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Nicolás García-Pedrajas

dblp:78/6955 · DBLP profile ↗
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69ranked-venue papers
32as first author
11since 2021 · last 2026
0000-0002-4488-6849ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 54 · 29 first-author · 8 since 2021Databases, data management, data science and information retrieval · 8 · 3 first-author · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 7 · 1 first-authorApplied, interdisciplinary, general and emerging computing · 7 · 2 since 2021Human-computer interaction and ubiquitous computing · 3

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
2 papers
Kernel, tree and ensemble methods · 84% Learning theory · 16%
Databases, data mining, and information retrieval
2 papers
Data mining · 100%
Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 9 heaviest of 9, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Data mining › text mining › text classification
sensitivity classification
0.312017
A Study of SVM Kernel Functions for Sensitivity Classification Ensembles with POS Sequences · SIGIR 2017
Bioinformatics and computational biology › genome annotation
gene prediction
0.212014
Improving translation initiation site and stop codon recognition by using more than two classes · Bioinform. 2014
Bioinformatics and computational biology › genome annotation
translation initiation site prediction
0.212014
Improving translation initiation site and stop codon recognition by using more than two classes · Bioinform. 2014
Machine learning › Kernel, tree and ensemble methods
ensemble learning
0.122007
Nonlinear Boosting Projections for Ensemble Construction · J. Mach. Learn. Res. 2007
Improving Multiclass Pattern Recognition by the Combination of Two Strategies · IEEE Trans. Pattern Anal. Mach. Intell. 2006
Data mining › data reduction
instance selection
0.112010
Democratic instance selection: A linear complexity instance selection algorithm based on classifier ensemble concepts · Artif. Intell. 2010
Machine learning › Kernel, tree and ensemble methods › ensemble learning
boosting
0.112007
Nonlinear Boosting Projections for Ensemble Construction · J. Mach. Learn. Res. 2007
Machine learning › Kernel, tree and ensemble methods › ensemble learning
random subspace method
0.112007
Nonlinear Boosting Projections for Ensemble Construction · J. Mach. Learn. Res. 2007
Machine learning › Kernel, tree and ensemble methods
classifier combination
0.112006
Improving Multiclass Pattern Recognition by the Combination of Two Strategies · IEEE Trans. Pattern Anal. Mach. Intell. 2006
Machine learning › Learning theory › classification
multiclass classification
0.112006
Improving Multiclass Pattern Recognition by the Combination of Two Strategies · IEEE Trans. Pattern Anal. Mach. Intell. 2006

Methods — techniques the papers use, named apart from their topics

support vector machine · 0.5part-of-speech sequence classification · 0.3ensemble learning · 0.3string kernel · 0.2multi-class classifier · 0.2classifier ensemble · 0.1nonlinear projection · 0.1neural network · 0.1boosting · 0.1bagging · 0.1one-vs-one · 0.1one-vs-all · 0.1
YearPublicationVenuePosition
2026 Sentiment analysis on review texts using category of words information and string kernels
abstract
Abstract With millions of opinions written every day around the internet, analyzing review sentiment has been shown to be an interesting and relevant problem. Support vector machines offer an excellent alternative when the amount of available data makes other models, such as deep learning, infeasible. A usual way to detect hidden sentiments in textual data is to address the mutual information through a corpus with a support vector machine or any other sophisticated classification algorithm. Approaches that are able to extract information from sequences of words, such as string kernels, have the potential for better performance. However, finding similarities can be difficult given the ample texts used to express opinions and the wide variety of vocabulary. To solve that problem, we suggest using clustering methods to automatically group words into categories based on a word vector, replacing the words in the dataset with their corresponding categories, and then using these categories to find mutual information in the text with support vector machines that use string kernels. This approach significantly reduces the token space and enhances the efficiency of the kernel methods. The proposed method showed better performance than state-of-the-art approaches for this task in a set of real-world problems. Different models were tested against our proposal. Results indicate that the proposed method has the ability to extract useful data from opinions in long texts and remains an interesting option for review sentiment analysis in general, even outperforming other state-of-the-art methods in certain datasets. It also opens the possibility of applying the same philosophy to deep learning and similar models.
José Manuel Cuevas-Muñoz, Nicolás García-Pedrajas, Aida de Haro-García
Appl. Intell.2
2024 Extensive experimental comparison among multilabel methods focused on ranking performance
abstract
Multilabel classification is a growing paradigm in the fields of data mining and machine learning. In multilabel learning, each input sample can belong to more than one binary class (termed “label”) in a multilabel framework, with contrasts with the standard single-label learning scenario. The challenge of producing a better classifier lies in the advantageous use of the correlations among different labels. In recent years, many multilabel models have been proposed, making it difficult to decide which methods to use. In this paper, we present the most comprehensive ranking performance comparison carried out thus far among numerous methods. We conduct a comprehensive analysis by comparing several configurations of 56 distinct methods, resulting in a total of 173 trained models. In addition, we utilize an extensive collection of problems involving 65 datasets. Furthermore, we analyze the effectiveness of the tested techniques by evaluating their performance with six different ranking performance metrics. Our findings indicate that while certain strategies consistently rank highly among the top-performing models, the most effective methods are strongly correlated with the specific metrics used to assess their performance. Finally, we examine many behavioral aspects of the different approaches.
