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2014 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing最新文献

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Dynamic Clustering of Gene Expression Data Using a Fuzzy Approach 基于模糊方法的基因表达数据动态聚类
A. Sirbu, G. Czibula, Maria-Iuliana Bocicor
The amount of gene expression data gathered in the last decade has increased exponentially due to modern technologies like micro array and next-generation sequencing, which allow measuring the levels of expression of thousands of genes simultaneously. Clustering is a data mining technique often used for analysing this kind of data, as it is able to discover patterns in genes that are very important for understanding functional genomics. To study biological processes which are dynamic by nature, researchers must analyse data gradually, as the processes evolve. There are two ways to achieve this: perform re-clustering from scratch every time new gene expression levels are available, or adapt the previously obtained partition using a dynamic clustering algorithm, which is more efficient. In this paper we propose a fuzzy approach for dynamic clustering of gene expression data and we prove its effectiveness through a set of experimental evaluations performed on a real-life data set.
由于微阵列和下一代测序等现代技术,在过去十年中收集的基因表达数据量呈指数级增长,这些技术可以同时测量数千个基因的表达水平。聚类是一种数据挖掘技术,经常用于分析这类数据,因为它能够发现基因中的模式,这对于理解功能基因组学非常重要。为了研究本质上是动态的生物过程,研究人员必须随着过程的演变逐渐分析数据。有两种方法可以实现这一点:每当有新的基因表达水平可用时,从头开始执行重新聚类,或者使用更有效的动态聚类算法调整先前获得的分区。本文提出了一种基因表达数据动态聚类的模糊方法,并通过对真实数据集进行的一组实验评估证明了其有效性。
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引用次数: 4
Implementing Powerlists with Bulk Synchronous Parallel ML 使用批量同步并行ML实现Powerlists
F. Loulergue, Virginia Niculescu, J. Tesson
Tools and methods able to simplify the development process of parallel software, but also to assure a high level of performance and robustness, are necessary. Power lists and their variants are data structures that can be successfully used in a simple, provably correct, functional description of parallel programs, which are divide-and-conquer in nature. The paper presents how programs defined based on power lists could be implemented in the functional language OCaml plus calls to the parallel functional programming library Bulk Synchronous Parallel ML. BSML functions follow the BSP model requirements, and so its advantages are introduced in OCaml parallel code. In order to write power list programs in BSML we provide a data type for power lists and a set of skeletons (higher-order functions implemented in parallel) to manipulate them. Examples are given and concrete experiments for their executions are conducted.
能够简化并行软件开发过程的工具和方法,同时保证高水平的性能和健壮性,是必要的。权力列表及其变体是一种数据结构,可以成功地用于并行程序的简单、可证明正确的功能描述,而并行程序本质上是分而治之的。本文介绍了如何在函数式语言OCaml中实现基于功率表定义的程序,并调用并行函数式编程库Bulk Synchronous parallel ML, BSML函数遵循BSP模型的要求,因此在OCaml并行代码中介绍了它的优点。为了在BSML中编写权力列表程序,我们提供了权力列表的数据类型和一组骨架(并行实现的高阶函数)来操作它们。给出了实例,并进行了具体的实验。
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引用次数: 5
Efficient Computation of Simplicial Homology through Acyclic Matching 非循环匹配简化同调的高效计算
Ulderico Fugacci, F. Iuricich, L. Floriani
We consider the problem of efficiently computing homology with Z coefficients as well as homology generators for simplicial complexes of arbitrary dimension. We analyze, compare and discuss the equivalence of different methods based on combining reductions, co reductions and discrete Morse theory. We show that the combination of these methods produces theoretically sound approaches which are mutually equivalent. One of these methods has been implemented for simplicial complexes by using a compact data structure for representing the complex and a compact encoding of the discrete Morse gradient. We present experimental results and discuss further developments.
