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Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space 全功能后缀树与bwt运行有界空间中的最优文本搜索
Pub Date : 2018-09-08 DOI: 10.1145/3375890
T. Gagie, G. Navarro, N. Prezza
Indexing highly repetitive texts—such as genomic databases, software repositories and versioned text collections—has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is r, the number of runs in their Burrows-Wheeler Transforms (BWTs). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used O(r) space and was able to efficiently count the number of occurrences of a pattern of length m in a text of length n (in O(m log log n) time, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of r. In this article, we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the occ occurrences efficiently (in O(occ log log n) time) within O(r) space. By raising the space to O(r log log n), our index counts the occurrences in optimal time, O(m), and locates them in optimal time as well, O(m + occ). By further raising the space by an O(w/ log σ) factor, where σ is the alphabet size and w = Ω (log n) is the RAM machine size in bits, we support count and locate in O(⌈ m log (σ)/w ⌉) and O(⌈ m log (σ)/w ⌉ + occ) time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using O(r log (n/r)) space that replaces the text and extracts any text substring of length ℓ in the almost-optimal time O(log (n/r)+ℓ log (σ)/w). Within that space, we similarly provide access to arbitrary suffix array, inverse suffix array, and longest common prefix array cells in time O(log (n/r)), and extend these capabilities to full suffix tree functionality, typically in O(log (n/r)) time per operation. Our experiments show that our O(r)-space index outperforms the space-competitive alternatives by 1--2 orders of magnitude in time. Competitive implementations of the original FM-index are outperformed by 1--2 orders of magnitude in space and/or 2--3 in time.
自世纪之交以来,索引高度重复的文本(如基因组数据库、软件库和版本化的文本集合)已成为一个重要问题。对于重复文本,一个相关的可压缩性度量是r,即它们的Burrows-Wheeler变换(BWTs)的运行次数。最早用于重复集合的索引之一是Run-Length FM-index,它使用O(r)空间,能够有效地计算长度为m的模式在长度为n的文本中出现的次数(使用当前技术需要O(m log log n)时间)。然而,它无法在以r为界的空间内有效地定位这些事件的位置。在本文中,我们解决了这个长期存在的问题,展示了如何扩展Run-Length FM-index,以便它能够在O(r)空间内有效地定位occ事件(在O(occ log log n)时间内)。通过将空间提升到O(r log log n),我们的索引计算在最优时间(O(m))内出现的次数,并将它们定位在最优时间(O(m + occ))内。通过将空间进一步提高一个O(w/ log σ)因子,其中σ为字母表大小,w = Ω (log n)为RAM机器大小(以位为单位),我们支持计数和定位于O(≤≤m log (σ)/w²)和O(≤≤m log (σ)/w²+ occ)时间,这在填充设置中是最优的,在压缩空间中是没有得到的。我们还描述了一个使用O(r log (n/r))空间的结构,该结构替换文本并在几乎最优的时间O(log (n/r)+ r log (σ)/w)内提取长度为r的任何文本子串。在该空间内,我们同样提供对任意后缀数组、逆后缀数组和最长公共前缀数组单元的访问,时间为O(log (n/r)),并将这些功能扩展为完整的后缀树功能,每次操作通常需要O(log (n/r))时间。我们的实验表明,我们的O(r)空间指数在时间上优于空间竞争方案1- 2个数量级。原始fm指数的竞争实现在空间上优于1- 2个数量级,在时间上优于2- 3个数量级。
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引用次数: 129
General Belief Revision 一般信念修正
Pub Date : 2018-09-07 DOI: 10.1145/3203409
J. Delgrande, P. Peppas, S. Woltran
In artificial intelligence, a key question concerns how an agent may rationally revise its beliefs in light of new information. The standard (AGM) approach to belief revision assumes that the underlying logic contains classical propositional logic. This is a significant limitation, since many representation schemes in AI don’t subsume propositional logic. In this article, we consider the question of what the minimal requirements are on a logic, such that the AGM approach to revision may be formulated. We show that AGM-style revision can be obtained even when extremely little is assumed of the underlying language and its semantics; in fact, one requires little more than a language with sentences that are satisfied at models, or possible worlds. The classical AGM postulates are expressed in this framework and a representation result is established between the postulate set and certain preorders on possible worlds. To obtain the representation result, we add a new postulate to the AGM postulates, and we add a constraint to preorders on worlds. Crucially, both of these additions are redundant in the original AGM framework, and so we extend, rather than modify, the AGM approach. As well, iterated revision is addressed and the Darwiche/Pearl postulates are shown to be compatible with our approach. Various examples are given to illustrate the approach, including Horn clause revision, revision in extended logic programs, and belief revision in a very basic logic called literal revision.