Nicolás García-Pedrajas, José Manuel Cuevas-Muñoz, Gonzalo Cerruela García, Aida de Haro-García
Inf. Sci.1
2024 Partial random under/oversampling for multilabel problems
abstract
Many current data mining applications address problems with instances that belong to more than one class. The term multilabel classification has been introduced as a way of describing this task. Advantageously using the correlation among the labels can provide better performance than methods that manage each label separately. One of the major challenges in multilabel datasets is the class-imbalance problem. In most cases, several or many of the labels are sparsely populated, producing heavily imbalanced datasets. Standard methods used for single-label class-imbalanced datasets are not easily applicable due to the lack of a proper concept of minority instance in the multilabel case. In this paper, we propose a new approach based on partial undersampling and/or oversampling of the instances that is more suitable for the multilabel case. The method modifies the concept of undersampling and oversampling to implement partial undersampling/oversampling of instances. In a large set of 55 real-world multilabel problems, our approach improves the results of current methods for dealing with class-imbalanced datasets in multilabel problems.
Nicolás García-Pedrajas
Knowl. Based Syst.1
2024 A thorough experimental comparison of multilabel methods for classification performance
abstract
Multilabel classification as a data mining task has recently attracted increasing interest from researchers. Many current data mining applications address problems with instances that belong to more than one class. These problems require the development of new, efficient methods. Advantageously using the correlation among different labels can provide better performance than methods that manage each label separately. In recent decades, many methods have been developed to deal with multilabel datasets, which makes it difficult to decide which method is the most appropriate for a given task. In this paper, we present the most comprehensive comparison carried out so far. We compare a total of 62 different methods and several configurations of each one for a total of 197 trained models. We also use a large set of problems comprising 65 datasets. In addition, we studied the efficiency of the methods considering six different classification performance metrics. Our results show that, although there are methods that repeatedly appear among the top-performing models, the best methods are closely related to the metric used for evaluating the performance. We also analyzed different aspects of the behavior of the methods.
Nicolás García-Pedrajas, José Manuel Cuevas-Muñoz, Gonzalo Cerruela García, Aida de Haro-García
Pattern Recognit.1
2022 Nonlinear physics opens a new paradigm for accurate transcription start site prediction
abstract
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learning (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors.
José Antonio Barbero-Aparicio, Santiago Cuesta-López, César Ignacio García-Osorio, Javier Pérez-Rodríguez, Nicolás García-Pedrajas
BMC Bioinform.5
2022 Local-based k values for multi-label k-nearest neighbors rule
abstract
Multi-label learning is a growing field in machine learning research. Many applications address instances that simultaneously belong to many categories, which cannot be disregarded if optimal results are desired. Among the many algorithms developed for multi-label learning, the multi-label k-nearest neighbor method is among the most successful. However, in a difficult classification task, such as multi-label learning, a challenge that arises in the k-nearest neighbor approach is the assignment of the appropriate value of k. Although a suitable value might be obtained using cross-validation, it is unlikely that the same value will be optimal for the whole space spanned by the training set. It is evident that different regions of the feature space would have different distributions of instances and labels that would require different values of k. The very complex boundaries among the many present labels make the necessity of local k values even more important than in the case with a single-label k-nearest neighbor. We present a simple yet powerful approach for setting a local value of k. We associate a potentially different k with every prototype and obtain the best value of that k by optimizing the criterion consisting of the local effect of the different k values in the neighborhood of the prototype. The proposed method has a fast training stage, as it only uses the neighborhood of each training instance to set the local k value. The complexity of the proposed method in terms of the testing time is similar to that of the standard multi-label k-nearest neighbor approach. Experiments performed on a set of 20 problems show that not only does our proposed method significantly outperform the standard multi-label k-nearest neighbor rule but also the locally adaptive multi-label k-nearest neighbor method can benefit from a local k value.
Juan Antonio Romero del Castillo, Manuel Mendoza-Hurtado, Domingo Ortiz-Boyer, Nicolás García-Pedrajas
Eng. Appl. Artif. Intell.4
2022 MABUSE: A margin optimization based feature subset selection algorithm using boosting principles
abstract
Feature subset selection is one of the most common procedures in machine learning tasks. In a broad sense, feature selection methods can be classified into three major groups, embedded, filter and wrapper methods. Although wrappers might attain superior classification performances, they suffer from scalability issues as they are more computationally expensive than the other methods. Filters are typically faster, and sometimes they are the only applicable methods when the datasets are large. In the field of classification, margin optimization has been proven to be an efficient approach for improving the generalization performance of many classification models. Although margins have been used as criteria for feature selection, in most cases, the most advanced methods are wrappers, which suffer from high computational costs and do not outperform the faster algorithms. In this paper, we propose MABUSE, which is a feature selection method that optimizes margins from a filter perspective. We consider a nearest-neighbor margin definition and, borrowing from the strategy of classifier ensemble construction using boosting, we develop a new method that uses a simple heuristic search. Extensive experimental validation demonstrates that our proposed approach outperforms the state-of-the-art algorithms in both classification and reduction, and has a computational cost that is similar to previous algorithms.