研究任意维简单复形的有效计算Z系数的同调和同调发生器问题。在结合约简、co约简和离散莫尔斯理论的基础上,对不同方法的等价性进行了分析、比较和讨论。我们表明,这些方法的组合产生了理论上合理的方法,它们是相互等效的。其中一种方法通过使用表示复数的紧凑数据结构和离散莫尔斯梯度的紧凑编码来实现简单复数。我们提出了实验结果并讨论了进一步的发展。
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引用次数: 8
A Lowest Level Rule Push-Relabel Algorithm for Submodular Flows and Matroid Optimization 子模块流的最低级规则推重标记算法及矩阵优化
E. F. Olariu, Cristian Frasinaru
We present a new strategy for combinatorial push-relabel algorithm used in sub modular flows and matroid optimization. In the case of matroid optimization, in contrast with other known algorithms, our strategy needs no lexicographic order of the elements. Combined with a reduction of the number of active basis the resulting procedure gives a time complexity of O(n6). Moreover our rule offers more interesting properties of the treated elements and suggests the adaptation of this rule to the sub modular flow algorithm. The above strategy applied for sub modular flows gives an O(n5) time complexity procedure, which is the same with the known best complexity given by a procedure based on highest level rule. This method starts a way for a simpler algorithm for finding a feasible sub modular flow which is described in the second part of the paper. Our method for sub modular flow is based on a lowest level rule combined with a bfs-like traversal. The lowest level rule does not work alone because new (ψ- or g-) larger nodes on lower levels can appear during treatment of the current node. Therefore, it is reinforced with a bfs traversal: the new larger nodes are added to a queue - restarted with a lowest level, larger node, whenever it becomes empty. The O(n5) time complexity is the same as the best known. Our strategy brings a forest structure of the treated nodes, where the basic operations (pushes and liftings) can be easily numbered and for this reason has a better potential for future improvements.
提出了一种用于子模块流和矩阵优化的组合推重标记算法。在矩阵优化的情况下,与其他已知算法相比,我们的策略不需要元素的字典顺序。结合减少活动基的数量,得到的过程的时间复杂度为0 (n6)。此外,我们的规则提供了处理元素更有趣的性质,并建议将该规则适用于子模块流算法。上述策略应用于子模块流给出了一个O(n5)时间复杂度的过程,这与基于最高级规则的过程给出的已知最佳复杂度相同。该方法为寻找可行子模块流的更简单算法开辟了一条道路,本文的第二部分将对此进行描述。我们的子模块流方法是基于一个最低级别的规则和一个类似bf的遍历相结合。最低能级规则不能单独工作,因为在处理当前节点的过程中,可能会出现较低能级上新的(ψ-或g-)较大的节点。因此,它通过bfs遍历得到加强:新的较大节点被添加到队列中——当队列变为空时,使用最低级别、更大的节点重新启动。O(n5)的时间复杂度与最著名的相同。我们的策略带来了处理节点的森林结构,其中基本操作(推动和提升)可以很容易地编号,因此具有更好的未来改进潜力。
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引用次数: 0
Multispace, Dynamic, Fixed-Radius, All Nearest Neighbours Problem 多空间、动态、固定半径、全近邻问题
B. Papis, A. Pacut
We present a solution to a specific version of one of the most fundamental computer science problem - the nearest neighbour problem (NN). The new, proposed variant of the NN problem is the multispace, dynamic, fixed-radius, all nearest neighbours problem, where the NN data structure handles queries that concern different subsets of input dimensions. In other words, solutions to this problem allow searching for closest points in terms of different features. This is an important issue in the context of practical applications of incremental state abstraction techniques for high dimensional Markov Decision Processes (MDP). The proposed solution is a set of simple, one-dimensional structures, that can handle range queries for arbitrary subset of input dimensions for the Chebyshev distance. We also provide version for other metrics, and a simplified version of the algorithm that yields approximate results but runs faster. The proposed approximation is deterministic in a way that ensures that the most important (in the context of the considered state abstraction task) parts of the result are returned with no accuracy loss. The presented experimental study demonstrates improvement in comparison to some state-of-the-art algorithms on uniformly random and MDP-generated data.
