Search results for "ComputingMethodologies_PATTERNRECOGNITION"
showing 10 items of 296 documents
X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification
2017
X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!Tandem…
Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource
2021
Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequenc…
Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
2021
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a…
Ant Colony Optimisation-Based Classification Using Two-Dimensional Polygons
2016
The application of Ant Colony Optimization to the field of classification has mostly been limited to hybrid approaches which attempt at boosting the performance of existing classifiers (such as Decision Trees and Support Vector Machines (SVM)) — often through guided feature reductions or parameter optimizations.
2D/3D Object Recognition and Categorization Approaches for Robotic Grasping
2017
International audience; Object categorization and manipulation are critical tasks for a robot to operate in the household environment. In this paper, we propose new methods for visual recognition and categorization. We describe 2D object database and 3D point clouds with 2D/3D local descriptors which we quantify with the k-means clustering algorithm for obtaining the Bag of Words (BOW). Moreover, we develop a new global descriptor called VFH-Color that combines the original version of Viewpoint Feature Histogram (VFH) descriptor with the color quantization histogram, thus adding the appearance information that improves the recognition rate. The acquired 2D and 3D features are used for train…
Predictive Model Markup Language (PMML) Representation of Bayesian Networks: An Application in Manufacturing
2018
International audience; Bayesian networks (BNs) represent a promising approach for the aggregation of multiple uncertainty sources in manufacturing networks and other engineering systems for the purposes of uncertainty quantification, risk analysis, and quality control. A standardized representation for BN models will aid in their communication and exchange across the web. This article presents an extension to the predictive model markup language (PMML) standard for the representation of a BN, which may consist of discrete variables, continuous variables, or their combination. The PMML standard is based on extensible markup language (XML) and used for the representation of analytical models…
George-Veeramani Fuzzy Metrics Revised
2018
In this note, we present an alternative approach to the concept of a fuzzy metric, calling it a revised fuzzy metric. In contrast to the traditional approach to the theory of fuzzy metric spaces which is based on the use of a t-norm, we proceed from a t-conorm in the definition of a revised fuzzy metric. Here, we restrict our study to the case of fuzzy metrics as they are defined by George-Veeramani, however, similar revision can be done also for some other approaches to the concept of a fuzzy metric.
An Artificial Bee Colony Approach for Classification of Remote Sensing Imagery
2018
This paper presents a novel Artificial Bee Colony (ABC) approach for supervised classification of remote sensing images. One proposes to apply an ABC algorithm to optimize the coefficients of the set of polynomial discriminant functions. We have experimented the proposed ABC-based classifier algorithm for a Landsat 7 ETM+ image database, evaluating the influence of the ABC model parameters on the classifier performances. Such ABC model parameters are: numbers of employed/onlooker/scout bees, number of epochs, and polynomial degree. One has compared the best ABC classifier Overall Accuracy (OA) with the performances obtained using a set of benchmark classifiers (NN, NP, RBF, and SVM). The re…
Engineering of a DNA Polymerase for Direct m6A Sequencing
2017
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6A-containing RNA prior to sequencing, since m6A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for…
CellMap visualizes protein-protein interactions and subcellular localization
2018
Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers.