Search results for "computational"
showing 10 items of 5884 documents
Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics.
2020
5 páginas, 2 figuras. AVAILABILITY AND IMPLEMENTATION: The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online: http://dx.doi.org/10.1093/bioinformatics/btz729
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures
2020
Abstract Motivation Mash is a popular hash-based genome analysis toolkit with applications to important downstream analyses tasks such as clustering and assembly. However, Mash is currently not able to fully exploit the capabilities of modern multi-core architectures, which in turn leads to high runtimes for large-scale genomic datasets. Results We present RabbitMash, an efficient highly optimized implementation of Mash which can take full advantage of modern hardware including multi-threading, vectorization and fast I/O. We show that our approach achieves speedups of at least 1.3, 9.8, 8.5 and 4.4 compared to Mash for the operations sketch, dist, triangle and screen, respectively. Furtherm…
Robust Mean Field Games
2015
Recently there has been renewed interest in large-scale games in several research disciplines, with diverse application domains as in the smart grid, cloud computing, financial markets, biochemical reaction networks, transportation science, and molecular biology. Prior works have provided rich mathematical foundations and equilibrium concepts but relatively little in terms of robustness in the presence of uncertainties. In this paper, we study mean field games with uncertainty in both states and payoffs. We consider a population of players with individual states driven by a standard Brownian motion and a disturbance term. The contribution is threefold: First, we establish a mean field syste…
The role of information in a two-traders market
2014
In a very simple stock market, made by only two \emph{initially equivalent} traders, we discuss how the information can affect the performance of the traders. More in detail, we first consider how the portfolios of the traders evolve in time when the market is \emph{closed}. After that, we discuss two models in which an interaction with the outer world is allowed. We show that, in this case, the two traders behave differently, depending on \textbf{i)} the amount of information which they receive from outside; and \textbf{ii)}the quality of this information.
Efficient change point detection in genomic sequences of continuous measurements
2010
Abstract Motivation: Knowing the exact locations of multiple change points in genomic sequences serves several biological needs, for instance when data represent aCGH profiles and it is of interest to identify possibly damaged genes involved in cancer and other diseases. Only a few of the currently available methods deal explicitly with estimation of the number and location of change points, and moreover these methods may be somewhat vulnerable to deviations of model assumptions usually employed. Results: We present a computationally efficient method to obtain estimates of the number and location of the change points. The method is based on a simple transformation of data and it provides re…
Discriminative pattern discovery for the characterization of different network populations
2023
Abstract Motivation An interesting problem is to study how gene co-expression varies in two different populations, associated with healthy and unhealthy individuals, respectively. To this aim, two important aspects should be taken into account: (i) in some cases, pairs/groups of genes show collaborative attitudes, emerging in the study of disorders and diseases; (ii) information coming from each single individual may be crucial to capture specific details, at the basis of complex cellular mechanisms; therefore, it is important avoiding to miss potentially powerful information, associated with the single samples. Results Here, a novel approach is proposed, such that two different input popul…
Steady-state and tracking analysis of a robust adaptive filter with low computational cost
2007
This paper analyses a new adaptive algorithm that is robust to impulse noise and has a low computational load [E. Soria, J.D. Martin, A.J. Serrano, J. Calpe, and J. Chambers, A new robust adaptive algorithm with low computacional cost, Electron. Lett. 42 (1) (2006) 60-62]. The algorithm is based on two premises: the use of the cost function often used in independent component analysis and a fuzzy modelling of the hyperbolic tangent function. The steady-state error and tracking capability of the algorithm are analysed using conservation methods [A. Sayed, Fundamentals of Adaptive Filtering, Wiley, New York, 2003], thus verifying the correspondence between theory and experimental results.
CFD Assisted Steady-State Modelling of Restrictive Counterbalance Valves
2020
The counterbalance valve is an important component in many hydraulic applications and its behaviour hugely impacts system stability and performance. Despite that, CBVs are rarely modelled accurately due to the effort required to obtain basic model parameters and the complexity involved in identifying expressions for flow forces and friction. This paper presents a CFD assisted approach to steady-state modelling of CBVs. It is applied to a 3-port restrictive commercially available counterbalance valve. The model obtained is based on detailed measurements of the valve geometry, a single data set and CFD modelling and includes flow forces and friction. The CFD assisted model is compared to expe…
Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.
2017
Oxidation of nucleic acids is ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases; however, the specific role of the biological environment remains relatively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations. It is shown…