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Using the GPU and Multi-core CPU to Generate a 3D Oviduct through Feature Extraction from Histology Slides 利用GPU和多核CPU对组织学切片进行特征提取,生成三维输卵管
Pub Date : 2010-09-30 DOI: 10.1109/PDMC-HIBI.2010.19
M. Burkitt, D. Walker, D. Romano, A. Fazeli
Extracting information about the structure of biological tissue from static image data is a complex task which requires a series of computationally intensive operations. Here we present how the power of multi-core CPUs and massively parallel GPUs have been utilised to extract information about the shape, size and path followed by the mammalian oviduct, called the fallopian tube in humans, from histology images, to create a realistic 3D virtual organ for use in predictive computational models. Histology images from a mouse oviduct were processed, using a combination of GPU and multi-core CPU techniques, to identify the individual cross-sections and determine the 3D path that the tube follows through the tissue. This information was then related back to the histology images, linking the 2D cross-sections with their corresponding 3D position along the oviduct. Measurements were then taken from the images and used to computationally generate a series of linear 2D spline cross-sections for the length of the oviduct, which were bound to the 3D path of the tube using a novel particle system based technique that provides smooth resolution of self intersections and crossovers from adjacent sections. This results in a unique 3D model of the oviduct, which is based on measurements of histology slides and therefore grounded in reality. The GPU is used for the processor intensive operations of image processing and particle physics based simulations, significantly reducing the time required to generate a complete model. A set of models created using this technique is being used to investigate the influence that the 3D structure of the oviductal environment has on sperm transport and navigation.
从静态图像数据中提取生物组织结构信息是一项复杂的任务,需要进行一系列计算密集型的操作。在这里,我们展示了如何利用多核cpu和大规模并行gpu的能力,从组织学图像中提取有关哺乳动物输卵管(人类称为输卵管)的形状,大小和路径的信息,以创建用于预测计算模型的逼真3D虚拟器官。使用GPU和多核CPU技术对小鼠输卵管的组织学图像进行处理,以识别单个横截面并确定输卵管穿过组织的3D路径。然后将这些信息与组织学图像联系起来,将2D横截面与其沿输卵管的相应3D位置联系起来。然后从图像中进行测量,并用于计算生成一系列关于输卵管长度的线性二维样条横截面,这些横截面使用基于新型粒子系统的技术绑定到管道的3D路径上,该技术提供了自相交和相邻截面交叉的平滑分辨率。这就产生了一个独特的输卵管3D模型,它是基于组织学切片的测量结果,因此是基于现实的。GPU用于图像处理和基于粒子物理的模拟的处理器密集型操作,大大减少了生成完整模型所需的时间。使用这种技术创建的一组模型被用来研究输卵管环境的3D结构对精子运输和导航的影响。
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引用次数: 0
GPU-PRISM: An Extension of PRISM for General Purpose Graphics Processing Units GPU-PRISM:用于通用图形处理单元的PRISM扩展
Pub Date : 2010-09-30 DOI: 10.1109/PDMC-HIBI.2010.11
D. Bosnacki, S. Edelkamp, Damian Sulewski, Anton Wijs
We present an extension of the model checker PRISM for (general purpose) graphics processing units (GPUs). The extension is based on parallel algorithms for probabilistic model checking which are tuned for GPUs. In particular, we parallelize the parts of the algorithms that boil down to linear algebraic operations, like solving systems of linear equations and matrix vector multiplication. These computations are performed very efficiently on GPGPUs which results inconsiderable runtime improvements compared to the standard versions of PRISM. We evaluated the extension of PRISM on several case studies in which we observed significant speedup over the standard CPU implementation of the tool.
