A heavy-tailed empirical Bayes method for replicated microarray data

DNA microarray has been recognized as being an important tool for studying the expression of thousands of genes simultaneously. These experiments allow us to compare two different samples of cDNA obtained under different conditions. A novel method for the analysis of replicated microarray experiments based upon the modelling of gene expression distribution as a mixture of α-stable distributions is presented. Some features of the distribution of gene expression, such as Pareto tails and the fact that the variance of any given array increases concomitantly with an increase in the number of genes studied, suggest the possibility of modelling gene expression distribution on the basis of α-stable density. The proposed methodology uses very well known properties of α-stable distribution, such as the scale mixture of normals. A Bayesian log-posterior odds is calculated, which allows us to decide whether a gene is expressed differentially or not. The proposed methodology is illustrated using simulated and experimental data and the results are compared with other existing statistical approaches. The proposed heavy-tail model improves the performance of other distributions and is easily applicable to microarray gene data, specially if the dataset contains outliers or presents high variance between replicates.     

Apparent mass matrix of standing subjects exposed to multi-axial whole-body vibration

This paper describes the experimental characterisation of the apparent mass matrix of eight male subjects in standing position and the identification of nonlinearities under both mono-axial and dual-axis whole-body vibration. The nonlinear behaviour of the response was studied using the conditioned response techniques considering models of increasing complexity. Results showed that the cross-axis terms are comparable to the diagonal terms. The contribution of the nonlinear effects are minor and can be endorsed to the change of modal parameters during the tests. The nonlinearity generated by the vibration magnitude is more evident in the subject response, since magnitude-dependent effects in the population are overlaid by the scatter in the subjects’ biometric data. The biodynamic response is influenced by the addition of a secondary vibration axis and, in case of dual-axis vibrations, the overall magnitude has a marginal contribution.

Practitioner Summary: We have measured both the diagonal and cross-axis elements of the apparent mass matrix. The effect of nonlinearities and the simultaneous presence of vibration along two axes are smaller than the inter-subject variability.     

Towards a set of agrosystem-specific cropland mapping methods to address the global cropland diversity

Accurate cropland information is of paramount importance for crop monitoring. This study compares five existing cropland mapping methodologies over five contrasting Joint Experiment for Crop Assessment and Monitoring (JECAM) sites of medium to large average field size using the time series of 7-day 250 m Moderate Resolution Imaging Spectroradiometer (MODIS) mean composites (red and near-infrared channels). Different strategies were devised to assess the accuracy of the classification methods: confusion matrices and derived accuracy indicators with and without equalizing class proportions, assessing the pairwise difference error rates and accounting for the spatial resolution bias. The robustness of the accuracy with respect to a reduction of the quantity of calibration data available was also assessed by a bootstrap approach in which the amount of training data was systematically reduced. Methods reached overall accuracies ranging from 85% to 95%, which demonstrates the ability of 250 m imagery to resolve fields down to 20 ha. Despite significantly different error rates, the site effect was found to persistently dominate the method effect. This was confirmed even after removing the share of the classification due to the spatial resolution of the satellite data (from 10% to 30%). This underlines the effect of other agrosystems characteristics such as cloudiness, crop diversity, and calendar on the ability to perform accurately. All methods have potential for large area cropland mapping as they provided accurate results with 20% of the calibration data, e.g. 2% of the study area in Ukraine. To better address the global cropland diversity, results advocate movement towards a set of cropland classification methods that could be applied regionally according to their respective performance in specific landscapes.     

Convolutional Sparse Coding for High Dynamic Range Imaging

Current HDR acquisition techniques are based on either (i) fusing multibracketed, low dynamic range (LDR) images, (ii) modifying existing hardware and capturing different exposures simultaneously with multiple sensors, or (iii) reconstructing a single image with spatially‐varying pixel exposures. In this paper, we propose a novel algorithm to recover high‐quality HDRI images from a single, coded exposure. The proposed reconstruction method builds on recently‐introduced ideas of convolutional sparse coding (CSC); this paper demonstrates how to make CSC practical for HDR imaging. We demonstrate that the proposed algorithm achieves higher‐quality reconstructions than alternative methods, we evaluate optical coding schemes, analyze algorithmic parameters, and build a prototype coded HDR camera that demonstrates the utility of convolutional sparse HDRI coding with a custom hardware platform.     

Applications of ontologies in requirements engineering: a systematic review of the literature

There is an increase use of ontology-driven approaches to support requirements engineering (RE) activities, such as elicitation, analysis, specification, validation and management of requirements. However, the RE community still lacks a comprehensive understanding of how ontologies are used in RE process. Thus, the main objective of this work is to investigate and better understand how ontologies support RE as well as identify to what extent they have been applied to this field. In order to meet our goal, we conducted a systematic literature review (SLR) to identify the primary studies on the use of ontologies in RE, following a predefined review protocol. We then identified the main RE phases addressed, the requirements modelling styles that have been used in conjunction with ontologies, the types of requirements that have been supported by the use of ontologies and the ontology languages that have been adopted. We also examined the types of contributions reported and looked for evidences of the benefits of ontology-driven RE. In summary, the main findings of this work are: (1) there are empirical evidences of the benefits of using ontologies in RE activities both in industry and academy, specially for reducing ambiguity, inconsistency and incompleteness of requirements; (2) the majority of studies only partially address the RE process; (3) there is a great diversity of RE modelling styles supported by ontologies; (4) most studies addressed only functional requirements; (5) several studies describe the use/development of tools to support different types of ontology-driven RE approaches; (6) about half of the studies followed W3C recommendations on ontology-related languages; and (7) a great variety of RE ontologies were identified; nevertheless, none of them has been broadly adopted by the community. Finally, we conclude this work by showing several promising research opportunities that are quite important and interesting but underexplored in current research and practice.     

Hand gesture recognition from depth and infrared Kinect data for CAVE applications interaction

This paper presents a real-time framework that combines depth data and infrared laser speckle pattern (ILSP) images, captured from a Kinect device, for static hand gesture recognition to interact with CAVE applications. At the startup of the system, background removal and hand position detection are performed using only the depth map. After that, tracking is started using the hand positions of the previous frames in order to seek for the hand centroid of the current one. The obtained point is used as a seed for a region growing algorithm to perform hand segmentation in the depth map. The result is a mask that will be used for hand segmentation in the ILSP frame sequence. Next, we apply motion restrictions for gesture spotting in order to mark each image as a ‘Gesture’ or ‘Non-Gesture’. The ILSP counterparts of the frames labeled as “Gesture” are enhanced by using mask subtraction, contrast stretching, median filter, and histogram equalization. The result is used as the input for the feature extraction using a scale invariant feature transform algorithm (SIFT), bag-of-visual-words construction and classification through a multi-class support vector machine (SVM) classifier. Finally, we build a grammar based on the hand gesture classes to convert the classification results in control commands for the CAVE application. The performed tests and comparisons show that the implemented plugin is an efficient solution. We achieve state-of-the-art recognition accuracy as well as efficient object manipulation in a virtual scene visualized in the CAVE.     

Time-relevant stability of 2D systems

For many 2D systems, one of the independent variables plays a distinct role in the evolution of the trajectories; since often this special independent variable is time, we call such systems ‘time-relevant’. In this paper, we introduce a stability notion for time-relevant systems described by higher-order difference equations. We give algebraic tests in terms of the location of the zeros of the determinant of a polynomial matrix describing the system. We also give an LMI characterization of time-relevant stability involving only constant matrices.