Nicolás García-Pedrajas, Gonzalo Cerruela García
Knowl. Based Syst.1
2022 Grab'Em: A Novel Graph-Based Method for Combining Feature Subset Selectors
abstract
Feature selection is one of the most frequent tasks in data mining applications. Its ability to remove useless and redundant features improves the classification performance and gains knowledge about a given problem makes feature selection a common first step in data mining. In many feature selection applications, we need to combine the results of different feature selection processes. The two most common scenarios are the ensembles of feature selectors and the scaling up of feature selection methods using a data division approach. The standard procedure is to store the number of times every feature has been selected as a vote for the feature and then evaluate different selection thresholds with a certain criterion to obtain the final subset of selected features. However, this method is suboptimal as the relationships of the features are not considered in the voting process. Two redundant features may be selected a similar number of times due to the different sets of instances used each time. Thus, a voting scheme would tend to select both of them. In this article, we present a new approach: instead of using only the number of times a feature has been selected, the approach considers how many times the features have been selected together by a feature selection algorithm. The proposal is based on constructing an undirected graph where the vertices are the features, and the edges count the number of times every pair of instances has been selected together. This graph is used to select the best subset of features, avoiding the redundancy introduced by the voting scheme. The proposal improves the results of the standard voting scheme in both ensembles of feature selectors and data division methods for scaling up feature selection.
Aida de Haro-García, José Pérez-Parras Toledano, Gonzalo Cerruela García, Nicolás García-Pedrajas
IEEE Trans. Cybern.4
2021 Cooperative coevolutionary instance selection for multilabel problems
Nicolás García-Pedrajas, Gonzalo Cerruela García
Knowl. Based Syst.1
2021 SI(FS)2: Fast simultaneous instance and feature selection for datasets with many features
Nicolás García-Pedrajas, Juan Antonio Romero del Castillo, Gonzalo Cerruela García
Pattern Recognit.1
2021 Floating Search Methodology for Combining Classification Models for Site Recognition in DNA Sequences
abstract
Recognition of the functional sites of genes, such as translation initiation sites, donor and acceptor splice sites and stop codons, is a relevant part of many current problems in bioinformatics. The best approaches use sophisticated classifiers, such as support vector machines. However, with the rapid accumulation of sequence data, methods for combining many sources of evidence are necessary as it is unlikely that a single classifier can solve this problem with the best possible performance. A major issue is that the number of possible models to combine is large and the use of all of these models is impractical. In this paper we present a methodology for combining many sources of information to recognize any functional site using "floating search", a powerful heuristics applicable when the cost of evaluating each solution is high. We present experiments on four functional sites in the human genome, which is used as the target genome, and use another 20 species as sources of evidence. The proposed methodology shows significant improvement over state-of-the-art methods. The results show an advantage of the proposed method and also challenge the standard assumption of using only genomes not very close and not very far from the human to improve the recognition of functional sites.
Javier Pérez-Rodríguez, Aida de Haro-García, Nicolás García-Pedrajas
IEEE ACM Trans. Comput. Biol. Bioinform.3
2020 Ensembles of feature selectors for dealing with class-imbalanced datasets: A proposal and comparative study
Aida de Haro-García, Gonzalo Cerruela García, Nicolás García-Pedrajas
Inf. Sci.3
2019 Improving the combination of results in the ensembles of prototype selectors
Gonzalo Cerruela García, Aida de Haro-García, José Pérez-Parras Toledano, Nicolás García-Pedrajas
Neural Networks4
2019 Instance selection based on boosting for instance-based learners
Aida de Haro-García, Gonzalo Cerruela García, Nicolás García-Pedrajas
Pattern Recognit.3
2017 A Study of SVM Kernel Functions for Sensitivity Classification Ensembles with POS Sequences
abstract
Freedom of Information (FOI) laws legislate that government documents should be opened to the public. However, many government documents contain sensitive information, such as confidential information, that is exempt from release. Therefore, government documents must be sensitivity reviewed prior to release, to identify and close any sensitive information. With the adoption of born-digital documents, such as email, there is a need for automatic sensitivity classification to assist digital sensitivity review. SVM classifiers and Part-of-Speech sequences have separately been shown to be promising for sensitivity classification. However, sequence classification methodologies, and specifically SVM kernel functions, have not been fully investigated for sensitivity classification. Therefore, in this work, we present an evaluation of five SVM kernel functions for sensitivity classification using POS sequences. Moreover, we show that an ensemble classifier that combines POS sequence classification with text classification can significantly improve sensitivity classification effectiveness (+6.09% F2) compared with a text classification baseline, according to McNemar's test of significance.
Graham McDonald, Nicolás García-Pedrajas, Craig Macdonald, Iadh Ounis
SIGIR2
2017 A Proposal for Local k Values for k-Nearest Neighbor Rule
abstract
The k -nearest neighbor ( k -NN) classifier is one of the most widely used methods of classification due to several interesting features, including good generalization and easy implementation. Although simple, it is usually able to match and even outperform more sophisticated and complex methods. One of the problems with this approach is fixing the appropriate value of k . Although a good value might be obtained using cross validation, it is unlikely that the same value could be optimal for the whole space spanned by the training set. It is evident that different regions of the feature space would require different values of k due to the different distributions of prototypes. The situation of a query instance in the center of a class is very different from the situation of a query instance near the boundary between two classes. In this brief, we present a simple yet powerful approach to setting a local value of k . We associate a potentially different k to every prototype and obtain the best value of k by optimizing a criterion consisting of the local and global effects of the different k values in the neighborhood of the prototype. The proposed method has a fast training stage and the same complexity as the standard k -NN approach at the testing stage. The experiments show that this simple approach can significantly outperform the standard k -NN rule for both standard and class-imbalanced problems in a large set of different problems.