在人工智能领域,一个关键问题是智能体如何根据新信息理性地修正其信念。信念修正的标准(AGM)方法假定底层逻辑包含经典命题逻辑。这是一个重要的限制,因为AI中的许多表示方案不包含命题逻辑。在本文中,我们考虑的问题是逻辑上的最小需求是什么,这样就可以制定AGM方法进行修订。我们证明,即使对底层语言及其语义的假设很少,也可以获得agm风格的修订;事实上,人们只需要一种语言,它的句子满足模型或可能世界的要求。在此框架中对经典的AGM公设进行了表达,并建立了公设集与可能世界上某些预定值之间的表示结果。为了得到表示结果,我们在AGM公设上增加了一个新的公设,并对世界上的预定量增加了一个约束。至关重要的是,这两个附加内容在原始的AGM框架中都是冗余的,因此我们扩展而不是修改AGM方法。此外,还讨论了迭代修订,并证明了达尔文/珀尔假设与我们的方法是兼容的。给出了各种例子来说明这种方法,包括霍恩子句修正,扩展逻辑程序中的修正,以及称为文字修正的非常基本逻辑中的信念修正。
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引用次数: 15
Weakest Precondition Reasoning for Expected Runtimes of Randomized Algorithms 随机算法预期运行时间的最弱前提推理
Pub Date : 2018-08-29 DOI: 10.1145/3208102
Benjamin Lucien Kaminski, J. Katoen, C. Matheja, Federico Olmedo
This article presents a wp--style calculus for obtaining bounds on the expected runtime of randomized algorithms. Its application includes determining the (possibly infinite) expected termination time of a randomized algorithm and proving positive almost--sure termination—does a program terminate with probability one in finite expected time? We provide several proof rules for bounding the runtime of loops, and prove the soundness of the approach with respect to a simple operational model. We show that our approach is a conservative extension of Nielson’s approach for reasoning about the runtime of deterministic programs. We analyze the expected runtime of some example programs including the coupon collector’s problem, a one--dimensional random walk and a randomized binary search.
本文提出了一种wp- style的计算方法,用于获得随机化算法的期望运行时边界。它的应用包括确定随机算法的(可能是无限的)预期终止时间,并证明几乎是肯定的终止——程序是否在有限的预期时间内以概率1终止?我们提供了几个循环运行时边界的证明规则,并在一个简单的操作模型上证明了该方法的正确性。我们表明,我们的方法是一个保守的扩展尼尔森的方法的推理关于确定性程序的运行时间。我们分析了一些示例程序的期望运行时间,包括优惠券收集问题、一维随机漫步和随机二分搜索。
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引用次数: 56
The Parameterized Complexity of the k-Biclique Problem k-比克形问题的参数化复杂度
Pub Date : 2018-08-29 DOI: 10.1145/3212622
Bingkai Lin
Given a graph G and an integer k, the k-Biclique problem asks whether G contains a complete bipartite subgraph with k vertices on each side. Whether there is an f(k) ċ |G|O(1)-time algorithm, solving k-Biclique for some computable function f has been a longstanding open problem. We show that k-Biclique is W[1]-hard, which implies that such an f(k) ċ |G|O(1)-time algorithm does not exist under the hypothesis W[1] ≠ FPT from parameterized complexity theory. To prove this result, we give a reduction which, for every n-vertex graph G and small integer k, constructs a bipartite graph H = (L⊍ R,E) in time polynomial in n such that if G contains a clique with k vertices, then there are k(k − 1)/2 vertices in L with nθ(1/k) common neighbors; otherwise, any k(k − 1)/2 vertices in L have at most (k+1)! common neighbors. An additional feature of this reduction is that it creates a gap on the right side of the biclique. Such a gap might have further applications in proving hardness of approximation results. Assuming a randomized version of Exponential Time Hypothesis, we establish an f(k) ċ |G|o(√k)-time lower bound for k-Biclique for any computable function f. Combining our result with the work of Bulatov and Marx [2014], we obtain a dichotomy classification of the parameterized complexity of cardinality constraint satisfaction problems.
