Federico Divina
Universidad Pablo de Olavide, Sports and Computer Science, Faculty Member
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Summary. This chapter provides a short overview of a GA-based system for in-ductive concept learning (in a fragment of rst-order logic). The described system exploits problem{speci c knowledge by means of ad-hoc selection, mutation... more
Summary. This chapter provides a short overview of a GA-based system for in-ductive concept learning (in a fragment of rst-order logic). The described system exploits problem{speci c knowledge by means of ad-hoc selection, mutation opera-tors and optimization applied to the single individuals. We focus on the experimental analysis of selection operators incorporating problem knowledge.
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Non-Universal Suffrage Selection Operators Favor Population Diversity in Genetic Algorithms Federico Divina, Maarten Keijzer, Elena Marchiori Vrije Universiteit ... rep-resenting a redundant set of partial solutions, where a chromosome... more
Non-Universal Suffrage Selection Operators Favor Population Diversity in Genetic Algorithms Federico Divina, Maarten Keijzer, Elena Marchiori Vrije Universiteit ... rep-resenting a redundant set of partial solutions, where a chromosome encodes a rule (typically a Horn clause). ...
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Research Interests: Algorithms, Evolutionary algorithms, Evolutionary Computation, Data Analysis, Swarm Intelligence, and 18 morePerformance, Biclustering, Particle Swarm Optimization, Gene expression, Genetic Algorithm, Electric Motor, Population Size, Experimentation, Evolutionary Computing, Evolutionary Algorithm, Electrical Machine, Search Space, Adaptive Algorithm, Euclidean Distance, Microarray Data, State dependence, Gene Expression Data, and Multiagent System
Protein structure prediction is one of the main challenges in Bioinformatics. An useful representation for protein D structure is the protein contact map. In this work, we propose an evolutionary approach for contact map prediction based... more
Protein structure prediction is one of the main challenges in Bioinformatics. An useful representation for protein D structure is the protein contact map. In this work, we propose an evolutionary approach for contact map prediction based on amino acids physicochemical properties. The evolutionary algorithm produces a set of rules that identifies contacts between amino acids. The rules obtained by the algorithm imposes a set of conditions on four amino acid properties in order to predict contacts. Results obtained confirm the validity of the proposal.
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This paper proposes two alternative methods for dealing with numeri- cal attributes in inductive concept learning systems based on genetic algo- rithms. The methods use constraints for restricting the range of values of the attributes and... more
This paper proposes two alternative methods for dealing with numeri- cal attributes in inductive concept learning systems based on genetic algo- rithms. The methods use constraints for restricting the range of values of the attributes and novel stochastic operators for modifying the constraints. These operators exploit information on a subset of thresholds on numer- ical attributes. The methods are embedded
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AbstractLearning concept descriptions from data is a challenging, and inherently multi-objective, optimization pro-blem. The model induced by the learner has to be complete, consistent and easily interpretable, and producing it should... more
AbstractLearning concept descriptions from data is a challenging, and inherently multi-objective, optimization pro-blem. The model induced by the learner has to be complete, consistent and easily interpretable, and producing it should take few ...
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Research Interests: Bioinformatics, Computer Science, Evolutionary Computation, Genetic Algorithms, Simulated Annealing, and 10 moreMultiobjective Optimization, Biclustering, Optimization Problem, Probabilistic reasoning, Evolutionary Computing, Evolutionary Algorithm, Search Space, Multimodal and Multiobjective Function Optimization, Microarray Data, and Optimal Solution
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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... more
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 ...
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ABSTRACT We present a multi-objective evolutionary approach to predict protein contact maps. The algorithm provides a set of rules, inferring whether there is contact between a pair of residues or not. Such rules are based on a set of... more
ABSTRACT We present a multi-objective evolutionary approach to predict protein contact maps. The algorithm provides a set of rules, inferring whether there is contact between a pair of residues or not. Such rules are based on a set of specific amino acid properties. These properties determine the particular features of each amino acid represented in the rules. In order to test the validity of our proposal, we have compared results obtained by our method with results obtained by other classification methods. The algorithm shows better accuracy and coverage rates than other contact map predictor algorithms. A statistical analysis of the resulting rules was also performed in order to extract conclusions of the protein folding problem.
