BACKGROUND: In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. RESULTS: Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. CONCLUSIONS: The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.

The microarray data classification is an open and active research field. The development of more accurate algorithms is of great interest and many of the developed techniques can be straightforwardly applied in analyzing different kinds of omics data. In this work, an ensemble learning algorithm is applied within a classification framework that already got good predictive results. Ensemble techniques take individual experts, (i.e. classifiers), to combine them to improve the individual expert results with a voting scheme. In this case, a thinning algorithm is proposed which starts by using all the available experts and removes them one by one focusing on improving the ensemble vote. Two versions of a state of the art ensemble thinning algorithm have been tested and three key elements have been introduced to work with microarray data: the ensemble cohort definition, the nonexpert notion, which defines a set of excluded expert from the thinning process, and a rule to break ties in the thinning process. Experiments have been done on seven public datasets from the Microarray Quality Control study, MAQC. The proposed key elements have shown to be useful for the prediction performance and the studied ensemble technique shown to improve the state of the art results by producing classifiers with better predictions.

Microarray data classification is a challenging problem due to the high number of variables compared to the small number of available samples. An effective methodology to output a precise and reliable classifier is proposed in this work as an improvement of the algorithm in [1]. It considers the sample scarcity problem and the lack of data structure typical of microarrays. Both problem are assessed by a two-step approach applying hierarchical clustering to create new features called metagenes and introducing a novel feature ranking criterion, inside the wrapper feature selection task. The classification ability has been evaluated on 4 publicly available datasets from Micro Array Quality Control study phase II (MAQC) classified by 7 different endpoints. The global results have showed how the proposed approach obtains better prediction accuracy than a wide variety of state of the art alternatives.

This paper deals with a class of morphological operators called connected operators. These operators filter the signal by merging its flat zones. As a result, they do not create any new contours and are very attractive for filtering tasks where the contour information has to be preserved. This paper shows that connected operators work implicitly on a structured representation of the image made of flat zones. The max-tree is proposed as a suitable and efficient structure to deal with the processing steps involved in antiextensive connected operators. A formal definition of the various processing steps involved in the operator is proposed and, as a result, several lines of generalization are developed. First, the notion of connectivity and its definition are analyzed. Several modifications of the traditional approach are presented. They lead to connected operators that are able to deal with texture. They also allow the definition of connected operators with less leakage than the classical ones. Second, a set of simplification criteria are proposed and discussed. They lead to simplicity-, entropy-, and motion-oriented operators. The problem of using a nonincreasing criterion is analyzed. Its solution is formulated as an optimization problem that can be very efficiently solved by a Viterbi algorithm. Finally, several implementation issues are discussed showing that these operators can be very efficiently implemented.

Connected operators are increasingly used in image processing due to their properties of simplifying the image with various criteria, without loosing contour's information. These properties are related to the connected operator approach that either preserves or completely eliminates a determined connected component, according to an established criterion of analysis. In this paper we will define a new connected operator for stereo images. The goal is to simplify one of the images (left) in the sense that the operator will eliminate the image components that are not present at a determined location in the other image (right). This filter let us select in a stereo image, objects as a function of their distance from the observer (for instance used in auto guided vehicles).