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Heart disease is currently one of the leading causes of death in developed countries. The electrocardiogram is an important source of information for identifying these conditions, therefore, becomes necessary to seek an advanced system of diagnosis based on these signals. In this paper we used samples of electrocardiograms of MIT-related database with ten types of pathologies and a rate corresponding to normal (healthy patient), which are processed and used for extraction from its two branches of a wide range of features. Next, various techniques have been applied to feature selection based on genetic algorithms, principal component analysis and mutual information. To carry out the task of intelligent classification, 3 different scenarios have been considered. These techniques allow us to achieve greater efficiency in the classification methods used, namely support vector machines (SVM) and decision trees (DT) to perform a comparative analysis between them. Finally, during the development of this contribution, the use of very non-invasive devices (2 channel ECG) was analyzed, we could practically classify them as wearable, which would not need interaction by the user, and whose energy consumption is very small to extend the average life of the user been on it.

The evaluation of multiple sequence alignments (MSAs) is still an open task in bioinformatics. Current MSA scores do not agree about how alignments must be accurately evaluated. Consequently, it is not trivial to know the quality of MSAs when reference alignments are not provided. Recent scores tend to use more complex evaluations adding supplementary biological features. In this work, a set of novel regression approaches are proposed for the MSA evaluation, comparing several supervised learning and mathematical methodologies. Therefore, the following models specifically designed for regression are applied: regression trees, a bootstrap aggregation of regression trees (bagging trees), least-squares support vector machines (LS-SVMs) and Gaussian processes. These algorithms consider a heterogeneous set of biological features together with other standard MSA scores in order to predict the quality of alignments. The most relevant features are then applied to build novel score schemes for the evaluation of alignments. The proposed algorithms are validated by using the BAliBASE benchmark. Additionally, an statistical ANOVA test is performed to study the relevance of these scores considering three alignment factors. According to the obtained results, the four regression models provide accurate evaluations, even outperforming other standard scores such as BLOSUM, PAM or STRIKE.

Motivation: Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, above all when sequences are less similar. Consequently, researchers and biologists do not agree about which is the most suitable way to evaluate MSAs. Recent evaluations tend to use more complex scores including further biological features. Among them, 3D structures are increasingly being used to evaluate alignments. Because structures are more conserved in proteins than sequences, scores with structural information are better suited to evaluate more distant relationships between sequences. Results: The proposed multiobjective algorithm, based on the non-dominated sorting genetic algorithm, aims to jointly optimize three objectives: STRIKE score, non-gaps percentage and totally conserved columns. It was significantly assessed on the BAliBASE benchmark according to the Kruskal–Wallis test (P < 0.01). This algorithm also outperforms other aligners, such as ClustalW, Multiple Sequence Alignment Genetic Algorithm (MSA-GA), PRRP, DIALIGN, Hidden Markov Model Training (HMMT), Pattern-Induced Multi-sequence Alignment (PIMA), MULTIALIGN, Sequence Alignment Genetic Algorithm (SAGA), PILEUP, Rubber Band Technique Genetic Algorithm (RBT-GA) and Vertical Decomposition Genetic Algorithm (VDGA), according to the Wilcoxon signed-rank test (P < 0.05), whereas it shows results not significantly different to 3D-COFFEE (P > 0.05) with the advantage of being able to use less structures. Structural information is included within the objective function to evaluate more accurately the obtained alignments. Availability: The source code is available at http://www.ugr.es/∼fortuno/MOSAStrE/MO-SAStrE.zip. Contact: fortuno@ugr.es Supplementary Information: Supplementary material is available at Bioinformatics online.

The analysis of daily living human behavior has proven to be of key importance to prevent unhealthy habits. The diversity of activities and the individuals' particular execution style determine that several sources of information are normally required. One of the main issues is to optimally combine them to guarantee performance, scalability and robustness. In this paper we present a fusion classification methodology which takes into account the potential of the individual decisions yielded at both activity and sensor classification levels. Particularly tested on a wearable sensors based system, the method reinforces the idea that some parts of the body (i.e., sensors) may be specially informative for the recognition of each particular activity, thus supporting the ranking of the decisions provided by each associated sensor decision entity. Our method systematically outperforms the results obtained by traditional multiclass models which otherwise may require a high-dimensional feature space to acquire a similar performance. The comparison with other activity-recognition fusion approaches also demonstrates our model scales significantly better for small sensor networks.