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In this paper we propose an approach based on evolutionary computation for the prediction of secondary protein structure motifs. The prediction model consists of a set of rules that predict both the beginning and the end of the regions... more
In this paper we propose an approach based on evolutionary computation for the prediction of secondary protein structure motifs. The prediction model consists of a set of rules that predict both the beginning and the end of the regions corresponding to a secondary structure state conformation (α-helix or β-strand). The prediction is based on a set of specific amino acid
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In this study, we present a residue-residue contact prediction approach based on evolutionary computation. Some amino acid properties are employed according to their importance in the folding process: hydrophobicity, polarity, charge and... more
In this study, we present a residue-residue contact prediction approach based on evolutionary computation. Some amino acid properties are employed according to their importance in the folding process: hydrophobicity, polarity, charge and residue size. Our evolutionary algorithm provides a set of rules which determine different cases where two amino acids are in contact. A rule represents two windows of three
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ABSTRACT Biclustering is a technique used in analysis of microarray data. It aims at discovering subsets of genes that presents the same tendency under a subset of experimental conditions. Various techniques have been introduced for... more
ABSTRACT Biclustering is a technique used in analysis of microarray data. It aims at discovering subsets of genes that presents the same tendency under a subset of experimental conditions. Various techniques have been introduced for discovering significant biclusters. One of the most popular heuristic was introduced by Cheng and Church. In the same work, a measure, called mean squared residue, for estimating the quality of biclusters was proposed. Even if this heuristic is successful in finding interesting biclusters, it presents a number of drawbacks. In this paper we expose these drawbacks and propose some solutions in order to overcome them. Experiments show that the proposed solutions are effective in order to improve the heuristic.
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Biclustering techniques aim at extracting significant subsets of genes and conditions from microarray gene expression data. This kind of algorithms is mainly based on two key aspects: the way in which they deal with gene similarity across... more
Biclustering techniques aim at extracting significant subsets of genes and conditions from microarray gene expression data. This kind of algorithms is mainly based on two key aspects: the way in which they deal with gene similarity across the experimental conditions, that determines the quality of biclusters; and the heuristic or search strategy used for exploring the search space. A measure
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This paper proposes a preliminary study of a new, real life propositional dataset, regarding the relation between patients and their doctors. The aim of this paper is to analyze this dataset from two point of view: the satisfaction of the... more
This paper proposes a preliminary study of a new, real life propositional dataset, regarding the relation between patients and their doctors. The aim of this paper is to analyze this dataset from two point of view: the satisfaction of the patient with his or her relation ...
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Biclustering is becoming a popular technique for the study of gene expression data. This is mainly due to the capability of biclustering to address the data using various dimensions simultaneously, as opposed to clustering, which can use... more
Biclustering is becoming a popular technique for the study of gene expression data. This is mainly due to the capability of biclustering to address the data using various dimensions simultaneously, as opposed to clustering, which can use only one dimension at the time. Different heuristics have been proposed in order to discover interesting biclusters in data. Such heuristics have one common characteristic: they are guided by a measure that determines the quality of biclusters. It follows that defining such a measure is probably the most important aspect. One of the popular quality measure is the mean squared residue (MSR). However, it has been proven that MSR fails at identifying some kind of patterns. This motivates us to introduce a novel measure, called virtual error (VE), that overcomes this limitation. Results obtained by using VE confirm that it can identify interesting patterns that could not be found by MSR.
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In this paper we discuss issues relating to modelling language evolution in large populations of au- tonomous agents that are situated in a realistic environment where they have to evolve and learn means to survive for extended periods of... more
In this paper we discuss issues relating to modelling language evolution in large populations of au- tonomous agents that are situated in a realistic environment where they have to evolve and learn means to survive for extended periods of time. As we intend to build such a model in relation to the recently started New Ties project, we identify three
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... Vrije Universiteit, Amsterdam, The Netherlands {divina,elena}@cs.vu.nl Abstract ... An ex-perimental evaluation of the algorithm indi-cates its effectiveness in learning short hy-potheses of satisfactory accuracy in a short amount of... more
... Vrije Universiteit, Amsterdam, The Netherlands {divina,elena}@cs.vu.nl Abstract ... An ex-perimental evaluation of the algorithm indi-cates its effectiveness in learning short hy-potheses of satisfactory accuracy in a short amount of time. 1 Introduction ...