Endika Bengoetxea

Towards a New Evolutionary Computation

Linking Entropy to Estimation of Distribution Algorithms.- Entropy-based Convergence Measurement in Discrete Estimation of Distribution Algorithms.- Real-coded Bayesian Optimization Algorithm.- The CMA Evolution Strategy: A Comparing Review.- Estimation of Distribution Programming: EDA-based Approach to Program Generation.- Multi-objective Optimization with the Naive ID A.- A Parallel Island Model for Estimation of Distribution Algorithms.- GA-EDA: A New Hybrid Cooperative Search Evolutionary Algorithm.- Bayesian Classifiers in Optimization: An EDA-like Approach.- Feature Ranking Using an EDA-based Wrapper Approach.- Learning Linguistic Fuzzy Rules by Using Estimation of Distribution Algorithms as the Search Engine in the COR Methodology.- Estimation of Distribution Algorithm with 2-opt Local Search for the Quadratic Assignment Problem.

Inexact graph matching by means of estimation of distribution algorithms

Abstract Estimation of distribution algorithms (EDAs) are a quite recent topic in optimization techniques. They combine two technical disciplines of soft computing methodologies: probabilistic reasoning and evolutionary computing. Several algorithms and approaches have already been proposed by different authors, but up to now there are very few papers showing their potential and comparing them to other evolutionary computational methods and algorithms such as genetic algorithms (GAs). This paper focuses on the problem of inexact graph matching which is NP-hard and requires techniques to find an approximate acceptable solution. This problem arises when a nonbijective correspondence is searched between two graphs. A typical instance of this problem corresponds to the case where graphs are used for structural pattern recognition in images. EDA algorithms are well suited for this type of problems. This paper proposes to use EDA algorithms as a new approach for inexact graph matching. Also, two adaptations of the EDA approach to problems with constraints are described as two techniques to control the generation of individuals, and the performance of EDAs for inexact graph matching is compared with the one of GAs.

Inexact graph matching for model-based recognition: Evaluation and comparison of optimization algorithms

A method for segmentation and recognition of image structures based on graph homomorphisms is presented in this paper. It is a model-based recognition method where the input image is over-segmented and the obtained regions are represented by an attributed relational graph (ARG). This graph is then matched against a model graph thus accomplishing the model-based recognition task. This type of problem calls for inexact graph matching through a homomorphism between the graphs since no bijective correspondence can be expected, because of the over-segmentation of the image with respect to the model. The search for the best homomorphism is carried out by optimizing an objective function based on similarities between object and relational attributes defined on the graphs. The following optimization procedures are compared and discussed: deterministic tree search, for which new algorithms are detailed, genetic algorithms and estimation of distribution algorithms. In order to assess the performance of these algorithms using real data, experimental results on supervised classification of facial features using face images from public databases are presented.

Bayesian classification for the selection of in vitro human embryos using morphological and clinical data

In vitro fertilization (IVF) is a medically assisted reproduction technique that enables infertile couples to achieve successful pregnancy. Given the uncertainty of the treatment, we propose an intelligent decision support system based on supervised classification by Bayesian classifiers to aid to the selection of the most promising embryos that will form the batch to be transferred to the womans uterus. The aim of the supervised classification system is to improve overall success rate of each IVF treatment in which a batch of embryos is transferred each time, where the success is achieved when implantation (i.e. pregnancy) is obtained. Due to ethical reasons, different legislative restrictions apply in every country on this technique. In Spain, legislation allows a maximum of three embryos to form each transfer batch. As a result, clinicians prefer to select the embryos by non-invasive embryo examination based on simple methods and observation focused on morphology and dynamics of embryo development after fertilization. This paper proposes the application of Bayesian classifiers to this embryo selection problem in order to provide a decision support system that allows a more accurate selection than with the actual procedures which fully rely on the expertise and experience of embryologists. For this, we propose to take into consideration a reduced subset of feature variables related to embryo morphology and clinical data of patients, and from this data to induce Bayesian classification models. Results obtained applying a filter technique to choose the subset of variables, and the performance of Bayesian classifiers using them, are presented.

