检索结果-内蒙古大学图书馆

29th International Symposium on String Processing and Information Retrieval (SPIRE)

作者： Fertin, Guillaume Jean, Geraldine Labarre, Anthony Nantes Univ LS2N CNRS UMR 6004 F-44000 Nantes France Univ Gustave Eiffel CNRS LIGM F-77454 Marne La Vallee France

ISBN: (纸本)9783031206429;9783031206436

In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and recombine the severed endpoints in one of two possible ways: one of these options corresponds to a prefix reversal, which reverses the order of elements between the two cuts (as well as their signs in the signed case). Depending on whether we consider both options or reversals only, our main results are: (1) new structural lower bounds based on the breakpoint graph for sorting by unsigned prefix reversals, unsigned prefix DCJs, or signed prefix DCJs;(2) a polynomial-time algorithm for sorting by signed prefix DCJs, thus answering an open question in [7];(3) a 3/2-approximation for sorting by unsigned prefix DCJs, which is, to the best of our knowledge, the first sorting by prefix rearrangements problem that admits an approximation ratio strictly smaller than 2 (with the obvious exception of the polynomial-time solvable problems);and finally, (4) an FPT algorithm for sorting by unsigned prefix DCJs parameterised by the number of breakpoints in the genome.

关键词： Genome rearrangements Prefix reversals Prefix DCJs Lower bounds algorithmics FPT Approximation algorithms

来源：评论

学校读者我要写书评

暂无评论

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

引用

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

来源：评论

学校读者我要写书评

暂无评论

Automatic Source Code Generation from Owl Pseudocode 13th

Automatic Source Code Generation from Owl Pseudocode

引用

13th International Conference on Interactive Mobile Communication, Technologies and Learning (IMCL)

作者： Diatta, Baboucar Basse, Adrien Deme, Cherif Bachir Ouya, Samuel Univ Alioune Diop Bambey Senegal Univ Cheikh Anta Diop Dakar Senegal

ISBN: (纸本)9783030499327;9783030499310

algorithmics is a crucial step in programming learning processes. It helps learners to propose a better writing and understanding of solutions without worrying about programming language syntactic complexity. Once algorithm is clearly established, the next step is to translate it into a given programming language. When writing programs, syntax errors are common mainly due to the multiplicity of programming languages and strict syntactic rules. We propose in this work a web and mobile interface to automatically generate, from algorithms based on Pseudocode ontology, the corresponding codes in several programming languages such as C, Pascal and Python.

关键词： Ontology algorithmics Pseudocode Programming languages

来源：评论

学校读者我要写书评

暂无评论

ReCombinatorics: The algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks

引用

2014年

作者： Dan Gusfield

ISBN: (纸本)0262027526;9780262027526

In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems. Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks. ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.

关键词： graphs explicit recombination ancestral algorithmics recombinatorics

来源：评论

学校读者我要写书评

暂无评论

Component-Graph Construction

引用

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

来源：评论

学校读者我要写书评

暂无评论

Meta-Alignment: Combining Sequence Aligners for Better Results 6th

Meta-Alignment: Combining Sequence Aligners for Better Resul...

引用

6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)

作者： Wolf, Beat Kuonen, Pierre Dandekar, Thomas Univ Appl Sci Western Switzerland Inst Complex Syst CH-1700 Fribourg Switzerland Univ Wurzburg Biozentrum Univ Wurzburg D-97074 Wurzburg Germany

ISBN: (纸本)9783319787220;9783319787237

Analysing next generation sequencing data often involves the use of a sequence aligner to map the sequenced reads against a reference. The output of this process is the basis of many downstream analyses and its quality thus critical. Many different alignment tools exist, each with a multitude of options, creating a vast amount of possibilities to align sequences. Choosing the correct aligner and options for a specific dataset is complex, and yet it can have a major impact on the quality of the data analysis. We propose a new approach in which we combine the output of multiple sequence aligners to create an improved sequence alignment files. Our novel approach can be used to either increase the sensitivity or the specificity of the alignment process. The software is freely available for non-commercial usage at http://***/.

关键词： Next generation sequencing Sequence alignment algorithmics

来源：评论

学校读者我要写书评

暂无评论

PictoMir - how and why do we teach textless programming for preschoolers, first graders and students of pedagogical universities 17

PictoMir - how and why do we teach textless programming for ...

