Search results for "Applied Mathematics"
showing 10 items of 4379 documents
IWCFTA2012 Keynote Speech I - Hidden attractors in dynamical systems: From hidden oscillation in Hilbert-Kolmogorov, Aizerman and Kalman problems to …
2012
Summary form only given. In this survey an attempt is made to reflect the current trends in the synthesis of analytical and numerical methods to develop efficient analytical-numerical methods, based on harmonic linearization, applied bifurcation theory and numerical methods, for searching hidden oscillations.
Big Data in metagenomics: Apache Spark vs MPI.
2020
The progress of next-generation sequencing has lead to the availability of massive data sets used by a wide range of applications in biology and medicine. This has sparked significant interest in using modern Big Data technologies to process this large amount of information in distributed memory clusters of commodity hardware. Several approaches based on solutions such as Apache Hadoop or Apache Spark, have been proposed. These solutions allow developers to focus on the problem while the need to deal with low level details, such as data distribution schemes or communication patterns among processing nodes, can be ignored. However, performance and scalability are also of high importance when…
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy
2021
Abstract Background Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic. Results We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy …
A Derivation of the Vlasov-Stokes System for Aerosol Flows from the Kinetic Theory of Binary Gas Mixtures
2016
In this short paper, we formally derive the thin spray equation for a steady Stokes gas, i.e. the equation consists in a coupling between a kinetic (Vlasov type) equation for the dispersed phase and a (steady) Stokes equation for the gas. Our starting point is a system of Boltzmann equations for a binary gas mixture. The derivation follows the procedure already outlined in [Bernard-Desvillettes-Golse-Ricci, arXiv:1608.00422 [math.AP]] where the evolution of the gas is governed by the Navier-Stokes equation.
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti
2013
Abstract Background Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstructed models may contain inconsistencies that appear as gap metabolites and blocked reactions. Although automatic methods for solving this problem have been previously developed, there are many situations where manual curation is still needed. Results We introduce a general definition of gap metabolite that allows its detection in a straightforward manner. Moreover, a method for the detection of Unconnected Modules, defined as isolated sets of blocked reactions connect…
A Coclustering Approach for Mining Large Protein-Protein Interaction Networks
2012
Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonove…
A motif-independent metric for DNA sequence specificity
2011
Abstract Background Genome-wide mapping of protein-DNA interactions has been widely used to investigate biological functions of the genome. An important question is to what extent such interactions are regulated at the DNA sequence level. However, current investigation is hampered by the lack of computational methods for systematic evaluating sequence specificity. Results We present a simple, unbiased quantitative measure for DNA sequence specificity called the Motif Independent Measure (MIM). By analyzing both simulated and real experimental data, we found that the MIM measure can be used to detect sequence specificity independent of presence of transcription factor (TF) binding motifs. We…
Mutual nonlinear prediction of cardiovascular variability series: Comparison between exogenous and autoregressive exogenous models
2007
A model-based approach to perform mutual nonlinear prediction of short cardiovascular variability series is presented. The approach is based on identifying exogenous (X) and autoregressive exogenous (ARX) models by K-nearest neighbors local linear approximation, and estimates the predictability of a series given the other as the squared correlation between original and predicted values of the series. The method was first tested on simulations reproducing different types of interaction between non-identical Henon maps, and then applied to heart rate (HR) and blood pressure (BP) variability series measured in healthy subjects at rest and after head-up tilt. Simulations showed that different c…
Power-Laws hereditariness of biomimetic ceramics for cranioplasty neurosurgery
2019
Abstract We discuss the hereditary behavior of hydroxyapatite-based composites used for cranioplasty surgery in the context of material isotropy. We classify mixtures of collagen and hydroxiapatite composites as biomimetic ceramic composites with hereditary properties modeled by fractional-order calculus. We assume isotropy of the biomimetic ceramic is assumed and provide thermodynamic of restrictions for the material parameters. We exploit the proposed formulation of the fractional-order isotropic hereditariness further by means of a novel mechanical hierarchy corresponding exactly to the three-dimensional fractional-order constitutive model introduced.
A biproportional filter to compare technical and allocation coefficient variations
1997
International audience; In input-output analysis there are two alternate possibilities between Leontief's mechanism (fixed technical coefficients) and Ghosh's mechanism (fixed allocation coefficients). Testing the long term consistency of these mechanisms entails comparing input-output matrices over time. This paper challenges the value of proportional filters (separate comparison of column and row coefficients) and introduces the biproportional filter which allows simultaneous comparison of column and rows. An application is proposed using French input-output tables for 1980 and 1993. The stability of column coefficients cannot be taken for granted and generally, for any sector, both rows …