In modern proteomics, prediction of protein-protein interactions (PPIs) is a key research line, as these interactions take part in most essential biological processes. In this paper, a new approach is proposed to PPI data classification based on the extraction of genomic and proteomic information from well-known databases and the incorporation of semantic measures. This approach is carried out through the application of data mining techniques and provides very accurate models with high levels of sensitivity and specificity in the classification of PPIs. The well-known support vector machine paradigm is used to learn the models, which will also return a new confidence score which may help expert researchers to filter out and validate new external PPIs. One of the most-widely analyzed organisms, yeast, will be studied. We processed a very high-confidence dataset by extracting up to 26 specific features obtained from the chosen databases, half of them calculated using two new similarity measures proposed in this paper. Then, by applying a filter-wrapper algorithm for feature selection, we obtained a final set composed of the eight most relevant features for predicting PPIs, which was validated by a ROC analysis. The prediction capability of the support vector machine model using these eight features was tested through the evaluation of the predictions obtained in a set of external experimental, computational, and literature-collected datasets.

Protein-protein interactions (PPIs) play a crucial role in cellular processes. In the present work, a new approach is proposed to construct a PPI predictor training a support vector machine model through a mutual information filter-wrapper parallel feature selection algorithm and an iterative and hierarchical clustering to select a relevance negative training set. By means of a selected suboptimum set of features, the constructed support vector machine model is able to classify PPIs with high accuracy in any positive and negative datasets.

Traditionally, the autoregressive moving average (ARMA) model has been one of the most widely used linear models in time series prediction. Recent research activities in forecasting with artificial neural networks (ANNs) suggest that ANNs can be a promising alternative to the traditional ARMA structure. These linear models and ANNs are often compared with mixed conclusions in terms of the superiority in forecasting performance. In this paper we propose a hybridization of intelligent techniques such as ANNs, fuzzy systems and evolutionary algorithms, so that the final hybrid ARIMA-ANN model could outperform the prediction accuracy of those models when used separately. More specifically, we propose the use of fuzzy rules to elicit the order of the ARMA or ARIMA model, without the intervention of a human expert, and the use of a hybrid ARIMA-ANN model that combines the advantages of the easy-to-use and relatively easy-to-tune ARIMA models, and the computational power of ANNs.

The challenge of predicting future values of a time series covers a variety of disciplines. The fundamental problem of selecting the order and identifying the time varying parameters of an autoregressive moving average model (ARMA) concerns many important fields of interest such as linear prediction, system identification and spectral analysis. Recent research activities in forecasting with artificial neural networks (ANNs) suggest that ANNs can be a promising alternative to the traditional ARMA structure. These linear models and ANNs are often compared with mixed conclusions in terms of the superiority in forecasting performance. This study was designed: (a) to investigate a hybrid methodology that combines ANN and ARMA models; (b) to resolve one of the most important problems in time series using ARMA structure and Box-Jenkins methodology: the identification of the model. In this paper, we present a new procedure to predict time series using paradigms such as: fuzzy systems, neural networks and evolutionary algorithms. Our goal is to obtain an expert system based on paradigms of artificial intelligence, so that the linear model can be identified automatically, without the need of human expert participation. The obtained linear model will be combined with ANN, making up an hybrid system that could outperform the forecasting result.

There are currently several biological databases related to proteins depending on the information we are interested to extract. Therefore, since a heterogeneous set of features will be needed (domains, structures, ontology terms, etc), several quite different databases should be consulted. The handling of different databases can become difficult, as each database could provide a different nomenclature for the same proteins. Anyway, these databases usually provides some mapping tools in order to determine the correspondence among the different nomenclatures used for the same protein. The main goal of this paper is to provide a biological database including a huge amount of protein information in order to be used for different purposes in bioinformatics. This database will be designed as a flexible and extensible tool and it could be extended and updated when new proteins are annotated or the included ones are modified.

The electrocardiogram (ECG) is a noninvasive technique used to reflect underlying heart conditions by measuring the electrical activity of the heart, and nowadays it is possible with just a few derivation (with just only two), obtain important information in order than an expert can recognize abnormal heart rhythms (the heart rate is very fast, very slow, or irregular) or a heart attack (myocardial infarction), and if it was recent or some time ago. In this paper, several intelligent classifiers are developed, focusing on the problem of diagnosing cardiac diseases based on the electrocardiogram (ECG), or more precisely, on the differentiation of several arrhythmia using a large data set. We will study and imitate the ECG treatment methodologies and the features extracted from the electrocardiograms used by the researchers, which obtained the best results in the PhysioNet Challenge (www.physionet.org/). We will extract a great amount of features, partly those used by these researchers and some additional others we considered to be important for the distinction previously mentioned. A new method based on different paradigms of intelligent computation (such as extreme learning machine, support vector machine, decision trees, genetic algorithms and feature selection) will be used to select the most relevant characteristics and to obtain a classifier capable of autonomously distinguishing the different types arrhythmia from the ECG signal.

Alzheimer's Disease (AD) is normally identified by several behavioral symptoms often mistakenly associated to age-related concerns or stress. However correct diagnosis and monitoring of the disease requires of additional resources. This paper presents a new methodology for classification of Alzheimer's disease from MR images for medical support. A large database with more than one thousand patients was used. Two different problems are tackled in this work: a first one where a classification method is developed to classify MR images as either normal or with the Alzheimer's disease and a second one for the identification and classification between normal subjects, MCI patients and AD patients. It is noteworthy that with this last study we could offer a tool to assist the early diagnosis of dementia. The outline of the methodology includes wavelet feature extraction from the MRIs, dimensionality reduction, training-test subdivision and classification using Support Vector Machines. Some concerns related to performance evaluation and dimensionality reduction are discussed.