我们提出了一个解决最基本的计算机科学问题之一的特定版本-最近邻问题(NN)。新提出的神经网络问题的变体是多空间、动态、固定半径、全近邻问题,其中神经网络数据结构处理涉及输入维度的不同子集的查询。换句话说,这个问题的解决方案允许根据不同的特征搜索最近的点。在高维马尔可夫决策过程(MDP)的增量状态抽象技术的实际应用中,这是一个重要的问题。提出的解决方案是一组简单的一维结构,可以处理切比雪夫距离输入维度的任意子集的范围查询。我们还提供了其他指标的版本,以及生成近似结果但运行速度更快的算法的简化版本。所建议的近似在某种程度上是确定的,它确保返回结果中最重要的部分(在所考虑的状态抽象任务的上下文中)而不损失准确性。所提出的实验研究表明,与一些最先进的算法相比,在均匀随机和mdp生成的数据上有所改进。
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引用次数: 0
A Practical Guide for Detecting the Java Script-Based Malware Using Hidden Markov Models and Linear Classifiers 使用隐马尔可夫模型和线性分类器检测基于Java脚本的恶意软件的实用指南
Doina Cosovan, Razvan Benchea, Dragos Gavrilut
The World Wide Web evolved so rapidly that it is no longer considered a luxury, but a necessity. That is why currently the most popular infection vectors used by cyber criminals are either web pages or commonly used documents (such as pdf files). In both of these cases, the malicious actions performed are written in Java Script. Because of this, Java Script has become the preferred language for spreading malware. In order to be able to stop malicious content from executing, detection of its infection vector is crucial. In this paper we propose various methods for detecting Java Script-based attack vectors. For achieving our goal we first need to fight metamorphism techniques usually used in Java Script malicious code, which are by no means trivial: garbage instruction insertion, variable renaming, equivalent instruction substitution, function permutation, instruction reordering, and so on. Our approach to deal with metamorphism starts with splitting the Java Script content in components and filtering the insignificant ones. We then use a data set, consisting in over one million Java Script files in order to test several machine learning algorithms such as Hidden Markov Models, linear classifiers and hybrid approaches for malware detection. Finally, we analyze these detection methods from a practical point of view, emphasizing the need for a very low false positive rate and the ability to be trained on large datasets.
万维网发展得如此之快,以至于它不再被认为是奢侈品,而是必需品。这就是为什么目前网络犯罪分子使用的最流行的感染媒介要么是网页,要么是常用的文档(如pdf文件)。在这两种情况下,所执行的恶意操作都是用Java Script编写的。正因为如此,Java脚本已经成为传播恶意软件的首选语言。为了能够阻止恶意内容的执行,检测其感染载体至关重要。在本文中,我们提出了各种检测基于Java脚本的攻击向量的方法。为了实现我们的目标,我们首先需要对抗通常在Java Script恶意代码中使用的变质技术,这些技术绝不是微不足道的:垃圾指令插入、变量重命名、等效指令替换、函数排列、指令重新排序等等。我们处理变形的方法是从在组件中拆分Java脚本内容并过滤不重要的内容开始的。然后,我们使用一个数据集,包含超过一百万个Java脚本文件,以测试几种机器学习算法,如隐马尔可夫模型,线性分类器和恶意软件检测的混合方法。最后,我们从实际的角度分析了这些检测方法,强调需要非常低的假阳性率和在大数据集上训练的能力。
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引用次数: 8
An Imperialistic Strategy Approach to Continuous Global Optimization Problem 连续全局优化问题的帝国策略方法
George Anescu
The paper is introducing the principles of a new global optimization strategy, Imperialistic Strategy (IS), applied to the Continuous Global Optimization Problem (CGOP). Inspired from existing multi-population strategies, like the Island Model (IM) approaches to parallel Evolutionary Algorithms (EA) and the Imperialistic Competitive Algorithm (ICA), the proposed IS method is considered an optimization strategy for the reason that it can integrate other well-known optimization methods, which in the context are regarded as sub-methods (although in other contexts they are prominent global optimization methods). Four optimization methods were implemented and tested in the roles of sub-methods: Genetic Algorithm (GA) (a floating-point representation variant), Differential Evolution (DE), Quantum Particle Swarm Optimization (QPSO) and Artificial Bee Colony (ABC). The optimization performances of the proposed optimization methods were compared on a test bed of 9 known multimodal optimization problems by applying an appropriate testing methodology. The obtained increased success rates of IS multi-population variants compared to the success rates of the optimization sub-methods run separately, combined with the increased computing efficiencies possible to be perceived for parallel and distributed implementations, demonstrated that IS is a promising approach to CGOP.