我们提出了(通用)图形处理单元(gpu)的模型检查器PRISM的扩展。扩展是基于并行算法的概率模型检查,这是调优的gpu。特别是,我们将算法的部分并行化,这些部分可以归结为线性代数运算,比如求解线性方程组和矩阵向量乘法。这些计算在gpgpu上非常有效地执行,与PRISM的标准版本相比,这导致了微不足道的运行时改进。我们在几个案例研究中评估了PRISM的扩展,在这些案例研究中,我们观察到与该工具的标准CPU实现相比有显著的加速。
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引用次数: 26
Parallel Computing Algorithms for Reverse-Engineering and Analysis of Genome-Wide Gene Regulatory Networks from Gene Expression Profiles 基于基因表达谱的全基因组基因调控网络逆向工程与分析的并行计算算法
Pub Date : 2010-09-30 DOI: 10.1109/PDMC-HIBI.2010.20
V. Belcastro, D. Bernardo, F. Gregoretti, G. Oliva
A Gene Regulatory Network links pairs of genes through an edge if they physically or functionally interact."Reverse engineering", a gene regulatory network means to infer the edges between genes from the available experimental data. Transcriptional responses (i.e. gene expression profiles obtained through micro array experiments) are often used to reverse-engineer a network of genes. Reverse-engineering consists in analyzing transcriptional responses to a set of treatments and adding an edge between genes if their expressions show a coordinated behavior on a subset of the treatments, according to some underlying model of gene regulation. Mammalian cells contain tens of thousands of genes, and it is necessary to analyze hundreds of transcriptional responses in order to have acceptable statistical evidence of interactions between genes. There currently exist several ready-to-use software packages able to infer gene networks, but few can be used to infer large-size networks from thousands of transcriptional responses as the dimension of the problem leads to high computational costs and memory requirements. We propose to exploit parallel computing techniques to overcome this problem. In this work, we designed and developed a parallel computing algorithm to reverse engineer large-scale gene regulatory networks from tens of thousands of gene expression profiles. The algorithm is based on computing pair-wise Mutual Information between each gene-pair. We successfully tested it to infer the Mus Musculus (mouse) gene regulatory network in liver from 312 expression profiles collected from a public Internet repository. Each profile measures the expression of 45,101 genes (more specifically, transcripts). We analyzed all of the possible gene-pairs for a total amount of about 1 billion identifying about 60 millions edges. We used a hierarchical clustering algorithm to discover communities within the gene network, and found a modular structure that highlights genes involved in the same biological functions.
如果一对基因在物理上或功能上相互作用,基因调控网络通过边缘将它们连接起来。“逆向工程”,一个基因调控网络意味着从现有的实验数据中推断出基因之间的边缘。转录反应(即通过微阵列实验获得的基因表达谱)通常用于对基因网络进行逆向工程。逆向工程包括分析对一系列处理的转录反应,如果它们的表达在处理的一个子集上显示出协调的行为,那么根据一些潜在的基因调控模型,在基因之间添加一个边缘。哺乳动物细胞包含数以万计的基因,有必要分析数以百计的转录反应,以便有可接受的基因之间相互作用的统计证据。目前有几个现成的软件包能够推断基因网络,但很少有软件可以从数千个转录反应中推断出大规模的网络,因为这个问题的规模导致了高计算成本和内存需求。我们建议利用并行计算技术来克服这个问题。在这项工作中,我们设计并开发了一种并行计算算法,从数万个基因表达谱中对大规模基因调控网络进行逆向工程。该算法基于计算每个基因对之间的成对互信息。我们成功地对其进行了测试,从公共互联网存储库收集的312个表达谱中推断出肝脏中的小家鼠(小鼠)基因调控网络。每个剖面测量45101个基因的表达(更具体地说,转录本)。我们分析了所有可能的基因对,总共有大约10亿对,确定了大约6000万条边。我们使用分层聚类算法来发现基因网络中的社区,并发现了一个模块化结构,突出了涉及相同生物功能的基因。
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引用次数: 1
HMMlib: A C++ Library for General Hidden Markov Models Exploiting Modern CPUs 利用现代cpu的通用隐马尔可夫模型的c++库
Pub Date : 2010-09-30 DOI: 10.1109/PDMC-HIBI.2010.24
Andreas Sand, Christian N. S. Pedersen, T. Mailund, Asbjorn Tolbol Brask
We present a C++ library for constructing and analyzing general hidden Markov models. The library consists of a number of template classes and generic functions, parameterized with the precision of floating point types and different types of hardware acceleration.
我们提出了一个c++库来构造和分析一般的隐马尔可夫模型。该库由许多模板类和泛型函数组成,使用浮点类型的精度和不同类型的硬件加速进行参数化。
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引用次数: 18
A Decidable Characterization of a Graphical Pi-calculus with Iterators 一类具有迭代器的图形pi -微积分的可定刻划
Pub Date : 2010-09-21 DOI: 10.4204/EPTCS.39.4
F. Peschanski, Hanna Klaudel, Raymond R. Devillers
This paper presents the Pi-graphs, a visual paradigm for the modelling and verification of mobile systems. The language is a graphical variant of the Pi-calculus with iterators to express non-terminating behaviors. The operational semantics of Pi-graphs use ground notions of labelled transition and bisimulation, which means standard verification techniques can be applied. We show that bisimilarity is decidable for the proposed semantics, a result obtained thanks to an original notion of causal clock as well as the automatic garbage collection of unused names.