引用

13th Central and Eastern European Software Engineering Conference in Russia (CEE-SECR)

作者： Besshaposhnikov, Nikita Kushnirenko, Anatoli Leonov, Alexander Russian Acad Sci Sci Res Inst Syst Dev Nakhimovsky Ave 35 B 1 Moscow 117218 Russia

ISBN: (纸本)9781450363969

The age reduction of acquaintance of children with programming is a worldwide trend. During long-term experiments, a freely distributed multiplatform educational and gaming system PictoMir was developed in the SRISA RAS, allowing preschoolers of the age 6+ to master a basic set of programming concepts: program, subroutine, repeater, feedback, command orders and command-questions, branching, repeaters, counters. In the 2016-2017 academic year, 902 children in 15 municipal kindergartens of Surgut successfully passed the annual cycle of "Algorithmic for Preschoolers", creating on the tablets programs for managing virtual robots and real robots-toys.

关键词： PiktoMir Mirera programming teaching algorithmics

来源：评论

学校读者我要写书评

暂无评论

Implicit Component-Graph: A Discussion 13th

Implicit Component-Graph: A Discussion

引用

13th International Symposium on Mathematical Morphology (ISMM)

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

ISBN: (纸本)9783319572406;9783319572390

Component-graphs are defined as the generalization of component-trees to images taking their values in partially ordered sets. Similarly to component-trees, component-graphs are a lossless image model, and can allow for the development of various image processing approaches (antiextensive filtering, segmentation by node selection). However, component-graphs are not trees, but directed acyclic graphs. This induces a structural complexity associated to a higher combinatorial cost. These properties make the handling of component-graphs a non-trivial task. We propose a preliminary discussion on a new way of building and manipulating component-graphs, with the purpose of reaching reasonable space and time costs. Tackling these complexity issues is indeed required for actually involving component-graphs in efficient image processing approaches.

关键词： Component-graph algorithmics Data-structure

来源：评论

学校读者我要写书评

暂无评论

Combinatorial Algorithms and Optimization

Combinatorial Algorithms and Optimization

引用

作者： George Manoussakis Universite Paris-Sud

学位级别：博士

We start by studying the class of $k$- degenerate graphs which are often used to model sparse real-world graphs. We focus on enumeration questions for these graphs. That is, we try and provide algorithms which must output, without duplication, all the occurrences of some input subgraph. We investigate the questions of finding all cycles of some given size and all maximal cliques in the graph. Our two contributions are a worst-case output size optimal algorithm for fixed-size cycle enumeration and an output sensitive algorithm for maximal clique enumeration for this restricted class of graphs. In a second part we consider graphs in a distributed manner. We investigate questions related to finding matchings of the network, when no assumption is made on the initial state of the system. These algorithms are often referred to as self- stabilizing. Our two main contributions are an algorithm returning an approximation of the maximum matching and a new algorithm for maximal matching when communication simulates message passing. Finally, we introduce and investigate some special families of polytopes, namely primitive zonotopes, which can be described as the Minkowski sum of short primitive vectors. We highlight connections with the largest possible diameter of the convex hull of a set of points in dimension d whose coordinates are integers between 0 and k. Our main contributions are new lower bounds for this diameter question as well as descriptions of small instances of these objects.

关键词： algorithmics graphs enumeration diameter polytopes

来源：评论

学校读者我要写书评

暂无评论

GNATY: Optimized NGS Variant Calling and Coverage Analysis 4th

GNATY: Optimized NGS Variant Calling and Coverage Analysis

引用

4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO)

作者： Wolf, Beat Kuonen, Pierre Dandekar, Thomas Univ Appl Sci Western Switzerland Inst Complex Syst CH-1700 Fribourg Switzerland Univ Wurzburg Biozentrum D-97074 Wurzburg Germany

ISBN: (纸本)9783319317441;9783319317434

Next generation sequencing produces an ever increasing amount of data, requiring increasingly fast computing infrastructures to keep up. We present GNATY, a collection of tools for NGS data analysis, aimed at optimizing parts of the sequence analysis process to reduce the hardware requirements. The tools are developed with efficiency in mind, using multithreading and other techniques to speed up the analysis. The architecture has been verified by implementing a variant caller based on the Varscan 2 variant calling model, achieving a speedup of nearly 18 times. Additionally, the flexibility of the algorithm is also demonstrated by applying it to coverage analysis. Compared to BEDtools 2 the same analysis results were found but in only half the time by GNATY. The speed increase allows for a faster data analysis and more flexibility to analyse the same sample using multiple settings.

关键词： Next generation sequencing Variant calling algorithmics

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：