Nicolás García-Pedrajas, Juan Antonio Romero del Castillo, Gonzalo Cerruela García
IEEE Trans. Neural Networks Learn. Syst.1
2016 Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences
abstract
BACKGROUND: Recognizing the different functional parts of genes, such as promoters, translation initiation sites, donors, acceptors and stop codons, is a fundamental task of many current studies in Bioinformatics. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels. However, with the rapid evolution of our ability to collect genomic information, it has been shown that combining many sources of evidence is fundamental to the success of any recognition task. With the advent of next-generation sequencing, the number of available genomes is increasing very rapidly. Thus, methods for making use of such large amounts of information are needed. RESULTS: In this paper, we present a methodology for combining tens or even hundreds of different classifiers for an improved performance. Our approach can include almost a limitless number of sources of evidence. We can use the evidence for the prediction of sites in a certain species, such as human, or other species as needed. This approach can be used for any of the functional recognition tasks cited above. However, to provide the necessary focus, we have tested our approach in two functional recognition tasks: translation initiation site and stop codon recognition. We have used the entire human genome as a target and another 20 species as sources of evidence and tested our method on five different human chromosomes. The proposed method achieves better accuracy than the best state-of-the-art method both in terms of the geometric mean of the specificity and sensitivity and the area under the receiver operating characteristic and precision recall curves. Furthermore, our approach shows a more principled way for selecting the best genomes to be combined for a given recognition task. CONCLUSIONS: Our approach has proven to be a powerful tool for improving the performance of functional site recognition, and it is a useful method for combining many sources of evidence for any recognition task in Bioinformatics. The results also show that the common approach of heuristically choosing the species to be used as source of evidence can be improved because the best combinations of genomes for recognition were those not usually selected. Although the experiments were performed for translation initiation site and stop codon recognition, any other recognition task may benefit from our methodology.
Javier Pérez-Rodríguez, Nicolás García-Pedrajas
BMC Bioinform.2
2014 Improving translation initiation site and stop codon recognition by using more than two classes
abstract
MOTIVATION: The recognition of translation initiation sites and stop codons is a fundamental part of any gene recognition program. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels. These methods all use two classes, one of positive instances and another one of negative instances that are constructed using sequences from the whole genome. However, the features of the negative sequences differ depending on the position of the negative samples in the gene. There are differences depending on whether they are from exons, introns, intergenic regions or any other functional part of the genome. Thus, the positive class is fairly homogeneous, as all its sequences come from the same part of the gene, but the negative class is composed of different instances. The classifier suffers from this problem. In this article, we propose the training of different classifiers with different negative, more homogeneous, classes and the combination of these classifiers for improved accuracy. RESULTS: The proposed method achieves better accuracy than the best state-of-the-art method, both in terms of the geometric mean of the specificity and sensitivity and the area under the receiver operating characteristic and precision recall curves. The method is tested on the whole human genome. The results for recognizing both translation initiation sites and stop codons indicated improvements in the rates of both false-negative results (FN) and false-positive results (FP). On an average, for translation initiation site recognition, the false-negative ratio was reduced by 30.2% and the FP ratio decreased by 10.9%. For stop codon prediction, FP were reduced by 41.4% and FN by 31.7%. AVAILABILITY AND IMPLEMENTATION: The source code is licensed under the General Public License and is thus freely available. The datasets and source code can be obtained from http://cib.uco.es/site-recognition. CONTACT: [email protected].
Javier Pérez-Rodríguez, Alexis G. Arroyo-Peña, Nicolás García-Pedrajas
Bioinform.3
2014 A Scalable Memetic Algorithm for Simultaneous Instance and Feature Selection
abstract
Instance selection is becoming increasingly relevant due to the huge amount of data that is constantly produced in many fields of research. At the same time, most of the recent pattern recognition problems involve highly complex datasets with a large number of possible explanatory variables. For many reasons, this abundance of variables significantly harms classification or recognition tasks. There are efficiency issues, too, because the speed of many classification algorithms is largely improved when the complexity of the data is reduced. One of the approaches to address problems that have too many features or instances is feature or instance selection, respectively. Although most methods address instance and feature selection separately, both problems are interwoven, and benefits are expected from facing these two tasks jointly. This paper proposes a new memetic algorithm for dealing with many instances and many features simultaneously by performing joint instance and feature selection. The proposed method performs four different local search procedures with the aim of obtaining the most relevant subsets of instances and features to perform an accurate classification. A new fitness function is also proposed that enforces instance selection but avoids putting too much pressure on removing features. We prove experimentally that this fitness function improves the results in terms of testing error. Regarding the scalability of the method, an extension of the stratification approach is developed for simultaneous instance and feature selection. This extension allows the application of the proposed algorithm to large datasets. An extensive comparison using 55 medium to large datasets from the UCI Machine Learning Repository shows the usefulness of our method. Additionally, the method is applied to 30 large problems, with very good results. The accuracy of the method for class-imbalanced problems in a set of 40 datasets is shown. The usefulness of the method is also tested using decision trees and support vector machines as classification methods.