给定一个图G和一个整数k, k- biclique问题问的是G是否包含一个每边有k个顶点的完全二部子图。是否有一个f (k)ċ| | G O(1)算法,解决k-Biclique对于一些可计算函数f是一个长期的开放问题。我们从参数化复杂性理论证明了k- biclique是W[1]-hard的,这意味着在W[1]≠FPT的假设下,f(k) * |G|O(1)时间算法不存在。为了证明这一结果,我们给出了一个约简,对于每一个n顶点图G和小整数k,在n的时间多项式上构造一个二部图H = (L R,E),使得如果G包含有k个顶点的团,则L中有k(k−1)/2个顶点具有nθ(1/k)个共邻;否则,L中的任何k(k−1)/2个顶点最多有(k+1)!常见的邻居。这种减少的另一个特点是,它在自行车的右侧产生一个间隙。这种差距可能在证明近似结果的硬度方面有进一步的应用。假设随机版本的指数时间的假设,我们建立一个f (k)ċ| | G o(√k) -下界为k-Biclique任何可计算函数f。将我们的结果与Bulatov和马克思的工作[2014],我们获得一个二分法分类的参数化基数约束满足问题的复杂性。
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引用次数: 36
The Cost of Unknown Diameter in Dynamic Networks 动态网络中未知直径的代价
Pub Date : 2018-08-29 DOI: 10.1145/3209665
Haifeng Yu, Yuda Zhao, Irvan Jahja
For dynamic networks with unknown diameter, we prove novel lower bounds on the time complexity of a range of basic distributed computing problems. Together with trivial upper bounds under dynamic networks with known diameter for these problems, our lower bounds show that the complexities of all these problems are sensitive to whether the diameter is known to the protocol beforehand: Not knowing the diameter increases the time complexities by a large poly(N) factor as compared to when the diameter is known, resulting in an exponential gap. Our lower bounds are obtained via communication complexity arguments and by reducing from the two-party DisjointnessCP problem. We further prove that sometimes this large poly(N) cost can be completely avoided if the protocol is given a good estimate on N. In other words, having such an estimate makes some problems no longer sensitive to unknown diameter.
对于直径未知的动态网络,我们证明了一系列基本分布式计算问题的时间复杂度的下界。与这些问题在已知直径的动态网络下的微不足道的上界一起,我们的下界表明,所有这些问题的复杂性对协议是否事先已知直径很敏感:与直径已知时相比,不知道直径会使时间复杂性增加一个大的poly(N)因子,从而导致指数差距。我们的下界是通过对通信复杂度的论证和对两方不连接问题的约简得到的。我们进一步证明,如果协议给出一个很好的N估计,有时可以完全避免这种大的poly(N)代价。换句话说,有了这样的估计,一些问题对未知直径不再敏感。
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引用次数: 4
Minimization of Tree Patterns 最小化树的图案
Pub Date : 2018-07-25 DOI: 10.1145/3180281
Wojciech Czerwinski, W. Martens, Matthias Niewerth, P. Parys
Many of today’s graph query languages are based on graph pattern matching. We investigate optimization of tree-shaped patterns that have transitive closure operators. Such patterns not only appear in the context of graph databases but also were originally studied for querying tree-structured data, where they can perform child, descendant, node label, and wildcard tests. The minimization problem aims at reducing the number of nodes in patterns and goes back to the early 2000s. We provide an example showing that, in contrast to earlier claims, tree patterns cannot be minimized by deleting nodes only. The example resolves the M =? NR problem, which asks if a tree pattern is minimal if and only if it is nonredundant. The example can be adapted to prove that minimization is ΣP2-complete, which resolves another question that was open since the early research on the problem. The latter result shows that, unless NP = ΠP2, more general approaches for minimizing tree patterns are also bound to fail in general.
今天的许多图查询语言都是基于图模式匹配的。我们研究了具有传递闭包操作符的树形模式的优化。这样的模式不仅出现在图数据库的上下文中,而且最初是为查询树结构数据而研究的,其中它们可以执行子、后代、节点标签和通配符测试。最小化问题旨在减少模式中的节点数量,这可以追溯到21世纪初。我们提供的示例表明,与前面的声明相反,树模式不能仅通过删除节点来最小化。这个例子解决了M =?NR问题,问一个树模式是否最小当且仅当它是非冗余的。这个例子可以用来证明最小化是ΣP2-complete,这解决了另一个问题,因为这个问题的早期研究是开放的。后一个结果表明,除非NP = ΠP2,否则用于最小化树模式的更一般的方法通常也注定会失败。
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引用次数: 8
Optimal Multi-Way Number Partitioning 最优多路数字分区
Pub Date : 2018-07-25 DOI: 10.1145/3184400
Ethan L. Schreiber
The NP-hard number-partitioning problem is to separate a multiset S of n positive integers into k subsets such that the largest sum of the integers assigned to any subset is minimized. The classic application is scheduling a set of n jobs with different runtimes on k identical machines such that the makespan, the elapsed time to complete the schedule, is minimized. The two-way number-partitioning decision problem is one of the original 21 problems that Richard Karp proved NP-complete. It is also one of Garey and Johnson’s six fundamental NP-complete problems and the only one based on numbers. This article explores algorithms for solving multi-way number-partitioning problems optimally. We explore previous algorithms as well as our own algorithms, which fall into three categories: sequential number partitioning (SNP), a branch-and-bound algorithm; binary-search improved bin completion (BSIBC), a bin-packing algorithm; and cached iterative weakening (CIW), an iterative weakening algorithm. We show experimentally that, for large random numbers, SNP and CIW are state-of-the-art algorithms depending on the values of n and k. Both algorithms outperform the previous state of the art by up to seven orders of magnitude in terms of runtime.
