Search results for " Mapping"
showing 10 items of 1411 documents
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
2015
This is a post-peer-review, pre-copyedit version of an article published in IEEE - ACM Transactions on Computational Biology and Bioinformatics. The final authenticated version is available online at: http://dx.doi.org/10.1109/TCBB.2015.2389958 [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. Computational methods to detect epistasis therefore suffer from prohibitively lon…
Executable Data Quality Models
2017
The paper discusses an external solution for data quality management in information systems. In contradiction to traditional data quality assurance methods, the proposed approach provides the usage of a domain specific language (DSL) for description data quality models. Data quality models consists of graphical diagrams, which elements contain requirements for data object's values and procedures for data object's analysis. The DSL interpreter makes the data quality model executable therefore ensuring measurement and improving of data quality. The described approach can be applied: (1) to check the completeness, accuracy and consistency of accumulated data; (2) to support data migration in c…
A Comparison of Advanced Regression Algorithms for Quantifying Urban Land Cover
2014
Quantitative methods for mapping sub-pixel land cover fractions are gaining increasing attention, particularly with regard to upcoming hyperspectral satellite missions. We evaluated five advanced regression algorithms combined with synthetically mixed training data for quantifying urban land cover from HyMap data at 3.6 and 9 m spatial resolution. Methods included support vector regression (SVR), kernel ridge regression (KRR), artificial neural networks (NN), random forest regression (RFR) and partial least squares regression (PLSR). Our experiments demonstrate that both kernel methods SVR and KRR yield high accuracies for mapping complex urban surface types, i.e., rooftops, pavements, gras…
Measuring the agreement between brain connectivity networks.
2016
Investigating the level of similarity between two brain networks, resulting from measures of effective connectivity in the brain, can be of interest from many respects. In this study, we propose and test the idea to borrow measures of association used in machine learning to provide a measure of similarity between the structure of (un-weighted) brain connectivity networks. The measures here explored are the accuracy, Cohen's Kappa (K) and Area Under Curve (AUC). We implemented two simulation studies, reproducing two contexts of application that can be particularly interesting for practical applications, namely: i) in methodological studies, performed on surrogate data, aiming at comparing th…
Dynamic 3D Scene Reconstruction and Enhancement
2017
International audience; In this paper, we present a 3D reconstruction and enhancement approach for high quality dynamic city scene reconstructions. We first detect and segment the moving objects using 3D Motion Segmenta-tion approach by exploiting the feature trajectories' behaviours. Getting the segmentations of both the dynamic scene parts and the static scene parts, we propose an efficient point cloud registration approach which takes the advantages of 3-point RANSAC and Iterative Closest Points algorithms to produce precise point cloud alignment. Furthermore, we proposed a point cloud smoothing and texture mapping framework to enhance the results of reconstructions for both the static a…
Reliability of Virtual Screening Methods in Prediction of PDE4Binhibitor Activity
2015
Identification of active ligands using computational methods is a challenging task. For example, molecular docking, pharmacophore modeling, and three dimensional quantitative structure-activity relationship models (3D-QSAR) are widely used methods to identify novel small molecules. However, all these methods have, in addition to advantages, also significant pitfalls. The aim of this study was to compare some commonly used computational methods to estimate their ability to separate highly active PDE4B-inhibitors from less active and inactive ones. Here, 152 molecules with pIC 50 -range of 3.4-10.5, originating from six original studies were used. High correlation coefficients by using dockin…
Atrial activity extraction for atrial fibrillation analysis using blind source separation.
2004
This contribution addresses the extraction of atrial activity (AA) from real electrocardiogram (ECG) recordings of atrial fibrillation (AF). We show the appropriateness of independent component analysis (ICA) to tackle this biomedical challenge when regarded as a blind source separation (BSS) problem. ICA is a statistical tool able to reconstruct the unobservable independent sources of bioelectric activity which generate, through instantaneous linear mixing, a measurable set of signals. The three key hypothesis that make ICA applicable in the present scenario are discussed and validated: 1) AA and ventricular activity (VA) are generated by sources of independent bioelectric activity; 2) AA …
Automatic Image Annotation Using Random Projection in a Conceptual Space Induced from Data
2018
The main drawback of a detailed representation of visual content, whatever is its origin, is that significant features are very high dimensional. To keep the problem tractable while preserving the semantic content, a dimen- sionality reduction of the data is needed. We propose the Random Projection techniques to reduce the dimensionality. Even though this technique is sub-optimal with respect to Singular Value Decomposition its much lower computational cost make it more suitable for this problem and in par- ticular when computational resources are limited such as in mobile terminals. In this paper we present the use of a "conceptual" space, automatically induced from data, to perform automa…
An Unsupervised Method for Suspicious Regions Detection in Mammogram Images
2015
Over the past years many researchers proposed biomedical imaging methods for computer-aided detection and classification of suspicious regions in mammograms. Mammogram interpretation is performed by radiologists by visual inspection. The large volume of mammograms to be analyzed makes such readings labour intensive and often inaccurate. For this purpose, in this paper we propose a new unsupervised method to automatically detect suspicious regions in mammogram images. The method consists mainly of two steps: preprocessing; feature extraction and selection. Preprocessing steps allow to separate background region from the breast profile region. In greater detail, gray levels mapping transform …
MIPPIE: the mouse integrated protein–protein interaction reference
2020
Abstract Cells operate and react to environmental signals thanks to a complex network of protein–protein interactions (PPIs), the malfunction of which can severely disrupt cellular homeostasis. As a result, mapping and analyzing protein networks are key to advancing our understanding of biological processes and diseases. An invaluable part of these endeavors has been the house mouse (Mus musculus), the mammalian model organism par excellence, which has provided insights into human biology and disorders. The importance of investigating PPI networks in the context of mouse prompted us to develop the Mouse Integrated Protein–Protein Interaction rEference (MIPPIE). MIPPIE inherits a robust infr…