Multicriteria group decision support system "Group Multichoice"

The paper presents a group multicriteria analysis decision support system called Group MultiChoice, designed to support decision makers in solving different multicriteria analysis problems in group manner. Various well-known methods and software systems are discussed. The basic features of the solving modules, the interface modules and the system modules are described

Towards Structural Classification of Proteins based on Contact Map Overlap

A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine estimation of the natural homology relation between proteins. Despite this large involvement of the bioinformatics and computer science community, the performance of known algorithms remains modest. Due to the complexity of the problem, they got stuck on relatively small instances and are not applicable for large scale comparison. This paper offers a clear improvement over past methods in this respect. We present a new integer programming model for CMO and propose an exact B &B algorithm with bounds computed by solving Lagrangian relaxation. The efficiency of the approach is demonstrated on a popular small benchmark (Skolnick set, 40 domains). On this set our algorithm significantly outperforms the best existing exact algorithms, and yet provides lower and upper bounds of better quality. Some hard CMO instances have been solved for the first time and within reasonable time limits. From the values of the running time and the relative gap (relative difference between upper and lower bounds), we obtained the right classification for this test. These encouraging result led us to design a harder benchmark to better assess the classification capability of our approach. We constructed a large scale set of 300 protein domains (a subset of ASTRAL database) that we have called Proteus 300. Using the relative gap of any of the 44850 couples as a similarity measure, we obtained a classification in very good agreement with SCOP. Our algorithm provides thus a powerful classification tool for large structure databases

N–Dimensional Orthogonal Tile Sizing Problem

AMS subject classification: 68Q22, 90C90We discuss in this paper the problem of generating highly efficient code when a n + 1-dimensional nested loop program is executed on a n-dimensional torus/grid of distributed-memory general-purpose machines. We focus on a class of uniform recurrences with non-negative components of the dependency matrix. Using tiling the iteration space strategy we show that minimizing the total running time reduces to solving a non-trivial non-linear integer optimization problem. For the later we present a mathematical framework that enables us to derive an O(n log n) algorithm for finding a good approximate solution. The theoretical evaluations and the experimental results show that the obtained solution approximates the original minimum sufficiently well in the context of the considered problem. Such algorithm is realtime usable for very large values of n and can be used as optimization techniques in parallelizing compilers as well as in performance tuning of parallel codes by hand

Project {\tt SANC} (former {\tt CalcPHEP}): Support of Analytic and Numeric calculations for experiments at Colliders

The project, aimed at the theoretical support of experiments at modern and future accelerators -- TEVATRON, LHC, electron Linear Colliders (TESLA, NLC, CLIC) and muon factories, is presented. Within this project a four-level computer system is being created, which must automatically calculate, at the one-loop precision level the pseudo- and realistic observables (decay rates and event distributions) for more and more complicated processes of elementary particle interaction, using the principle of knowledge storing. It was already used for a recalculation of the EW radiative corrections for Atomic Parity Violation [1] and complete one-loop corrections for the process $e^+ e^-\to t\bar{t}$ [2-4]; for the latter an, agreement up to 11 digits with FeynArts and the other results is found. The version of {\tt SANC} that we describe here is capable of automatically computing the decay rates and the distributions for the decays $Z(H,W)\to f\bar{f}$ in the one-loop approximation.Comment: 3 Latex, Presented at ICHEP2002, Amsterdam, July 24-30, 2000; Submitted to Proceeding

Solving Maximum Clique Problem for Protein Structure Similarity

A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein structures is therefore a crucial task and has been extensively investigated. Evaluating the similarity of two proteins can be done by finding an optimal one-to-one matching between their components, which is equivalent to identifying a maximum weighted clique in a specific "alignment graph". In this paper we present a new integer programming formulation for solving such clique problems. The model has been implemented using the ILOG CPLEX Callable Library. In addition, we designed a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST (Vector Alignment Search Tool) - a software for aligning protein 3D structures largely used in NCBI (National Center for Biotechnology Information). The original VAST clique solver uses the well known Bron and Kerbosh algorithm (BK). Our computational results on real life protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK for the largest proteins

Theoretical and probability analysis of frequency selective circuits

The deviations of the circuit characteristics from their nominal values are random quantities and appear as a result of different destabilizing factors. With designing frequency selective circuits, two mutually connected problems are solved. The one is a study on the possible variations of circuit characteristics with given probability indices for the instability of the characteristics of their elements. The other is to synthesize the circuit and to determine the nominal parameters of its elements considering the requirements for stability of its characteristics. Both problems are solved by the methods of the theory of circuit sensitivity. The paper presents a new approach to theoretical probability analysis of the characteristics of frequency selective circuits depending on the relative changes of their parameters

Comparison of SANC with KORALZ and PHOTOS

Using the SANC system we study the one-loop electroweak standard model prediction, including virtual and real photon emissions, for the decays of on-shell vector and scalar bosons B --> f anti-f (gamma), where B is a vector boson, Z or W, or a Standard Model Higgs. The complete one-loop corrections and exact photon emission matrix element are taken into account. For the phase-space integration, the Monte Carlo technique is used. For Z decay the QED part of the calculation is first cross-checked with the exact one-loop QED prediction of KORALZ. For Higgs boson and W decays, a comparison is made with the approximate QED calculation of PHOTOS Monte Carlo. This provides a useful element for the evaluation of the theoretical uncertainty of PHOTOS, very interesting for its application in ongoing LEP2 and future LC and LHC phenomenology.Comment: Submitted to Acta Physica Polonica. 9 pages, 6 figure

News on PHOTOS Monte Carlo: gamma^* -> pi^+ pi^-(gamma) and K^\pm -> pi^+ pi^- e^\pm nu (gamma)

PHOTOS Monte Carlo is widely used for simulating QED effects in decay of intermediate particles and resonances. It can be easily connected to other main process generators. In this paper we consider decaying processes gamma^* -> pi^+ pi^-(gamma) and K^\pm -> pi^+ pi^- e^\pm nu (gamma) in the framework of Scalar QED. These two processes are interesting not only for the technical aspect of PHOTOS Monte Carlo, but also for precision measurement of alpha_{QED}(M_Z), g-2, as well as pi pi scattering lengths.Comment: 6 pages, 11 figures, proceedings of the PhiPsi09, Oct. 13-16, 2009, Beijing, Chin