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Computing the graph-based parallel complexity of gene assembly

THEORETICAL COMPUTER SCIENCE 2010年第25期411卷 2359-2367页

作者： Alhazov, Artiom Li, Chang Petre, Ion Acad Finland Helsinki Finland Abo Akad Univ Dept Informat Technol Turku Finland Moldavian Acad Sci Inst Math & Comp Sci MD-2028 Kishinev Moldova Turku Ctr Comp Sci FIN-20520 Turku Finland

We consider a graph-theoretical formalization of the process of gene assembly in ciliates introduced in Ehrenfeucht et al. (2003)[3], where a gene is modeled as a signed graph. The gene assembly, based on three types of operations only, is then modeled as a graph reduction process (to the empty graph). Motivated by the robustness of the gene assembly process, the notions of parallel reduction and parallel complexity of signed graphs have been considered in Harju et al. (2006)[7]. We describe in this paper an exact algorithm for computing the parallel complexity of a given signed graph and for finding an optimal parallel reduction for it. Checking the parallel applicability of a given set of operations and scanning all possible selections amount to a high computational complexity. We also briefly discuss a faster approximate algorithm that however, cannot guarantee finding the optimal reduction. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Gene assembly Parallelism Signed graphs Parallel complexity algorithmics

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INFORMATION-PROCESSING AND ARTIFICIAL-INTELLIGENCE

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ANNALES DES TELECOMMUNICATIONS-ANNALS OF TELECOMMUNICATIONS 1987年第7-8期42卷 470-489页

作者： SIMON, JC UNIV PARIS 06 INST PROGRAMMAT4 PL JUSSIEUF-75230 PARIS 05FRANCE

Les systèmes informatiques sont les machines les plus générales, propres au traitement de l’information. Leur emploi, de plus en plus courant, conduit à ne considérer que des modèles constructifs, par opposition à certaines modélisations formelles ou mathématiques. La calculabilité et la programmabilité deviennent ainsi des facteurs essentiels au succès d’un modèle informatique. La nécessité d’échapper aux contraintes imposees par la complexité de calcul conduit à dégager des idées et des méthodes nouvelles, particulièrement mises en évidence dans les domaines de l’intelligence artificielle et de la reconnaissance des formes.

关键词： Traitement information Intelligence artificielle Traitement informatique Algorithmique Arbre recherche Complexité calcul Reconnaissance forme Information processing Artificial intelligence Computerized processing algorithmics Research tree Computing complexity Pattern recognition

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An algorithmic view of gene teams

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THEORETICAL COMPUTER SCIENCE 2004年第2-3期320卷 395-418页

作者： Béal, MP Bergeron, A Corteel, S Raffinot, M Univ Marne La Vallee Inst Gaspard Monge F-77454 Marne La Vallee 2 France Univ Quebec LaCIM Montreal PQ H3C 3P8 Canada Univ Versailles CNRS Lab PRiSM F-78035 Versailles France CNRS Lab Genome & Informat F-91034 Evry France

Comparative genomics is a growing field in computational biology, and one of its typical problem is the identification of sets of orthologous genes that have virtually the same function in several genomes. Many different bioinformatics approaches have been proposed to define these groups, often based on the detection of sets of genes that are "not too far" in all genomes. In this paper, we propose a unifying concept, called gene teams, which can be adapted to various notions of distance. We present two algorithms for identifying gene teams formed by n genes placed on m linear chromosomes. The first one runs in O(mn log(2) n) and uses a divide and conquer approach based on the formal properties of gene teams. We next propose an optimization of the original algorithm, and, in order to better understand the complexity bound of the algorithms, we recast the problem in the Hopcroft's partition refinement framework. This allows us to analyze the complexity of the algorithms with elegant amortized techniques. Both algorithms require linear space. We also discuss extensions to circular chromosomes that achieve the same complexity. (C) 2004 Elsevier B.V. All rights reserved.