Nicolás García-Pedrajas, Aida de Haro-García, Javier Pérez-Rodríguez
Evol. Comput.1
2014 Boosting instance selection algorithms
Nicolás García-Pedrajas, Aida de Haro-García
Knowl. Based Syst.1
2013 A scalable approach to simultaneous evolutionary instance and feature selection
Nicolás García-Pedrajas, Aida de Haro-García, Javier Pérez-Rodríguez
Inf. Sci.1
2013 OligoIS: Scalable Instance Selection for Class-Imbalanced Data Sets
abstract
In current research, an enormous amount of information is constantly being produced, which poses a challenge for data mining algorithms. Many of the problems in extremely active research areas, such as bioinformatics, security and intrusion detection, or text mining, share the following two features: large data sets and class-imbalanced distribution of samples. Although many methods have been proposed for dealing with class-imbalanced data sets, most of these methods are not scalable to the very large data sets common to those research fields. In this paper, we propose a new approach to dealing with the class-imbalance problem that is scalable to data sets with many millions of instances and hundreds of features. This proposal is based on the divide-and-conquer principle combined with application of the selection process to balanced subsets of the whole data set. This divide-and-conquer principle allows the execution of the algorithm in linear time. Furthermore, the proposed method is easy to implement using a parallel environment and can work without loading the whole data set into memory. Using 40 class-imbalanced medium-sized data sets, we will demonstrate our method's ability to improve the results of state-of-the-art instance selection methods for class-imbalanced data sets. Using three very large data sets, we will show the scalability of our proposal to millions of instances and hundreds of features.
Nicolás García-Pedrajas, Javier Pérez-Rodríguez, Aida de Haro-García
IEEE Trans. Cybern.1
2012 Linear Projection Methods - An Experimental Study for Regression Problems
Carlos Pardo-Aguilar, José-Francisco Díez-Pastor, Nicolás García-Pedrajas, Juan José Rodríguez Diez, César Ignacio García-Osorio
ICPRAM (1)3
2012 A Comparative Study of Content Statistics of Coding Regions in an Evolutionary Computation Framework for Gene Prediction
Javier Pérez-Rodríguez, Alexis G. Arroyo-Peña, Nicolás García-Pedrajas
IEA/AIE3
2012 Evolutionary response surfaces for classification: an interpretable model
Rafael del Castillo Gomariz, Nicolás García-Pedrajas
Appl. Intell.2
2012 Large scale instance selection by means of federal instance selection
Aida de Haro-García, Nicolás García-Pedrajas, Juan Antonio Romero del Castillo
Data Knowl. Eng.2
2012 Supervised subspace projections for constructing ensembles of classifiers
Nicolás García-Pedrajas, Jesús Maudes, César Ignacio García-Osorio, Juan José Rodríguez Diez
Inf. Sci.1
2012 Special issue on "New Trends in Data Mining" NTDM
José Manuel Benítez 0001, Nicolás García-Pedrajas, Francisco Herrera
Knowl. Based Syst.2
2012 Class imbalance methods for translation initiation site recognition in DNA sequences
Nicolás García-Pedrajas, Javier Pérez-Rodríguez, María D. García-Pedrajas, Domingo Ortiz-Boyer, Colin Fyfe
Knowl. Based Syst.1
2011 Translation Initiation Site Recognition by Means of Evolutionary Response Surfaces
Rafael del Castillo Gomariz, Nicolás García-Pedrajas
IEA/AIE (2)2
2011 Feature Selection for Translation Initiation Site Recognition
Aida de Haro-García, Javier Pérez-Rodríguez, Nicolás García-Pedrajas
IEA/AIE (2)3
2011 An Evolutionary Algorithm for Gene Structure Prediction
Javier Pérez-Rodríguez, Nicolás García-Pedrajas
IEA/AIE (2)2
2011 A scalable method for instance selection for class-imbalance datasets
abstract
Instance selection is becoming more and more relevant due to the huge amount of data that is constantly being produced. Research areas such as bioinformatics, text mining and intrusion detection, are generating huge amounts of information that must be dealt with. Instance selection is a powerful tool to reduce that information to manageable datasets. Most of the datasets in these areas shares a common property, they are heavily class-imbalanced. The class of interest, or positive or minority class, is outnumbered many times by the negative, or majority, class. Thus, any instance selection algorithm addressing these problems must take into account two important features of such problems. Firstly, the large size of the datasets that makes scalability issues very relevant. Secondly, the class-imbalanced distribution of the instances. In this paper, we propose a new methodology for instance selection that it is specifically designed for large class-imbalanced datasets. We use a divide-and-conquer approach to deal with the scalability of the algorithms, and a combination of different rounds of instance selection to improve the results in terms of class-imbalance error measures. The validity of the proposed framework is assured using 45 datasets. Our proposal improves the results of standard methods in accuracy and storage reduction, and at the same time is able to reduce the time needed by the algorithms with a time complexity O(n log(n)).