本文介绍了应用于连续全局优化问题的一种新的全局优化策略——帝国主义策略(is)的原理。受现有多种群策略的启发,如并行进化算法(EA)和帝国主义竞争算法(ICA)的岛屿模型(IM)方法,所提出的IS方法被认为是一种优化策略,因为它可以整合其他已知的优化方法,这些方法在上下文中被视为子方法(尽管在其他上下文中它们是突出的全局优化方法)。采用遗传算法(GA)、差分进化(DE)、量子粒子群优化(QPSO)和人工蜂群优化(ABC)四种子方法分别对四种优化方法进行了实现和测试。在9个已知多模态优化问题的实验台上,采用适当的测试方法对所提优化方法的优化性能进行了比较。与单独运行的优化子方法的成功率相比,所获得的IS多种群变体的成功率增加了,结合并行和分布式实现可能感知到的计算效率的提高,表明IS是一种有前途的CGOP方法。
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引用次数: 3
Enhancing Dental Radiographic Images in Spline-Type Spaces 在样条空间增强牙科放射图像
D. Onchis, S. Gotia
The aim of this paper is to propose a method to enhance the acquisition resolution of dental radiographic images to facilitate the clinical examination and interpretation. The algorithm is based on the approximation properties of spline-type spaces with multiple generators. These spaces are obtained by applying a discrete group of translation operators to a finite set of smooth functions, forming a Riesz basis for its closed linear span within the Hilbert space L2(R2). For computational efficiency a parallel approach to the algorithm is also proposed. The experiments show that the algorithm allows to increase the resolution of dental radiographic images to sub -- pixel levels.
本文的目的是提出一种提高牙科放射图像采集分辨率的方法,以方便临床检查和解释。该算法基于具有多个生成器的样条空间的逼近性质。这些空间是通过将一组离散平移算子应用于有限光滑函数集而得到的,形成了Hilbert空间L2(R2)内的闭线性张成的Riesz基。为了提高计算效率,本文还提出了一种并行算法。实验表明,该算法可以将牙科放射图像的分辨率提高到亚像素级。
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引用次数: 0
An Ontology Selection and Ranking System Based on the Analytic Hierarchy Process 基于层次分析法的本体选择与排序系统
Adrian Groza, Irina Dragoste, Iulia Sincai, Ioana Jimborean, Vasile Moraru
Selecting the desired ontology from a collection of available ones is essential for ontology reuse. We address the problem of evaluating, ranking and selecting ontologies according to user preferences. We exploit the Analytic Hierarchy Process (AHP) to solve the multiple-criteria decision problem and to model the preferences of the users. We use AHP to analyze the available ontologies from different perspectives and at different abstraction levels. The decision is based on the concrete end-node measurements and their relative importance at higher levels. For supporting the selection decision, we developed an ontology representation, reasoning and management system. The system applies different metrics on ontologies in order to feed the Analytic Hierarchy Process with facts. The running scenario applies our method to the task of reusing ontologies from the tourism domain.
从可用的本体集合中选择所需的本体对于本体重用至关重要。我们解决了根据用户偏好评估、排序和选择本体的问题。我们利用层次分析法(AHP)来解决多准则决策问题,并对用户的偏好进行建模。我们使用AHP从不同的角度和不同的抽象级别分析可用的本体。决策是基于具体的终端节点测量及其在更高级别上的相对重要性。为了支持选择决策,我们开发了本体表示、推理和管理系统。系统在本体上应用不同的度量,以便向层次分析过程提供事实。正在运行的场景将我们的方法应用于重用来自旅游领域的本体的任务。
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引用次数: 8
CSPs and Connectedness: P/NP Dichotomy for Idempotent, Right Quasigroups csp与连通性:幂等右拟群的P/NP二分法
Robert W. McGrail, James M. Belk, Solomon Garber, J. Wood, Benjamin Fish
In the 1990's, Jeavons showed that every finite algebra corresponds to a class of constraint satisfaction problems. Vardi later conjectured that idempotent algebras exhibit P/NP dichotomy: Every non NP-complete algebra in this class must be tractable. Here we discuss how tractability corresponds to connectivity in Cayley graphs. In particular, we show that dichotomy in finite idempotent, right quasi groups follows from a very strong notion of connectivity. Moreover, P/NP membership is first-order axiomatizable in involutory quandles.
在20世纪90年代,Jeavons证明了每一个有限代数对应于一类约束满足问题。Vardi后来推测幂等代数表现出P/NP二分性:这门课中的每一个非NP完全代数都必须是可处理的。这里我们讨论了在Cayley图中可跟踪性是如何对应于连通性的。特别地,我们证明了有限幂等右拟群的二分类遵循一个很强的连通性概念。此外,P/NP隶属关系是一阶公理化的。
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引用次数: 2
期刊
2014 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing
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