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Identifying gene-specific variations in biomedical text

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Journal of Bioinformatics and Computational Biology 2007年第6期5卷 1277-1296页

作者： Klinger, Roman Friedrich, Christoph M. Mevissen, Heinz Theodor Fluck, Juliane Hofmann-apitius, Martin Furlong, Laura I. Sanz, Ferran Department of Bioinformatics Fraunhofer Institute for Algorithms and Scientific Computing 53754 Sankt Augustin Schloss Birlinghoven Germany Research Unit on Biomedical Informatics (GRIB) IMIM UPF PRBB E-08003 Barcelona c/ Dr. Aiguader 88 Spain

The influence of genetic variations on diseases or cellular processes is the main focus of many investigations, and results of biomedical studies are often only accessible through scientific publications. Automatic extraction of this information requires recognition of the gene names and the accompanying allelic variant information. In a previous work, the OSIRIS system for the detection of allelic variation in text based on a query expansion approach was communicated. Challenges associated with this system are the relatively low recall for variation mentions and gene name recognition. To tackle this challenge, we integrate the ProMiner system developed for the recognition and normalization of gene and protein names with a conditional random field (CRF)-based recognition of variation terms in biomedical text. Following the newly developed normalization of variation entities, we can link textual entities to Single Nucleotide Polymorphism database (dbSNP) entries. The performance of this novel approach is evaluated, and improved results in comparison to state-of-the-art systems are reported. © 2007 Imperial College Press.

关键词： Conditional random field Named entity recognition Normalization Single nucleotide polymorphism SNP Variants

Grid Added Value to Address Malaria 06

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Grid Added Value to Address Malaria

Proceedings of the Sixth IEEE International Symposium on Cluster computing and the Grid

作者： V. Breton N. Jacq M. Hofmann Université Blaise Pascal/IN2P3 France Communication & Systèmes CS-SI France Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Germany

ISBN: (纸本)9780769525853

Through this paper, we call for a distributed, internet-based collaboration to address one of the worst plagues of our present world, malaria. The spirit is a non-proprietary peer-production of informationembedding goods. And we propose to use the grid technology to enable such a world wide "open source" like collaboration. The first step towards this vision has been achieved during the summer on the EGEE grid infrastructure where 46 million ligands were docked for a total amount of 80 CPU years in 6 weeks in the quest for new drugs.

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RDM-stars and galactic rotation curves

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arXiv 2019年

作者： Nikitin, Igor Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 Germany

The recently formulated model of black holes coupled to the radial flows of dark matter (RDM-stars) is considered and the shape of the galactic rotation curves predicted by the model is evaluated. Under the assumption that the density of black holes is proportional to the density of luminous matter, the model perfectly fits the experimental data, both for the universal rotation curve, describing the spiral galaxies of a general form, and for the grand rotation curve, describing the orbital velocities of Milky Way galaxy in a wide range of distances. The modeling of the galactic gravitational field at large distances from the center and out of the galactic plane is also discussed. Copyright © 2019, The Authors. All rights reserved.

关键词： Stars

Galactic model with a phase transition from dark matter to dark energy

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arXiv 2021年

作者： Nikitin, Igor Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 Germany

This work continues the construction of a recently proposed model of dark matter stars. In this model, dark matter quanta are sterile massless particles that are emitted from the central regions of the galaxy in the radial direction. As a result, at large distances r from the center of the galaxy, the mass density of dark matter has the form ρ ∼ r−2, in contrast to the homogeneous model ρ = Const. In the cosmological context, the homogeneous model with massless particles corresponds to the radiation epoch of the expansion of the universe, while the proposed inhomogeneous model turns out to be equivalent to ΛCDM. In this paper, scenarios will be considered in which the radial emission of dark matter is brought into hydrostatic equilibrium with a uniform background. It is shown that solutions exist if the uniform background has an equation of state typical for dark energy. Thus, this model describes a phase transition from dark matter inside the galaxy to dark energy outside of it. The specific mechanism for such a transition could be Bose-Einstein condensation. In addition, the question of what happens if dark matter particles are not sterile, for example, are photons of the Standard Model, is considered. © 2021, CC BY.

关键词： Galaxies

Coupling fluids and structures codes on MPI

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Coupling fluids and structures codes on MPI

Proceedings of the MPI Developer's Conference

作者： K. Wolf E. Brakkee GMD-German National Research Center for Computer Science SCAI-Institute for Algorithms and Scientific Computing Sankt Augustin Germany

In the last few years lots of industrial simulation applications were ported onto parallel systems to gain more computational power. Besides other parallelisation techniques message-passing seems to be the most powerful and accepted one. Since MPI is the upcoming standard definition for message-passing libraries, portability and adaptation among different hardware- and software-environments becomes more and more realistic. However some problems are still unsolved, if two or more independent parallel MPI-applications are coupled and work together. This article shows some of the problems which might arise in coupling independent parallel codes: e.g. management of separate address spaces, definition of dedicated neighborhoods, integration of dynamic process sets and synchronisation events.