NP-hard数字划分问题是将n个正整数的多集S分成k个子集,使得分配给任意子集的整数的最大和最小。经典的应用程序是在k台相同的机器上调度一组n个具有不同运行时的作业,以便最小化makespan(完成调度所花费的时间)。双向数字划分决策问题是Richard Karp最早证明np完全的21个问题之一。它也是gary和Johnson的六个基本np完全问题之一,也是唯一一个基于数字的np完全问题。本文探讨了最优地解决多路数字划分问题的算法。我们探索了以前的算法以及我们自己的算法,它们分为三类:序列号划分(SNP),一种分支定界算法;二叉搜索改进箱补全(BSIBC),一种装箱算法;缓存迭代弱化(CIW),一种迭代弱化算法。我们通过实验证明,对于大随机数,SNP和CIW是最先进的算法,取决于n和k的值。就运行时间而言,这两种算法的性能都比以前的最先进的算法高出七个数量级。
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引用次数: 55
Invited Article Foreword 特邀文章前言
Pub Date : 2018-07-25 DOI: 10.1145/3231052
É. Tardos
The Invited Article section of this issue consists of the article “Minimization of Tree Patterns” by Wojciech Czerwiński, Wim Martens, Matthias Niewerth, and Paweł Parys, which was invited from the 35th Annual ACM Symposium on Principles of Distributed Computing (PODC’16). We want to thank the PODC’16 Program Committee, the PC chair Wang-Chiew Tan, and JACM editor Georg Gottlob for their help in selecting this invited article, and editor Dan Suciu for handling the article.
本期的特邀文章部分由Wojciech Czerwiński, Wim Martens, Matthias Niewerth和paweowparys的文章“最小化树模式”组成,这篇文章来自第35届ACM分布式计算原理研讨会(PODC ' 16)。我们要感谢PODC ' 16项目委员会,PC主席Wang-Chiew Tan和JACM编辑Georg Gottlob在选择这篇特邀文章方面的帮助,以及编辑Dan Suciu对这篇文章的处理。
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引用次数: 0
Silence 沉默
Pub Date : 2018-07-23 DOI: 10.1145/3377883
G. Goren, Y. Moses
The cost of communication is a substantial factor affecting the scalability of many distributed applications. Every message sent can incur a cost in storage, computation, energy, and bandwidth. Consequently, reducing the communication costs of distributed applications is highly desirable. The best way to reduce message costs is by communicating without sending any messages whatsoever. This article initiates a rigorous investigation into the use of silence in synchronous settings, in which processes can fail. We formalize sufficient conditions for information transfer using silence, as well as necessary conditions for particular cases of interest. This allows us to identify message patterns that enable communication through silence. In particular, a pattern called a silent choir is identified, and shown to be central to information transfer via silence in failure-prone systems. The power of the new framework is demonstrated on the atomic commitment problem (AC). A complete characterization of the tradeoff between message complexity and round complexity in the synchronous model with crash failures is provided, in terms of lower bounds and matching protocols. In particular, a new message-optimal AC protocol is designed using silence, in which processes decide in three rounds in the common case. This significantly improves on the best previously known message-optimal AC protocol, in which decisions were performed in Θ(n) rounds. And in the naked light I saw Ten thousand people, maybe more People talking without speaking … People writing songs that voices never share And no one dared Disturb the sound of silence Paul Simon, 1964
