César Germán Castellanos-Domínguez

Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins

BackgroundProteins are the key elements on the path from genetic information to the development of life. The roles played by the different proteins are difficult to uncover experimentally as this process involves complex procedures such as genetic modifications, injection of fluorescent proteins, gene knock-out methods and others. The knowledge learned from each protein is usually annotated in databases through different methods such as the proposed by The Gene Ontology (GO) consortium. Different methods have been proposed in order to predict GO terms from primary structure information, but very few are available for large-scale functional annotation of plants, and reported success rates are much less than the reported by other non-plant predictors. This paper explores the predictability of GO annotations on proteins belonging to the Embryophyta group from a set of features extracted solely from their primary amino acid sequence.ResultsHigh predictability of several GO terms was found for Molecular Function and Cellular Component. As expected, a lower degree of predictability was found on Biological Process ontology annotations, although a few biological processes were easily predicted. Proteins related to transport and transcription were particularly well predicted from primary structure information. The most discriminant features for prediction were those related to electric charges of the amino-acid sequence and hydropathicity derived features.ConclusionsAn analysis of GO-slim terms predictability in plants was carried out, in order to determine single categories or groups of functions that are most related with primary structure information. For each highly predictable GO term, the responsible features of such successfulness were identified and discussed. In addition to most published studies, focused on few categories or single ontologies, results in this paper comprise a complete landscape of GO predictability from primary structure encompassing 75 GO terms at molecular, cellular and phenotypical level. Thus, it provides a valuable guide for researchers interested on further advances in protein function prediction on Embryophyta plants.

Comparison of the nearest feature classifiers for face recognition

This paper presents an experimental comparison of the nearest feature classifiers, using an approach based on binomial tests in order to evaluate their strengths and weaknesses. In addition, classification accuracies and the accuracy-dimensionality tradeoff have been considered as comparison criteria. We extend two of the nearest feature classifiers to label the query point by a majority vote of the samples. Comparisons were carried out for face recognition using ORL database. We apply the eigenface representation for feature extraction. Experimental results showed that even though the classification accuracy of k-NFP outperforms k-NFL in some dimensions, these rate differences do not have statistical significance.

Identification and monitoring of brain activity based on stochastic relevance analysis of short–time EEG rhythms

BackgroundThe extraction of physiological rhythms from electroencephalography (EEG) data and their automated analyses are extensively studied in clinical monitoring, to find traces of interictal/ictal states of epilepsy.MethodsBecause brain wave rhythms in normal and interictal/ictal events, differently influence neuronal activity, our proposed methodology measures the contribution of each rhythm. These contributions are measured in terms of their stochastic variability and are extracted from a Short Time Fourier Transform to highlight the non–stationary behavior of the EEG data. Then, we performed a variability–based relevance analysis by handling the multivariate short–time rhythm representation within a subspace framework. This maximizes the usability of the input information and preserves only the data that contribute to the brain activity classification. For neural activity monitoring, we also developed a new relevance rhythm diagram that qualitatively evaluates the rhythm variability throughout long time periods in order to distinguish events with different neuronal activities.ResultsEvaluations were carried out over two EEG datasets, one of which was recorded in a noise–filled environment. The method was evaluated for three different classification problems, each of which addressed a different interpretation of a medical problem. We perform a blinded study of 40 patients using the support–vector machine classifier cross–validation scheme. The obtained results show that the developed relevance analysis was capable of accurately differentiating normal, ictal and interictal activities.ConclusionsThe proposed approach provides the reliable identification of traces of interictal/ictal states of epilepsy. The introduced relevance rhythm diagrams of physiological rhythms provides effective means of monitoring epileptic seizures; additionally, these diagrams are easily implemented and provide simple clinical interpretation. The developed variability–based relevance analysis can be translated to other monitoring applications involving time–variant biomedical data.