本文介绍了pi图,一种用于移动系统建模和验证的可视化范例。该语言是pi演算的图形化变体,使用迭代器来表达非终止行为。pi -graph的操作语义使用标记转换和双仿真的基本概念,这意味着可以应用标准验证技术。我们表明,对于所提出的语义,双相似性是可确定的,这一结果得益于因果时钟的原始概念以及未使用名称的自动垃圾收集。
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引用次数: 2
An Inverse Method for Policy-Iteration Based Algorithms 一种基于策略迭代算法的逆方法
Pub Date : 2009-11-17 DOI: 10.4204/EPTCS.10.4
L. Fribourg, É. André
We present an extension of two policy-iteration based algorithms on weighted graphs (viz., Markov Decision Problems and Max-Plus Algebras). This extension allows us to solve the following inverse problem: considering the weights of the graph to be unknown constants or parameters, we suppose that a reference instantiation of those weights is given, and we aim at computing a constraint on the parameters under which an optimal policy for the reference instantiation is still optimal. The original algorithm is thus guaranteed to behave well around the reference instantiation, which provides us with some criteria of robustness. We present an application of both methods to simple examples. A prototype implementation has been done.
我们提出了两种基于策略迭代的加权图算法(即马尔可夫决策问题和Max-Plus代数)的扩展。这个扩展允许我们解决以下反问题:考虑到图的权重是未知的常量或参数,我们假设这些权重的参考实例化是给定的,我们的目标是计算一个参数约束,在这个参数约束下,参考实例化的最优策略仍然是最优的。从而保证了原始算法在引用实例化周围的良好行为,为我们提供了一些鲁棒性准则。我们给出了两种方法在简单例子中的应用。已经完成了原型实现。
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引用次数: 6
On external presentations of infinite graphs 论无穷图的外部表示
Pub Date : 2009-11-17 DOI: 10.4204/EPTCS.10.2
Christophe Morvan
The vertices of a finite state system are usually a subset of the natural numbers. Most algorithms relative to these systems only use this fact to select vertices. For infinite state systems, however, the situation is different: in particular, for such systems having a finite description, each state of the system is a configuration of some machine. Then most algorithmic approaches rely on the structure of these configurations. Such characterisations are said internal. In order to apply algorithms detecting a structural property (like identifying connected components) one may have first to transform the system in order to fit the description needed for the algorithm. The problem of internal characterisation is that it hides structural properties, and each solution becomes ad hoc relatively to the form of the configurations. On the contrary, external characterisations avoid explicit naming of the vertices. Such characterisation are mostly defined via graph transformations. In this paper we present two kind of external characterisations: deterministic graph rewriting, which in turn characterise regular graphs, deterministic context-free languages, and rational graphs. Inverse substitution from a generator (like the complete binary tree) provides characterisation for prefix-recognizable graphs, the Caucal Hierarchy and rational graphs. We illustrate how these characterisation provide an efficient tool for the representation of infinite state systems.
有限状态系统的顶点通常是自然数的一个子集。与这些系统相关的大多数算法只使用这一事实来选择顶点。然而,对于无限状态系统,情况是不同的:特别是,对于具有有限描述的系统,系统的每个状态都是某个机器的配置。然后,大多数算法方法依赖于这些配置的结构。这种特征被称为内部特征。为了应用检测结构属性的算法(如识别连接的组件),可能首先要对系统进行转换,以适应算法所需的描述。内部表征的问题在于它隐藏了结构属性,并且每个解决方案相对于配置的形式都变得特别。相反,外部特征避免了对顶点的显式命名。这样的刻画主要是通过图变换来定义的。在本文中,我们提出了两种外部表征:确定性图重写,它们反过来表征正则图、确定性上下文无关语言和有理图。来自生成器的逆代换(如完全二叉树)为前缀可识别的图、caual Hierarchy和有理图提供了表征。我们说明了这些表征如何为无限状态系统的表示提供了有效的工具。
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引用次数: 1
A Tighter Bound for the Determinization of Visibly Pushdown Automata 确定可见下推自动机的一个更紧界
Pub Date : 2009-11-17 DOI: 10.4204/EPTCS.10.5
Nguyen Van Tang
Visibly pushdown automata (VPA), introduced by Alur and Madhusuan in 2004, is a subclass of pushdown automata whose stack behavior is completely determined by the input symbol according to a fixed partition of the input alphabet. Since its introduce, VPAs have been shown to be useful in various context, e.g., as specification formalism for verification and as automaton model for processing XML streams. Due to high complexity, however, implementation of formal verification based on VPA framework is a challenge. In this paper we consider the problem of implementing VPA-based model checking algorithms. For doing so, we first present an improvement on upper bound for determinization of VPA. Next, we propose simple on-the-fly algorithms to check universality and inclusion problems of this automata class. Then, we implement the proposed algorithms in a prototype tool. Finally, we conduct experiments on randomly generated VPAs. The experimental results show that the proposed algorithms are considerably faster than the standard ones.