通信成本是影响许多分布式应用程序可伸缩性的一个重要因素。发送的每条消息都可能在存储、计算、能源和带宽方面产生成本。因此,减少分布式应用程序的通信成本是非常可取的。减少消息成本的最佳方法是不发送任何消息就进行通信。本文开始对同步设置中静默的使用进行严格的调查,在同步设置中,进程可能会失败。我们形式化了使用沉默传递信息的充分条件,以及特殊情况下的必要条件。这使我们能够识别通过沉默进行交流的信息模式。特别地,一种被称为沉默合唱团的模式被识别出来,并被证明是在容易发生故障的系统中通过沉默传递信息的核心。在原子承诺问题(AC)上展示了新框架的强大功能。从下限和匹配协议的角度,提供了具有崩溃故障的同步模型中消息复杂性和循环复杂性之间权衡的完整特征。特别地,设计了一种新的消息最优交流协议,该协议采用静默方式,通常情况下进程需要三轮决定。这大大改进了先前已知的最佳消息最优AC协议,其中决策以Θ(n)轮执行。在那赤裸的灯光下,我看见一万个人,也许更多的人在无声地交谈着,人们谱写着无人分享的歌曲,没有人敢去打破这寂静之声
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引用次数: 1
Tight Bounds for Undirected Graph Exploration with Pebbles and Multiple Agents 基于卵石和多智能体的无向图探索的紧边界
Pub Date : 2018-05-09 DOI: 10.1145/3356883
Y. Disser, J. Hackfeld, Max Klimm
We study the problem of deterministically exploring an undirected and initially unknown graph with n vertices either by a single agent equipped with a set of pebbles or by a set of collaborating agents. The vertices of the graph are unlabeled and cannot be distinguished by the agents, but the edges incident to a vertex have locally distinct labels. The graph is explored when all vertices have been visited by at least one agent. In this setting, it is known that for a single agent without pebbles Θ(log n) bits of memory are necessary and sufficient to explore any graph with at most n vertices. We are interested in how the memory requirement decreases as the agent may mark vertices by dropping and retrieving distinguishable pebbles or when multiple agents jointly explore the graph. We give tight results for both questions showing that for a single agent with constant memory Θ(log log n) pebbles are necessary and sufficient for exploration. We further prove that using collaborating agents instead of pebbles does not help as Θ(log log n) agents with constant memory each are necessary and sufficient for exploration. For the upper bounds, we devise an algorithm for a single agent with constant memory that explores any n-vertex graph using O(log log n) pebbles, even when n is not known a priori. The algorithm terminates after polynomial time and returns to the starting vertex. We further show that the algorithm can be realized with additional constant-memory agents rather than pebbles, implying that O(log log n) agents with constant memory can explore any n-vertex graph. For the lower bound, we show that the number of agents needed for exploring any graph with at most n vertices is already Ω(log log n) when we allow each agent to have at most O((log n)1-ε) bits of memory for any ε > 0. Our argument also implies that a single agent with sublogarithmic memory needs Θ(log log n) pebbles to explore any n-vertex graph.
我们研究了确定性地探索具有n个顶点的无向和初始未知图的问题,无论是由单个智能体配备一组鹅卵石还是由一组协作智能体。图的顶点是未标记的,不能被代理区分,但是与顶点相关的边具有局部不同的标签。当至少有一个代理访问了所有顶点时,将探索图。在这种情况下,对于没有鹅卵石Θ(log n)位内存的单个智能体来说,对于探索最多有n个顶点的任何图来说,这些内存位是必要的,也是足够的。我们感兴趣的是,当智能体通过丢弃和检索可区分的鹅卵石来标记顶点时,或者当多个智能体共同探索图时,内存需求是如何减少的。我们对这两个问题给出了严密的结果,表明对于具有恒定内存Θ(log log n)的单个代理,卵石对于探索是必要和充分的。我们进一步证明,使用协作代理而不是鹅卵石并没有帮助,因为Θ(log log n)具有恒定内存的代理对于探索来说是必要和足够的。对于上限,我们为具有恒定内存的单个代理设计了一种算法,该算法使用O(log log n)个卵石来探索任何n顶点图,即使n不是先验已知的。该算法在多项式时间后终止并返回到起始顶点。我们进一步证明,该算法可以通过额外的恒定内存代理而不是鹅卵石来实现,这意味着O(log log n)个具有恒定内存的代理可以探索任何n顶点的图。对于下界,我们表明,当我们允许每个智能体最多拥有O((log n)1-ε)位内存时,探索任何至多有n个顶点的图所需的智能体数量已经是Ω(log log n)。我们的论证还表明,具有次对数内存的单个代理需要Θ(log log n)个卵石来探索任何n顶点的图。
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引用次数: 14
期刊
Journal of the ACM (JACM)
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