Machine Learning: An Indispensable Tool in Bioinformatics

The increase in the number and complexity of biological databases has raised the need for modern and powerful data analysis tools and techniques. In order to fulfill these requirements, the machine learning discipline has become an everyday tool in bio-laboratories. The use of machine learning techniques has been extended to a wide spectrum of bioinformatics applications. It is broadly used to investigate the underlying mechanisms and interactions between biological molecules in many diseases, and it is an essential tool in any biomarker discovery process. In this chapter, we provide a basic taxonomy of machine learning algorithms, and the characteristics of main data preprocessing, supervised classification, and clustering techniques are shown. Feature selection, classifier evaluation, and two supervised classification topics that have a deep impact on current bioinformatics are presented. We make the interested reader aware of a set of popular web resources, open source software tools, and benchmarking data repositories that are frequently used by the machine learning community.

Inexact graph matching using stochastic optimization techniques for facial feature recognition

We propose a formalization of model-based facial feature recognition as an inexact graph matching problem, one graph representing a model of a face and the other an image where recognition has to be performed. The graphs are built from regions and relationships between regions. Both nodes and edges are attributed. A global dissimilarity function is defined based on comparison of attributes of the two graphs, and accounting for the fact that several image regions can correspond to the same model region. This junction is then minimized using several stochastic algorithms.

A parallel framework for loopy belief propagation

There are many innovative proposals introduced in the literature under the evolutionary computation field, from which estimation of distribution algorithms (EDAs) is one of them. Their main characteristic is the use of probabilistic models to represent the (in) dependencies between the variables of a concrete problem. Such probabilistic models have also been applied to the theoretical analysis of EDAs, providing a platform for the implementation of other optimization methods that can be incorporated into the EDA framework. Some of these methods, typically used for probabilistic inference, are belief propagation algorithms. In this paper we present a parallel approach for one of these inference-based algorithms, the loopy belief propagation algorithm for factor graphs. Our parallel implementation was designed to provide an algorithm that can be executed in clusters of computers or multiprocessors in order to reduce the total execution time. In addition, this framework was also designed as a flexible tool where many parameters, such as scheduling rules or stopping criteria, can be adjusted according to the requirements of each particular experiment and problem.

Experimental Results in Function Optimization with EDAs in Continuous Domain

This chapter shows experimental results of applying continuous Estimation of Distribution Algorithms to some well known optimization problems. For this UMDAC, MIMICe, EGNABIc, EGNABGe, EGNAee, EMNAglob, 1, and EMNAa algorithms were implemented. Their performance was compared to such of Evolution Strategies (Schwefel, 1995). The optimization problems of choice were Summation cancellation, Griewangk, Sphere model, Rosenbrock generalized, and Ackley.

Predicting dementia development in Parkinson's disease using Bayesian network classifiers

Parkinsons disease (PD) has broadly been associated with mild cognitive impairment (PDMCI) and dementia (PDD). Researchers have studied surrogate, neuroanatomic biomarkers provided by magnetic resonance imaging (MRI) that may help in the early diagnosis of this condition. In this article, four classification models (naïve Bayes, multivariate filter-based naïve Bayes, filter selective naïve Bayes and support vector machines, SVM) have been applied to evaluate their capacity to discriminate between cognitively intact patients with Parkinsons disease (PDCI), PDMCI and PDD. For this purpose, the MRI studies of 45 subjects (16 PDCI, 15 PDMCI and 14 PDD) were acquired and post-processed with Freesurfer, obtaining 112 variables (volumes of subcortical structures and thickness of cortical parcels) per subject. A multivariate filter-based naïve Bayes model was found to be the best classifier, having the highest cross-validated sensitivity, specificity and accuracy. Additionally, the most relevant variables related to dementia in PD, as predicted by our classifiers, were cerebral white matter, and volumes of the lateral ventricles and hippocampi.

The new multidimensional and user-driven higher education ranking concept of the European Union

Higher education rankings constitute a important but controversial topic due to the methodologies applied in existing rankings and to the use being done of these interpreting their results for purposes which they were not designed for. At present there is no international ranking can responds to the needs of all users and that is methodologically sound by considering the various missions of higher education institutions, mainly due to a narrow focus on research giving less importance to other missions in which higher education institutions can excel beyond research such as teaching quality, knowledge transfer, international orientation, regional engagement etc. The European Commission is currently involved in the implementation of a new higher education ranking methodology, characterised by taking into account a diversity of missions and the diversity of existing higher education institutions. The final aim is to create a tool allowing users to choose the performance indicators of their interest and providing them with a personalised ranking according to their interests. This paper describes the motivation for designing such a tool, the principles of the methodology proposed, as well as the steps foreseen to have it ready for end users by 2014.