Jose A. Seoane

Classification of EEG signals using relative wavelet energy and artificial neural networks

Electroencephalographms (EEGs) are records of brain electrical activity. It is an indispensable tool for diagnosing neurological diseases, such as epilepsy. Wavelet transform (WT) is an effective tool for analysis of non-stationary signal, such as EEGs. Relative wavelet energy (RWE) provides information about the relative energy associated with different frequency bands present in EEG signals and their corresponding degree of importance. This paper deals with a novel method of analysis of EEG signals using relative wavelet energy, and classification using Artificial Neural Networks (ANNs). The obtained classification accuracy confirms that the proposed scheme has potential in classifying EEG signals.

An artificial neural network improves the non-invasive diagnosis of significant fibrosis in HIV/HCV coinfected patients

OBJECTIVE To develop an artificial neural network to predict significant fibrosis (F≥2) (ANN-SF) in HIV/Hepatitis C (HCV) coinfected patients using clinical data derived from peripheral blood. METHODS Patients were randomly divided into an estimation group (217 cases) used to generate the ANN and a test group (145 cases) used to confirm its power to predict F≥2. Liver fibrosis was estimated according to the METAVIR score. RESULTS The values of the area under the receiver operating characteristic curve (AUC-ROC) of the ANN-SF were 0.868 in the estimation set and 0.846 in the test set. In the estimation set, with a cut-off value of <0.35 to predict the absence of F≥2, the sensitivity (Se), specificity (Sp), and positive (PPV) and negative predictive values (NPV) were 94.1%, 41.8%, 66.3% and 85.4% respectively. Furthermore, with a cut-off value of >0.75 to predict the presence of F≥2, the ANN-SF provided Se, Sp, PPV and NPV of 53.8%, 94.9%, 92.8% and 62.8% respectively. In the test set, with a cut-off value of <0.35 to predict the absence of F≥2, the Se, Sp, PPV and NPV were 91.8%, 51.7%, 72.9% and 81.6% respectively. Furthermore, with a cut-off value of >0.75 to predict the presence of F≥2, the ANN-SF provided Se, Sp, PPV and NPV of 43.5%, 96.7%, 94.9% and 54.7% respectively. CONCLUSION The ANN-SF accurately predicted significant fibrosis and outperformed other simple non-invasive indices for HIV/HCV coinfected patients. Our data suggest that ANN may be a helpful tool for guiding therapeutic decisions in clinical practice concerning HIV/HCV coinfection.

Drug Discovery and Design for Complex Diseases through QSAR Computational Methods

There is a need for a study of the complex diseases due to their important impact on our society. One of the solutions involves the theoretical methods which are fast and efficient tools that can lead to the discovery of new active drugs specially designed for these diseases. The Quantitative Structure - Activity Relationship models (QSAR) and the complex network theory become important solutions for screening and designing efficient pharmaceuticals by coding the chemical information of the molecules into molecular descriptors. This review presents the most recent studies on drug discovery and design using QSAR of several complex diseases in the fields of Neurology, Cardiology and Oncology.

A pathway-based data integration framework for prediction of disease progression

Motivation: Within medical research there is an increasing trend toward deriving multiple types of data from the same individual. The most effective prognostic prediction methods should use all available data, as this maximizes the amount of information used. In this article, we consider a variety of learning strategies to boost prediction performance based on the use of all available data. Implementation: We consider data integration via the use of multiple kernel learning supervised learning methods. We propose a scheme in which feature selection by statistical score is performed separately per data type and by pathway membership. We further consider the introduction of a confidence measure for the class assignment, both to remove some ambiguously labeled datapoints from the training data and to implement a cautious classifier that only makes predictions when the associated confidence is high. Results: We use the METABRIC dataset for breast cancer, with prediction of survival at 2000 days from diagnosis. Predictive accuracy is improved by using kernels that exclusively use those genes, as features, which are known members of particular pathways. We show that yet further improvements can be made by using a range of additional kernels based on clinical covariates such as Estrogen Receptor (ER) status. Using this range of measures to improve prediction performance, we show that the test accuracy on new instances is nearly 80%, though predictions are only made on 69.2% of the patient cohort. Availability: https://github.com/jseoane/FSMKL Contact: J.Seoane@bristol.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Alternative Consent Models for Biobanks: The New Spanish Law on Biomedical Research

This article provides an overview of recent contributions to the debate on the ethical use of previously collected biobank samples, as well as a country report about how this issue has been regulated in Spain by means of the new Biomedical Research Act, enacted in the summer of 2007. By contrasting the Spanish legal situation with the wider discourse of international bioethics, we identify and discuss a general trend moving from the traditional requirements of informed consent towards new models more favourable to research in a post-genomic context.

Naïve Bayes QSDR classification based on spiral-graph Shannon entropies for protein biomarkers in human colon cancer.