关键词： Application software Software libraries Computer industry Computational modeling Automotive engineering Concurrent computing Vehicle dynamics Visualization Computer science scientific computing

Stability of white holes revisited

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arXiv 2018年

作者： Nikitin, Igor Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 Germany

It is shown that the models of white hole interacting with external matter can be made stable by introduction of a negative central mass. Similar results are obtained for the models of white hole, interacting with null shells, with radial flows of matter and with photon gas. In realistic models, a naked timelike singularity corresponding to the negative mass is hidden under a coat of positive mass, providing an extremely strong redshift for photons born in the Planck neighborhood of the singularity and observed at infinity, thereby realizing the principle of cosmic censorship in a relaxed form. Copyright © 2018, The Authors. All rights reserved.

关键词： Stars

Wormholes and Teleporters

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arXiv 2021年

作者： Nikitin, Igor Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 Germany

In general relativity, there is a class of solutions that currently do not have observed analogues, but on which the theory is shaped, giving an understanding what is fundamentally possible within its framework. Such solutions include wormholes, tunnels that connect distant regions in spacetime. Although not a single wormhole has yet been discovered, there is a large number of works devoted to their study, thanks to which wormholes as a class of solutions become firmly established in modern science. In this paper, we consider two topologically nontrivial types of solutions related to wormholes. First: Wormholes that can open and close. In this relation, we will discuss topological censorship theorems, which under certain conditions prohibit changing topology. We will also discuss known ways to circumvent these theorems. Using analytical and numerical methods, as well as visualization, we will construct an example of an opening and closing wormhole with the dimensions of the central black hole in the Milky Way galaxy. Our construction continues the work by Kardashev, Novikov and Shatskiy, in which a static wormhole with the same parameters was considered. The second type is a modification of Visser's dihedral wormhole solution for a dynamic case, which can be considered as a model of a teleportation event. © 2021, CC BY.

关键词： Topology

A representer theorem for deep kernel learning

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arXiv 2017年

作者： Bohn, Bastian Griebel, Michael Rieger, Christian Institute for Numerical Simulation University of Bonn Wegelerstr. 6 Bonn53115 Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53754 Germany

In this paper we provide a finite-sample and an infinite-sample representer theorem for the concatenation of (linear combinations of) kernel functions of reproducing kernel Hilbert spaces. These results serve as mathematical foundation for the analysis of machine learning algorithms based on compositions of functions. As a direct consequence in the finite-sample case, the corresponding infinite-dimensional minimization problems can be recast into (nonlinear) finite-dimensional minimization problems, which can be tackled with nonlinear optimization algorithms. Moreover, we show how concatenated machine learning problems can be reformulated as neural networks and how our representer theorem applies to a broad class of state-of-the-art deep learning methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Sampling

A Dimension-adaptive Combination Technique for Uncertainty Quantification

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arXiv 2022年

作者： Seidler, Uta Griebel, Michael Institute for Numerical Simulation University of Bonn Friedrich-Hirzebruch-Allee 7 Bonn53115 Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53754 Germany

We present an adaptive algorithm for the computation of quantities of interest involving the solution of a stochastic elliptic PDE where the diffusion coefficient is parametrized by means of a Karhunen-Loève expansion. The approximation of the equivalent parametric problem requires a restriction of the countably infinite-dimensional parameter space to a finite-dimensional parameter set, a spatial discretization and an approximation in the parametric variables. We consider a sparse grid approach between these approximation directions in order to reduce the computational effort and propose a dimension-adaptive combination technique. In addition, a sparse grid quadrature for the high-dimensional parametric approximation is employed and simultaneously balanced with the spatial and stochastic approximation. Our adaptive algorithm constructs a sparse grid approximation based on the benefit-cost ratio such that the regularity and thus the decay of the Karhunen-Loève coefficients is not required beforehand. The decay is detected and exploited as the algorithm adjusts to the anisotropy in the parametric variables. We include numerical examples for the Darcy problem with a lognormal permeability field, which illustrate a good performance of the algorithm: For sufficiently smooth random fields, we essentially recover the spatial order of convergence as asymptotic convergence rate with respect to the computational *** Codes 65N35, 65C20, 65D30, 65N30, 60H35 © 2022, CC BY.

关键词： Diffusion