关键词： comparative genomics algorithmics gene team Hopcroft's framework

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A comparison of techniques to find mirrored hosts on the WWW

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JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE 2000年第12期51卷 1114-1122页

作者： Bharat, K Broder, A Dean, J Henzinger, MR Google Inc Mountain View CA 94043 USA AltaVista Co San Mateo CA 94402 USA

We compare several algorithms for identifying mirrored hosts on the World Wide Web. The algorithms operate on the basis of URL strings and linkage data: the type of information about Web pages easily available from Web proxies and crawlers. Identification of mirrored hosts can improve Web-based information retrieval in several ways: first, by identifying mirrored hosts, search engines can avoid storing and returning duplicate documents. Second, several new information retrieval techniques for the Web make inferences based on the explicit links among hypertext documents-mirroring perturbs their graph model and degrades performance. Third, mirroring information can be used to redirect users to alternate mirror sites to compensate for various failures, and can thus improve the performance of Web browsers and proxies. We evaluated four classes of "top-down" algorithms for detecting mirrored host pairs (that is, algorithms that are based on page attributes such as URL, IP address, and hyperlinks between pages, and not on the page content) on a collection of 140 million URLs (on 230,000 hosts) and their associated connectivity information. Our best approach is one which combines five algorithms and achieved a precision of 0.57 for a recall of 0.86 considering 100,000 ranked host pairs.

关键词： Comparative Analysis Data Analysis Information Retrieval Information Sources Online Searching Online Systems World Wide WebConnectivity algorithmics

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Scheduling periodic I/O access with bi-colored chains: models and algorithms

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JOURNAL OF SCHEDULING 2021年第5期24卷 469-481页

作者： Jeannot, Emmanuel Pallez, Guillaume Vidal, Nicolas Univ Bordeaux INRIA LaBRI F-33405 Talence France

Observations show that some HPC applications periodically alternate between (i) operations (computations, local data accesses) executed on the compute nodes, and (ii) I/O transfers of data and this behavior can be predicted before-hand. While the compute nodes are allocated separately to each application, the storage is shared, and thus, I/O access can be a bottleneck leading to contention. To tackle this issue, we design new static I/O scheduling algorithms that prescribe when each application can access the storage. To design a static algorithm, we emphasize on the periodic behavior of most applications. Scheduling the I/O volume of the different applications is repeated over time. This is critical since often the number of application runs is very high. In the following article, we develop a formal background for I/O scheduling. First, we define a model, bi-colored chain scheduling, and then, we go through related results existing in the literature and explore the complexity of this problem variants. Finally, to match the HPC context, we perform experiments based on use cases matching highly parallel applications or distributed learning framework

关键词： High-performance computing Complexity algorithmics Approximations

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An algorithmic toolbox for network calculus

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DISCRETE EVENT DYNAMIC SYSTEMS-THEORY AND APPLICATIONS 2008年第1期18卷 3-49页

作者： Bouillard, Anne Thierry, Eric ENS IRISA F-35170 Bruz France CNRS ENS INRIA LIP UMR 5668UCBL F-69364 Lyon 07 France

Network calculus offers powerful tools to analyze the performances in communication networks, in particular to obtain deterministic bounds. This theory is based on a strong mathematical ground, notably by the use of (min,+) algebra. However, the algorithmic aspects of this theory have not been much addressed yet. This paper is an attempt to provide some efficient algorithms implementing network calculus operations for some classical functions. Some functions which are often used are the piecewise affine functions which ultimately have a constant growth. As a first step towards algorithmic design, we present a class containing these functions and closed under the main network calculus operations (min, max, +, -, convolution, subadditive closure, deconvolution): the piecewise affine functions which are ultimately pseudo-periodic. They can be finitely described, which enables us to propose some algorithms for each of the network calculus operations. We finally analyze their computational complexity.