Motor Imagery Classification for BCI Using Common Spatial Patterns and Feature Relevance Analysis

Recently, there have been many efforts to develop Brain Computer Interface (BCI) systems, allowing to identify and discriminate brain activity. In this work, a Motor Imagery (MI) discrimination framework is proposed, which employs Common Spatial Patterns (CSP) as preprocessing stage, and a feature relevance analysis approach based on an eigendecomposition method to identify the main features that allow to discriminate the studied EEG signals. The CSP is employed to reveal the dynamics of interest from EEG signals, and then we select a set of features representing the best as possible the studied process. EEG signals modeling is done by feature estimation of three frequency-based and one time-based. Besides, a relevance analysis over the EEG channels is performed, which gives to the user an idea about the channels that mainly contribute for the MI discrimination. Our approach is tested over a well known MI dataset. Attained results (95.21±4.21 [%] mean accuracy) show that presented framework can be used as a tool to support the discrimination of MI brain activity.

Managing Imbalanced Data Sets in Multi-label Problems: A Case Study with the SMOTE Algorithm

Multi-label learning has been becoming an increasingly active area into the machine learning community since a wide variety of real world problems are naturally multi-labeled. However, it is not uncommon to find disparities among the number of samples of each class, which constitutes an additional challenge for the learning algorithm. Smote is an oversampling technique that has been successfully applied for balancing single-labeled data sets, but has not been used in multi-label frameworks so far. In this work, several strategies are proposed and compared in order to generate synthetic samples for balancing data sets in the training of multi-label algorithms. Results show that a correct selection of seed samples for oversampling improves the classification performance of multi-label algorithms. The uniform generation oversampling, provides an efficient methodology for a wide scope of real world problems.

New Cues in Low-Frequency of Speech for Automatic Detection of Parkinson's Disease

In this paper, the analysis of low-frequency zone of the speech signals from the five Spanish vowels, by means of the Teager energy operator (TEO) and the modified group delay functions (MGDF) is proposed for the automatic detection of Parkinson’s disease.

Predictability of protein subcellular locations by pattern recognition techniques

An analysis of the predictability of subcellular locations is performed by using simple pattern recognition techniques in an attempt to capture the real dimensions of the problem at hand. Results show that there are some particular locations that does not need of high complexity classification models to be predicted with high accuracies, and some partial biological explanations are formulated. All the experiments were carried out over a set of Arabidopsis Thaliana proteins and classes were defined according to the plants GO slim.

Video Segmentation Framework by Dynamic Background Modelling

Detecting moving objects in video streams is the first relevant step of information extraction in many computer vision applications, e.g. video surveillance systems. In this work, a video segmentation framework by dynamic background modelling is presented. Our approach aims to update suitably the background model of a scene that is recorded by a static camera. For such purpose, we develop an optical flow based methodology to suitable track moving objects, which can stop or change smoothly their movement along the video. Moreover, a light variations identification stage, is employed to avoid possible confusions between illumination changes and objects in movement. Regarding this, our approach is able to ensure a suitable background modelling in real world scenarios. Attained results show that our framework outperforms, in well-known datasets, state of the art methodologies.

Multiple manifold learning by nonlinear dimensionality reduction

Methods for nonlinear dimensionality reduction have been widely used for different purposes, but they are constrained to single manifold datasets. Considering that in real world applications, like video and image analysis, datasets with multiple manifolds are common, we propose a framework to find a low-dimensional embedding for data lying on multiple manifolds. Our approach is inspired on the manifold learning algorithm Laplacian Eigenmaps - LEM, computing the relationships among samples of different datasets based on an intra manifold comparison to unfold properly the data underlying structure. According to the results, our approach shows meaningful embeddings that outperform the results obtained by the conventional LEM algorithm and a previous close related work that analyzes multiple manifolds.

Generalizing dissimilarity representations using feature lines

A crucial issue in dissimilarity-based classification is the choice of the representation set. In the small sample case, classifiers capable of a good generalization and the injection or addition of extra information allow to overcome the representational limitations. In this paper, we present a new approach for enriching dissimilarity representations. It is based on the concept of feature lines and consists in deriving a generalized version of the original dissimilarity representation by using feature lines as prototypes. We use a linear normal density-based classifier and the nearest neighbor rule, as well as two different methods for selecting prototypes: random choice and a length-based selection of the feature lines. An important observation is that just a few long feature lines are needed to obtain a significant improvement in performance over the other representation sets and classifiers. In general, the experiments show that this alternative representation is especially profitable for some correlated datasets.