可见下推自动机(visible pushdown automata, VPA)由Alur和Madhusuan于2004年提出,它是下推自动机的一个子类,其堆栈行为完全由输入符号根据输入字母表的固定划分来决定。自引入以来,vpa已被证明在各种上下文中都很有用,例如,作为验证的规范形式和处理XML流的自动模型。然而,由于VPA框架的高复杂性,实现形式化验证是一个挑战。本文研究了基于vpa的模型检验算法的实现问题。为此,我们首先提出了确定VPA的上界的改进。接下来,我们提出了简单的实时算法来检验这类自动机的通用性和包容性问题。然后,我们在原型工具中实现了所提出的算法。最后,我们对随机生成的vpa进行了实验。实验结果表明,所提算法的速度明显快于标准算法。
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引用次数: 14
Automated Predicate Abstraction for Real-Time Models 实时模型的自动谓词抽象
Pub Date : 2009-11-01 DOI: 10.4204/EPTCS.10.3
Bahareh Badban, S. Leue, J. Smaus
Introduction Model checking has been widely successful in validating and debugging hardware de- signs and communication protocols. However, state-space explosion is an intrinsic problem which limits the applicability of model checking tools. To overcome this limitation software model checkers have suggested different approaches, among which abstraction methods have been highly esteemed. modern techniques. Among others, predicate abstraction is a prominent technique which has been widely used in modern model checking. This technique has been shown to enhance the effectiveness of the reachability computation technique in infinite-state systems. In this te chnique an infinite-state system is represented abstractly by a finite-state system, where states of the abst ract model correspond to the truth valuations of a chosen set of atomic predicates. Predicate abstraction was first introduced in (8) as a method for auto- matically determining invariant properties of infinite-st ate systems. This technique involves abstracting a concrete transition system using a set of formulas called predicates which usually denote some state properties of the concrete system. The practical applicability of predicate abstraction is im peded by two problems. First, predicates need to be provided manually (11, 7). This means that the selection of appropriate abstraction predicates is based on a user-driven trial-and-error process. The high degree of user intervention also stands in the way of a seamless integration into practical software development processes. Second, very often the abstraction is too coarse in order to allow relevant system properties to be verified. This calls for abstrac- tion refinement (6), often following a counterexample guide d abstraction refinement scheme (5, 3). Real time models are one example of systems with a large state space as time adds much complexity to the system. In this event, recently there have been increasing number of research to provide a means for the abstraction of such models. It is the objective of this paper to provide support for an automated predicate abstraction technique for concurrent dense real-time models according to the timed automaton model of (1). We propose a method to generate an efficient set of pred icates than a manual, ad-hoc process would be able to provide. We use the results from our recent work (2) to analyze the behavior of the system under verification to discover its local state invari ants and to remove transitions that can never be traversed. We then describe a method to compute a predicate abstraction based on these state invariants. We use information regarding the control state labels as well as the newly computed invariants in the considered control states when determining the abstraction predicates. We have developed a prototype
模型检查在验证和调试硬件设计和通信协议方面已经取得了广泛的成功。然而,状态空间爆炸是一个固有的问题,限制了模型检验工具的适用性。为了克服这一限制,软件模型检查人员提出了不同的方法,其中抽象方法受到高度重视。现代技术。其中,谓词抽象是一种突出的技术,在现代模型检测中得到了广泛的应用。该方法提高了可达性计算技术在无限状态系统中的有效性。在这种技术中,无限状态系统被抽象地表示为有限状态系统,其中抽象模型的状态对应于一组选定的原子谓词的真值。谓词抽象在(8)中首次被引入,作为一种自动确定无限状态系统不变性质的方法。该技术涉及使用一组称为谓词的公式抽象具体的转换系统,谓词通常表示具体系统的一些状态属性。谓词抽象的实际适用性受到两个问题的制约。首先,需要手动提供谓词(11,7)。这意味着选择适当的抽象谓词是基于用户驱动的试错过程。高度的用户干预也阻碍了与实际软件开发过程的无缝集成。其次,为了验证相关的系统属性,通常抽象过于粗糙。这需要抽象细化(6),通常遵循反例指导抽象细化方案(5,3)。实时模型是具有大状态空间的系统的一个例子,因为时间增加了系统的复杂性。在这种情况下,最近有越来越多的研究为这种模型的抽象提供了一种方法。本文的目标是根据(1)的时间自动机模型,为并发密集实时模型的自动谓词抽象技术提供支持。我们提出了一种方法来生成一组有效的谓词,而不是手动的,特别的过程能够提供。我们使用我们最近工作(2)的结果来分析验证下系统的行为,以发现其局部状态不变性,并删除永远无法遍历的转换。然后,我们描述了一种基于这些状态不变量计算谓词抽象的方法。在确定抽象谓词时,我们使用有关控制状态标签的信息以及在考虑的控制状态中新计算的不变量。我们已经开发了一个原型
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引用次数: 4
More infinite results 更多无限结果
Pub Date : 2001-05-01 DOI: 10.1016/S1571-0661(05)80680-2
Olaf Burkart, J. Esparza
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引用次数: 64
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Infinity
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