关键词： network calculus functional (min, plus ) algebra algorithmics computational complexity

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Graph encoding of 2D-gon tilings

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THEORETICAL COMPUTER SCIENCE 2005年第2-3期346卷 226-253页

作者： Chavanon, F Latapy, M Morvan, M Rémila, E Vuillon, L Univ Lyon 1 CNRS INRIA UMR 5668LIPENS Lyon F-69364 Lyon France Univ St Etienne Grp Rech Informat & Math Appl F-42334 Roanne France Univ Paris 07 LIAFA F-75005 Paris France Univ Savoie CNRS UMR 5127 Math Lab F-73376 Le Bourget Du Lac France

2D-gon tilings with parallelograms are a model used in physics to study quasicrystals, and they are also important in combinatorics for the study of aperiodic structures. In this paper, we study the graph induced by the adjacency relation between tiles. This relation can been used to encode simply and efficiently 2D-gon tilings for algorithmic manipulation. We show for example how it can be used to sample random 2D-gon tilings. (c) 2005 Elsevier B.V. All rights reserved.

关键词： tilings algorithmics graph theory

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Component-Graph Construction

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JOURNAL OF MATHEMATICAL IMAGING AND VISION 2019年第6期61卷 798-823页

作者： Passat, Nicolas Naegel, Benoit Kurtz, Camille Univ Reims CReSTIC Reims France Univ Strasbourg ICube CNRS Strasbourg France Univ Paris 05 LIPADE Paris France

Component-trees are classical tree structures for grey-level image modelling. Component-graphs are defined as a generalization of component-trees to images taking their values in any (totally or partially) ordered sets. Similar to component-trees, component-graphs are a lossless image model;then, they can allow for the development of various image processing approaches. However, component-graphs are not trees, but directed acyclic graphs. This makes their construction non-trivial, leading to nonlinear time cost and resulting in nonlinear space data structures. In this theoretical article, we discuss the notion(s) of component-graph, and we propose a strategy for their efficient building and representation, which are necessary conditions for further involving them in image processing approaches.

关键词： Component-graph algorithmics Mathematical morphology Multivalued images

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Onion routing circuit construction via latency graphs

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COMPUTERS & SECURITY 2013年 37卷 197-214页

作者： Castillo-Perez, Sergio Garcia-Alfaro, Joaquin Autonomous Univ Barcelona Dept Informat & Commun Engn E-08193 Barcelona Spain CNRS Samovar UMR 5157 TELECOM SudParis Inst MINES TELECOM Evry France

The use of anonymity-based infrastructures and anonymisers is a plausible solution to mitigate privacy problems on the Internet. Tor (short for The onion router) is a popular low-latency anonymity system that can be installed as an end-user application on a wide range of operating systems to redirect the traffic through a series of anonymising proxy circuits. The construction of these circuits determines both the latency and the anonymity degree of the Tor anonymity system. While some circuit construction strategies lead to delays which are tolerated for activities like Web browsing, they can make the system vulnerable to linking attacks. We evaluate in this paper three classical strategies for the construction of Tor circuits, with respect to their de-anonymisation risk and latency performance. We then develop a new circuit selection algorithm that considerably reduces the success probability of linking attacks while keeping a good degree of performance. We finally conduct experiments on a real-world Tor deployment over Planet Lab. Our experimental results confirm the validity of our strategy and its performance increase for Web browsing. (c) 2013 Elsevier Ltd. All rights reserved.

关键词： Onion routing Anonymity Privacy Entropy Graphs algorithmics

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Algorithmic computation of optimal capacity in multiservice mobile wireless networks

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IEICE TRANSACTIONS ON COMMUNICATIONS 2005年第2期E88B卷 797-799页

作者： Pla, V Martínez, J Casares-Giner, V Univ Politecn Valencia Dept Commun Valencia 46022 Spain

In this paper we propose a new algorithm for computing the optimal configuration of the Multiple Fractional Guard Channel (MFGC) admission policy in multiservice mobile wireless networks. The optimal configuration maximizes the offered traffic that the system can handle while meeting certain QoS requirements. The proposed algorithm is shown to be more efficient than previous algorithms appeared in the literature.

关键词： mobile wireless network multiservice admission control capacity algorithmics

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