This paper is focused on the development of intelligent classifiers in the area of biomedicine, focusing on the problem of diagnosing cardiac diseases based on the electrocardiogram (ECG), or more precisely, on the differentiation of several arrhythmia using a large data set, by an autonomous intelligent system which can be used as an expert system to support human experts in the diagnosis and, moreover, to autonomously display an alarm to the user in case of a dangerous situation. We will study and imitate the ECG treatment methodologies and the features extracted from the electrocardiograms used by the researchers, which obtained the best results in the PhysioNet Challenge. We will extract a great amount of features, partly those used by these researchers and some additional others we considered to be important for the distinction previously mentioned. A new method based on different paradigms of intelligent computation (such as extreme learning machine, support vector machine and feature selection) will be used to select the most relevant characteristics and to obtain a classifier capable of autonomously distinguishing the different types arrhythmia from the ECG signal. Finally, the behavior and performance of the classifier have been tested using data from several cardiac pathologies, obtaining good classification results.

Multiple sequence alignment (MSA) is an essential approach to apply in other outstanding bioinformatics tasks such as structural predictions, biological function analyses or phylogenetic modeling. However, current MSA methodologies do not reach a consensus about how sequences must be accurately aligned. Moreover, these tools usually provide partially optimal alignments, as each one is focused on specific features. Thus, the same set of sequences can provide quite different alignments, overall when sequences are less related. Consequently, researchers and biologists do not agree on how the quality of MSAs should be evaluated in order to decide the most adequate methodology. Therefore, recent evaluations tend to use more complex scores including supplementary biological features. In this work, we address the evaluation of MSAs by using a novel supervised learning approach based on Least Square Support Vector Machine (LS-SVM). This algorithm will include a set of heterogeneous features and scores in order to determine the alignment accuracies. It is assessed by means of the benchmark BAliBASE.

There are several dementias but Alzheimer's Disease (AD) is leading cause of dementia in the world. In this paper, a new methodology for classification of MR images is proposed, using a large data base (more than one thousand patient). We have two main objectives in this paper: a first one where a classification method is developed to classify MR images as either normal or with the Alzheimer's disease and a second which is the ambitious goal of this study, the identification and classification between normal subjects, MCI patients and AD patients. It is noteworthy that with this last study we could offer a tool to assist the early diagnosis of dementia.

Intrusion Detection System (IDS) which are increasingly a key part of system defense are used to identify abnormal activities in a computer system. In general, the traditional IDS relies on the extensive knowledge of security experts, in particular, on their familiarity with the computer system to be protected. To reduce this dependence, various data-mining and machine learning techniques have been used in the literature. The experiments and evaluations of the proposed intrusion detection system are performed with the NSL-KDD intrusion detection dataset. We will apply different learning algorithms on NSL-KDD data set, to recognize between normal and attack connections and compare their performing in different scenarios- discretization, features selections and algorithm method for classification- using a powerful statistical analysis: ANOVA. In this study, both the accuracy of the configuration of different system and methodologies used, and also the computational time and complexity of the methodologies are analyzed.

This article focuses on the development of intelligent classifiers in the area of biomedicine, focusing on the problem of diagnosing cardiac diseases based on the electrocardiogram (ECG), or more precisely, on the differentiation of the types of atrial fibrillations. First of all, we will study the ECG, and the treatment of the ECG in order to work with it with this specific pathology. In order to achieve this we will study different ways of elimination, in the best possible way, of any activity that is not caused by the auriculars. We will study and imitate the ECG treatment methodologies and the characteristics extracted from the electrocardiograms that were used by the researchers who obtained the best results in the Physionet Challenge, where the classification of ECG recordings according to the type of atrial fibrillation (AF) that they showed, was realized. We will extract a great amount of characteristics, partly those used by these researchers and additional characteristics that we consider to be important for the distinction previously mentioned. A new method based on evolutionary algorithms will be used to realize a selection of the most relevant characteristics and to obtain a classifier that will be capable of distinguishing the different types of this pathology.

The main architectures, learning abilities and applications of fuzzy systems are well documented. However, to the best of our knowledge, no in-depth analyses have been carried out into the influence on the behaviour of the fuzzy system arising from the use of different alternatives for the design of the fuzzy inference process (mainly, different implication operators and T-norm). Thus, as a complement to the existing intuitive knowledge, it is necessary to have a more precise understanding of the significance of the different alternatives. In the present contribution, the relevance and relative importance of the parameters involved in such a design are investigated by using a statistical tool, the ANalysis Of the VAriance (ANOVA).