Fast cancer diagnosis represents a real necessity in applied medicine due to the importance of this disease. Thus, theoretical models can help as prediction tools. Graph theory representation is one option because it permits us to numerically describe any real system such as the protein macromolecules by transforming real properties into molecular graph topological indices. This study proposes a new classification model for proteins linked with human colon cancer by using spiral graph topological indices of protein amino acid sequences. The best quantitative structure-disease relationship model is based on eleven Shannon entropy indices. It was obtained with the Naïve Bayes method and shows excellent predictive ability (90.92%) for new proteins linked with this type of cancer. The statistical analysis confirms that this model allows diagnosing the absence of human colon cancer obtaining an area under receiver operating characteristic of 0.91. The methodology presented can be used for any type of sequential information such as any protein and nucleic acid sequence.

RRegrs: an R package for computer-aided model selection with multiple regression models

AbstractBackgroundPredictive regression models can be created with many different modelling approaches. Choices need to be made for data set splitting, cross-validation methods, specific regression parameters and best model criteria, as they all affect the accuracy and efficiency of the produced predictive models, and therefore, raising model reproducibility and comparison issues. Cheminformatics and bioinformatics are extensively using predictive modelling and exhibit a need for standardization of these methodologies in order to assist model selection and speed up the process of predictive model development. A tool accessible to all users, irrespectively of their statistical knowledge, would be valuable if it tests several simple and complex regression models and validation schemes, produce unified reports, and offer the option to be integrated into more extensive studies. Additionally, such methodology should be implemented as a free programming package, in order to be continuously adapted and redistributed by others.ResultsWe propose an integrated framework for creating multiple regression models, called RRegrs. The tool offers the option of ten simple and complex regression methods combined with repeated 10-fold and leave-one-out cross-validation. Methods include Multiple Linear regression, Generalized Linear Model with Stepwise Feature Selection, Partial Least Squares regression, Lasso regression, and Support Vector Machines Recursive Feature Elimination. The new framework is an automated fully validated procedure which produces standardized reports to quickly oversee the impact of choices in modelling algorithms and assess the model and cross-validation results. The methodology was implemented as an open source R package, available at https://www.github.com/enanomapper/RRegrs, by reusing and extending on the caret package.ConclusionThe universality of the new methodology is demonstrated using five standard data sets from different scientific fields. Its efficiency in cheminformatics and QSAR modelling is shown with three use cases: proteomics data for surface-modified gold nanoparticles, nano-metal oxides descriptor data, and molecular descriptors for acute aquatic toxicity data. The results show that for all data sets RRegrs reports models with equal or better performance for both training and test sets than those reported in the original publications. Its good performance as well as its adaptability in terms of parameter optimization could make RRegrs a popular framework to assist the initial exploration of predictive models, and with that, the design of more comprehensive in silico screening applications.Graphical abstractRRegrs is a computer-aided model selection framework for R multiple regression models; this is a fully validated procedure with application to QSAR modelling

Breast density classification to reduce false positives in CADe systems

This paper describes a novel weighted voting tree classification scheme for breast density classification. Breast parenchymal density is an important risk factor in breast cancer. Moreover, it is known that mammogram interpretation is more difficult when dense tissue is involved. Therefore, automated breast density classification may aid in breast lesion detection and analysis. Several classification methods have been compared and a novel hierarchical classification procedure of combined classifiers with linear discriminant analysis (LDA) is proposed as the best solution to classify the mammograms into the four BIRADS tissue classes. The classification scheme is based on 298 texture features. Statistical analysis to test the normality and homoscedasticity of the data was carried out for feature selection. Thus, only features that are influenced by the tissue type were considered. The novel classification techniques have been incorporated into a CADe system to drive the detection algorithms and tested with 1459 images. The results obtained on the 322 screen-film mammograms (SFM) of the mini-MIAS dataset show that 99.75% of samples were correctly classified. On the 1137 full-field digital mammograms (FFDM) dataset results show 91.58% agreement. The results of the lesion detection algorithms were obtained from modules integrated within the CADe system developed by the authors and show that using breast tissue classification prior to lesion detection leads to an improvement of the detection results. The tools enhance the detectability of lesions and they are able to distinguish their local attenuation without local tissue density constraints.

Texture classification using feature selection and kernel-based techniques

The interpretation of the results in a classification problem can be enhanced, specially in image texture analysis problems, by feature selection techniques, knowing which features contribute more to the classification performance. This paper presents an evaluation of a number of feature selection techniques for classification in a biomedical image texture dataset (2-DE gel images), with the aim of studying their performance and the stability in the selection of the features. We analyse three different techniques: subgroup-based multiple kernel learning (MKL), which can perform a feature selection by down-weighting or eliminating subsets of features which shares similar characteristic, and two different conventional feature selection techniques such as recursive feature elimination (RFE), with different classifiers (naive Bayes, support vector machines, bagged trees, random forest and linear discriminant analysis), and a genetic algorithm-based approach with an SVM as decision function. The different classifiers were compared using a ten times tenfold cross-validation model, and the best technique found is SVM-RFE, with an AUROC score of (