Aida de Haro-García, Nicolás García-Pedrajas
ISDA2
2011 Evolutionary computation, combined with support vector machines, for gene structure prediction
abstract
Gene structure prediction consists of determining which parts of a genomic sequence of the cell are coding, and constructing the whole gene from its start site to its stop codon. Gene recognition is one of the most important open problems in bioinformatics. The subtle sources of evidence and the many pitfalls of the problem make gene recognition in eukaryotes one of the most challenging tasks in this field. Gene recognition may be considered as a search problem, where many evidence sources are combined in a scoring function that must be maximized to obtain the structure of a probable gene. Using an intrinsic method, we propose a combination of evolutionary computation and support vector machines for gene structure prediction. Specifically, we use support vector machines (SVMs) to localize and score the functional sites along the genomic sequence, reducing the search space. Evolutionary computation is used to evolve a population where the individuals are correct gene structures. The flexibility of evolutionary computation can be used to account for the complexities of the problem, which are growing as our knowledge of the molecular processes of transcription and translation deepens. Our results show that with a very simple program we are able to achieve very good accuracies in the recognition of genes in human chromosome 19.
Javier Pérez-Rodríguez, Nicolás García-Pedrajas
ISDA2
2011 Special issue on the trends in applied intelligence systems
Nicolás García-Pedrajas, Francisco Herrera, Colin Fyfe
Appl. Intell.1
2011 Constructing ensembles of classifiers using supervised projection methods based on misclassified instances
Nicolás García-Pedrajas, César Ignacio García-Osorio
Expert Syst. Appl.1
2010 Large Scale Instance Selection by Means of a Parallel Algorithm
Aida de Haro-García, Juan Antonio Romero del Castillo, Nicolás García-Pedrajas
IDEAL3
2010 Class Imbalance Methods for Translation Initiation Site Recognition
Nicolás García-Pedrajas, Domingo Ortiz-Boyer, María D. García-Pedrajas, Colin Fyfe
IEA/AIE (1)1
2010 Scaling Up Feature Selection by Means of Democratization
Aida de Haro-García, Nicolás García-Pedrajas
IEA/AIE (2)2
2010 Democratic instance selection: A linear complexity instance selection algorithm based on classifier ensemble concepts
César Ignacio García-Osorio, Aida de Haro-García, Nicolás García-Pedrajas
Artif. Intell.3
2010 A cooperative coevolutionary algorithm for instance selection for instance-based learning
Nicolás García-Pedrajas, Juan Antonio Romero del Castillo, Domingo Ortiz-Boyer
Mach. Learn.1
2009 A divide-and-conquer recursive approach for scaling up instance selection algorithms
Aida de Haro-García, Nicolás García-Pedrajas
Data Min. Knowl. Discov.2
2009 Boosting k-nearest neighbor classifier by means of input space projection
Nicolás García-Pedrajas, Domingo Ortiz-Boyer
Expert Syst. Appl.1
2009 Supervised projection approach for boosting classifiers
Nicolás García-Pedrajas
Pattern Recognit.1
2009 Constructing Ensembles of Classifiers by Means of Weighted Instance Selection
abstract
In this paper, we approach the problem of constructing ensembles of classifiers from the point of view of instance selection. Instance selection is aimed at obtaining a subset of the instances available for training capable of achieving, at least, the same performance as the whole training set. In this way, instance selection algorithms try to keep the performance of the classifiers while reducing the number of instances in the training set. Meanwhile, boosting methods construct an ensemble of classifiers iteratively focusing each new member on the most difficult instances by means of a biased distribution of the training instances. In this work, we show how these two methodologies can be combined advantageously. We can use instance selection algorithms for boosting using as objective to optimize the training error weighted by the biased distribution of the instances given by the boosting method. Our method can be considered as boosting by instance selection. Instance selection has mostly been developed and used for k -nearest neighbor ( k -NN) classifiers. So, as a first step, our methodology is suited to construct ensembles of k -NN classifiers. Constructing ensembles of classifiers by means of instance selection has the important feature of reducing the space complexity of the final ensemble as only a subset of the instances is selected for each classifier. However, the methodology is not restricted to k-NN classifier. Other classifiers, such as decision trees and support vector machines (SVMs), may also benefit from a smaller training set, as they produce simpler classifiers if an instance selection algorithm is performed before training. In the experimental section, we show that the proposed approach is able to produce better and simpler ensembles than random subspace method (RSM) method for k-NN and standard ensemble methods for C4.5 and SVMs.
Nicolás García-Pedrajas
IEEE Trans. Neural Networks1
2008 Constructing ensembles of classifiers using linear projections based on misclassified instances
César Ignacio García-Osorio, Nicolás García-Pedrajas
ESANN2
2008 A tool for teaching LL and LR parsing algorithms
abstract
In this paper we present a tool to assist in teaching top-down and bottom-up analysis algorithms. The tool provides simulation for the following analysis algorithms: LL, SLR, LALR and LR. During the simulation the student can simultaneously see the pending input, the analysis stack and tables, the generated output and the parse tree.
César Ignacio García-Osorio, Carlos Gómez-Palacios, Nicolás García-Pedrajas
ITiCSE3
2008 Teaching push-down automata and turing machines
abstract
In this paper we present the new version of a tool to assist in teaching formal languages and automata theory. In the previous version the tool provided algorithms for regular expressions, finite automata and context free grammars. The new version can simulate as well push-down automata and Turing machines.
