a second language, the substitution of native language phonology being a common process. Such substitution leads to fuzziness between the phoneme boundaries and phoneme classes, which reduces out-of-class variations, and increases the similarities between the different sets of phonemes. Thus, this fuzziness is the main cause of reduced NLCR system performance. The main requirement for commercial enterprises using an NLCR system is to have a robust NLCR system that provides call understanding and routing to appropriate destinations. The chief motivation for this present work is to develop an NLCR system that eliminates multilayered menus and employs a sophisticated speaker accent-based automated voice response system around the clock. Currently, NLCRs are not fully equipped with accent classification capability. Our main objective is to develop both speaker-independent and speaker-dependent accent classification systems that understand a caller's query, classify the caller's accent, and route the call to the acoustic model that has been thoroughly trained on a database of speech utterances recorded by such speakers. In the field of accent classification, the dominant approaches are the Gaussian Mixture Model (GMM) and Hidden Markov Model (HMM). Of the two, GMM is the most widely implemented for accent classification. However, GMM performance depends on the initial partitions and number of Gaussian mixtures, both of which can reduce performance if poorly chosen. To overcome these shortcomings, we propose a speaker-independent accent classification system based on a distance metric learning approach and evolution strategy. This approach depends on side information from dissimilar pairs of accent groups to transfer data points to a new feature space where the Euclidean distances between similar and dissimilar points are at their minimum and maximum, respectively. Finally, a Non-dominated Sorting Evolution Strategy (NSES)-based k-means clustering algorithm is employed on the training data set processed by the distance metric learning approach. The main objectives of the NSES-based k-means approach are to find the cluster centroids as well as the optimal number of clusters for a GMM classifier. In the case of a speaker-dependent application, a new method is proposed based on the fuzzy canonical correlation analysis to find appropriate Gaussian mixtures for a GMM-based accent classification system. In our proposed method, we implement a fuzzy clustering approach to minimize the within-group sum-of-square-error and canonical correlation analysis to maximize the correlation between the speech feature vectors and cluster centroids. We conducted a number of experiments using the TIMIT database, the speech accent archive, and the foreign accent English databases for evaluating the performance of speaker-independent and speaker-dependent applications. Assessment of the applications and analysis shows that our proposed methodologies outperform the HMM, GMM, vector quantization GMM, and radial basis neural networks

A Genetic Clustering Algorithm for Automatic Text Summarization

Abstract. Automatic text summarization has become a relevant topic due to the information overload. This automatization aims to help humans and machines to deal with the vast amount of text data (structured and un-structured) offered on the web and deep web. In this research a novel approach for automatic extractive text summarization called SENCLUS is presented. Using a genetic clustering algorithm, SENCLUS clusters the sentences as close representation of the text topics using a fitness function based on redundancy and coverage, and applies a scoring function to select the most relevant sentences of each topic to be part of the extractive summary. The approach was validated using the DUC2002 data set and ROUGE summary quality measures. The results shows that the approach is representative against the state of the art methods for extractive automatic text summarization.La generación automática de resúmenes se ha posicionado como un tema de gran importancia debido a la sobrecarga informativa. El objetivo de esta tecnología es el ayudar humanos y maquinas a lidiar con el gran volumen de información en forma de texto (estructurada y no estructurada) que se encuentra en la red y en la red profunda. Esta investigación presenta un nuevo algoritmo para la generación automática de resúmenes extractivos llamado SENCLUS. Este algoritmo es capaz de detectar los temas presentes en un texto usando una técnica de agrupación genética para formar grupos de oraciones. Estos grupos de oraciones son una representación aproximada de los temas del texto y estos son formados usando una función aptitud basada en cobertura y redundancia. Una vez los grupos de oraciones son encontrados, se aplica una función puntuación para seleccionar las oraciones mas relevantes de cada tema hasta que las restricciones de longitud del resumen lo permitan. SENCLUS fue validado en una serie de experimentos en los cuales se usò el conjunto de datos DUC2002 para la generación de resúmenes de un solo documento y se usò la medida ROUGE para medir de forma automática la calidad de cada resumen. Los resultados mostraron que el enfoque propuesto es representativo al ser comparado con los algoritmos presentes en el estado del arte para la generación de resúmenes extractivos.Maestrí

INVESTIGATIONS INTO THE COGNITIVE ABILITIES OF ALTERNATE LEARNING CLASSIFIER SYSTEM ARCHITECTURES

The Learning Classifier System (LCS) and its descendant, XCS, are promising paradigms for machine learning design and implementation. Whereas LCS allows classifier payoff predictions to guide system performance, XCS focuses on payoff-prediction accuracy instead, allowing it to evolve optimal classifier sets in particular applications requiring rational thought. This research examines LCS and XCS performance in artificial situations with broad social/commercial parallels, created using the non-Markov Iterated Prisoner\u27s Dilemma (IPD) game-playing scenario, where the setting is sometimes asymmetric and where irrationality sometimes pays. This research systematically perturbs a conventional IPD-playing LCS-based agent until it results in a full-fledged XCS-based agent, contrasting the simulated behavior of each LCS variant in terms of a number of performance measures. The intent is to examine the XCS paradigm to understand how it better copes with a given situation (if it does) than the LCS perturbations studied.Experiment results indicate that the majority of the architectural differences do have a significant effect on the agents\u27 performance with respect to the performance measures used in this research. The results of these competitions indicate that while each architectural difference significantly affected its agent\u27s performance, no single architectural difference could be credited as causing XCS\u27s demonstrated superiority in evolving optimal populations. Instead, the data suggests that XCS\u27s ability to evolve optimal populations in the multiplexer and IPD problem domains result from the combined and synergistic effects of multiple architectural differences.In addition, it is demonstrated that XCS is able to reliably evolve the Optimal Population [O] against the TFT opponent. This result supports Kovacs\u27 Optimality Hypothesis in the IPD environment and is significant because it is the first demonstrated occurrence of this ability in an environment other than the multiplexer and Woods problem domains.It is therefore apparent that while XCS performs better than its LCS-based counterparts, its demonstrated superiority may not be attributed to a single architectural characteristic. Instead, XCS\u27s ability to evolve optimal classifier populations in the multiplexer problem domain and in the IPD problem domain studied in this research results from the combined and synergistic effects of multiple architectural differences

Multi-Objective Evolutionary Simultaneous Feature Selection and Outlier Detection for Regression

When investigating the causes of contamination in specific contexts, such as in underground water wells, multivariate regression is commonly used to establish possible links between the chemical-physical values of the samples and the levels of contaminant. Two issues often arise from such a statistical analysis: selecting the best predicting variables and detecting the instances that can be suspected to be outliers. In this paper, we propose a comprehensive, integrated, and general optimization model that solves these two problems simultaneously in such a way that outliers can be detected in reference to the specific variables that are selected for the regression, and we implement such an optimization model with a well-known evolutionary algorithm. We test our proposal on data extracted from a project whose aim is to establish the causes of the contamination of underwater water wells in a very specific area of northeastern Italy. The results show that our variable selection and outlier detection algorithm allows the synthesis of very reliable, interpretable, and clean regression models