César Ignacio García-Osorio, Iñigo Mediavilla-Sáiz, Javier Jimeno-Visitación, Nicolás García-Pedrajas
ITiCSE4
2008 Boosting random subspace method
Nicolás García-Pedrajas, Domingo Ortiz-Boyer
Neural Networks1
2008 Robust confidence intervals applied to crossover operator for real-coded genetic algorithms
Domingo Ortiz-Boyer, César Hervás-Martínez, Nicolás García-Pedrajas
Soft Comput.3
2008 Evolving Output Codes for Multiclass Problems
abstract
In this paper, we propose an evolutionary approach to the design of output codes for multiclass pattern recognition problems. This approach has the advantage of taking into account the different aspects that are relevant for a code matrix to achieve a good performance. We define a fitness function made up of five terms that refer to overall classifier accuracy, binary classifiers' accuracy, classifiers' diversity, minimum Hamming distance among codewords, and margin of classification. These five factors have not been considered together in previous works. We perform a study of these five terms to obtain a fitness function with three of them. We test our approach on 27 datasets from the UCI Machine Learning Repository, using three different base learners: C4.5, neural networks, and support vector machines. We show a better performance than most of the current standard methods, namely, randomly generated codes with approximately equal random split, codes designed using a CHC algorithm, and one-vs-all and one-vs-one methods.
Nicolás García-Pedrajas, Colin Fyfe
IEEE Trans. Evol. Comput.1
2007 Immune network based ensembles
Nicolás García-Pedrajas, Colin Fyfe
Neurocomputing1
2007 Nonlinear Boosting Projections for Ensemble Construction
abstract
In this paper we propose a novel approach for ensemble construction based on the use of nonlinear projections to achieve both accuracy and diversity of individual classifiers. The proposed approach combines the philosophy of boosting, putting more effort on difficult instances, with the basis of the random subspace method. Our main contribution is that instead of using a random subspace, we construct a projection taking into account the instances which have posed most difficulties to previous classifiers. In this way, consecutive nonlinear projections are created by a neural network trained using only incorrectly classified instances. The feature subspace induced by the hidden layer of this network is used as the input space to a new classifier. The method is compared with bagging and boosting techniques, showing an improved performance on a large set of 44 problems from the UCI Machine Learning Repository. An additional study showed that the proposed approach is less sensitive to noise in the data than boosting methods.
Nicolás García-Pedrajas, César Ignacio García-Osorio, Colin Fyfe
J. Mach. Learn. Res.1
2007 A cooperative constructive method for neural networks for pattern recognition
Nicolás García-Pedrajas, Domingo Ortiz-Boyer
Pattern Recognit.1
2006 Immune Network based Ensembles
Nicolás García-Pedrajas, Colin Fyfe
ESANN1
2006 Classification by means of Evolutionary Response Surfaces
Rafael del Castillo Gomariz, Nicolás García-Pedrajas
ESANN2
2006 An alternative approach for neural network evolution with a genetic algorithm: Crossover by combinatorial optimization
Nicolás García-Pedrajas, Domingo Ortiz-Boyer, César Hervás-Martínez
Neural Networks1
2006 Evolutionary product unit based neural networks for regression
Alfonso C. Martínez-Estudillo, Francisco J. Martínez-Estudillo, César Hervás-Martínez, Nicolás García-Pedrajas
Neural Networks4
2006 Improving Multiclass Pattern Recognition by the Combination of Two Strategies
abstract
We present a new method of multiclass classification based on the combination of one-vs-all method and a modification of one-vs-one method. This combination of one-vs-all and one-vs-one methods proposed enforces the strength of both methods. A study of the behavior of the two methods identifies some of the sources of their failure. The performance of a classifier can be improved if the two methods are combined in one, in such a way that the main sources of their failure are partially avoided.
Nicolás García-Pedrajas, Domingo Ortiz-Boyer
IEEE Trans. Pattern Anal. Mach. Intell.1
2006 Hybridization of evolutionary algorithms and local search by means of a clustering method
abstract
This paper presents a hybrid evolutionary algorithm (EA) to solve nonlinear-regression problems. Although EAs have proven their ability to explore large search spaces, they are comparatively inefficient in fine tuning the solution. This drawback is usually avoided by means of local optimization algorithms that are applied to the individuals of the population. The algorithms that use local optimization procedures are usually called hybrid algorithms. On the other hand, it is well known that the clustering process enables the creation of groups (clusters) with mutually close points that hopefully correspond to relevant regions of attraction. Local-search procedures can then be started once in every such region. This paper proposes the combination of an EA, a clustering process, and a local-search procedure to the evolutionary design of product-units neural networks. In the methodology presented, only a few individuals are subject to local optimization. Moreover, the local optimization algorithm is only applied at specific stages of the evolutionary process. Our results show a favorable performance when the regression method proposed is compared to other standard methods.
Alfonso C. Martínez-Estudillo, César Hervás-Martínez, Francisco J. Martínez-Estudillo, Nicolás García-Pedrajas
IEEE Trans. Syst. Man Cybern. Part B4
2005 Crossover effect over penalty methods in function optimization with constraints
abstract
One of the most common and versatile techniques for coping with constraints consists of the penalty of the solutions whose variables do not fulfill the constraints. The genetic algorithm (GA) is one of the main tools used for the optimization of functions with constraints. In this context the crossover operator must tend to generate individuals within or near the feasible region in order to converge to useful solutions. In this work we make an analysis of the influence of the crossover operator in this kind of problems. We have used a test set that includes functions with linear and nonlinear constraints. The results confirm the importance of the crossover operator.
Domingo Ortiz-Boyer, Rafael del Castillo Gomariz, Nicolás García-Pedrajas, César Hervás-Martínez
Congress on Evolutionary Computation3
2005 CIXL2: A Crossover Operator for Evolutionary Algorithms Based on Population Features
abstract
In this paper we propose a crossover operator for evolutionary algorithms with real values that is based on the statistical theory of population distributions. The operator is based on the theoretical distribution of the values of the genes of the best individuals in the population. The proposed operator takes into account the localization and dispersion features of the best individuals of the population with the objective that these features would be inherited by the offspring. Our aim is the optimization of the balance between exploration and exploitation in the search process. In order to test the efficiency and robustness of this crossover, we have used a set of functions to be optimized with regard to different criteria, such as, multimodality, separability, regularity and epistasis. With this set of functions we can extract conclusions in function of the problem at hand. We analyze the results using ANOVA and multiple comparison statistical tests. As an example of how our crossover can be used to solve artificial intelligence problems, we have applied the proposed model to the problem of obtaining the weight of each network in a ensemble of neural networks. The results obtained are above the performance of standard methods.
Domingo Ortiz-Boyer, César Hervás-Martínez, Nicolás García-Pedrajas
J. Artif. Intell. Res.3
2005 Cooperative coevolution of artificial neural network ensembles for pattern classification
abstract
This paper presents a cooperative coevolutive approach for designing neural network ensembles. Cooperative coevolution is a recent paradigm in evolutionary computation that allows the effective modeling of cooperative environments. Although theoretically, a single neural network with a sufficient number of neurons in the hidden layer would suffice to solve any problem, in practice many real-world problems are too hard to construct the appropriate network that solve them. In such problems, neural network ensembles are a successful alternative. Nevertheless, the design of neural network ensembles is a complex task. In this paper, we propose a general framework for designing neural network ensembles by means of cooperative coevolution. The proposed model has two main objectives: first, the improvement of the combination of the trained individual networks; second, the cooperative evolution of such networks, encouraging collaboration among them, instead of a separate training of each network. In order to favor the cooperation of the networks, each network is evaluated throughout the evolutionary process using a multiobjective method. For each network, different objectives are defined, considering not only its performance in the given problem, but also its cooperation with the rest of the networks. In addition, a population of ensembles is evolved, improving the combination of networks and obtaining subsets of networks to form ensembles that perform better than the combination of all the evolved networks. The proposed model is applied to ten real-world classification problems of a very different nature from the UCI machine learning repository and proben1 benchmark set. In all of them the performance of the model is better than the performance of standard ensembles in terms of generalization error. Moreover, the size of the obtained ensembles is also smaller.
Nicolás García-Pedrajas, César Hervás-Martínez, Domingo Ortiz-Boyer
IEEE Trans. Evol. Comput.1
2004 Cooperative coevolution of generalized multi-layer perceptrons
Nicolás García-Pedrajas, Domingo Ortiz-Boyer, César Hervás-Martínez
Neurocomputing1
2003 COVNET: a cooperative coevolutionary model for evolving artificial neural networks
abstract
This paper presents COVNET, a new cooperative coevolutionary model for evolving artificial neural networks. This model is based on the idea of coevolving subnetworks that must cooperate to form a solution for a specific problem, instead of evolving complete networks. The combination of this subnetworks is part of a coevolutionary process. The best combinations of subnetworks must be evolved together with the coevolution of the subnetworks. Several subpopulations of subnetworks coevolve cooperatively and genetically isolated. The individual of every subpopulation are combined to form whole networks. This is a different approach from most current models of evolutionary neural networks which try to develop whole networks. COVNET places as few restrictions as possible over the network structure, allowing the model to reach a wide variety of architectures during the evolution and to be easily extensible to other kind of neural networks. The performance of the model in solving three real problems of classification is compared with a modular network, the adaptive mixture of experts and with the results presented in the bibliography. COVNET has shown better generalization and produced smaller networks than the adaptive mixture of experts and has also achieved results, at least, comparable with the results in the bibliography.
Nicolás García-Pedrajas, César Hervás-Martínez, José Muñoz-Pérez
IEEE Trans. Neural Networks1
2002 Theoretical Analysis of the Confidence Interval Based Crossover for Real-Coded Genetic Algorithms
César Hervás-Martínez, Domingo Ortiz-Boyer, Nicolás García-Pedrajas
PPSN3
2002 Crossover Operator Effect in Function Optimization with Constraints
Domingo Ortiz-Boyer, César Hervás-Martínez, Nicolás García-Pedrajas
PPSN3
2002 Multi-objective cooperative coevolution of artificial neural networks (multi-objective cooperative networks)
Nicolás García-Pedrajas, César Hervás-Martínez, José Muñoz-Pérez
Neural Networks1
1992 Comparison Between Artificial Neural Networks and Classical Statsitical Methods in Pattern Recognition
César Hervás-Martínez, E. J. Romero Soto, Nicolás García-Pedrajas, Rafael Medina Carnicer
IPMU3