{"title":"Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space","authors":"T. Gagie, G. Navarro, N. Prezza","doi":"10.1145/3375890","DOIUrl":"https://doi.org/10.1145/3375890","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"70 1","pages":"1 - 54"},"PeriodicalIF":0.0,"publicationDate":"2018-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83790121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"General Belief Revision","authors":"J. Delgrande, P. Peppas, S. Woltran","doi":"10.1145/3203409","DOIUrl":"https://doi.org/10.1145/3203409","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"55 1","pages":"1 - 34"},"PeriodicalIF":0.0,"publicationDate":"2018-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84819320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Benjamin Lucien Kaminski, J. Katoen, C. Matheja, Federico Olmedo
{"title":"Weakest Precondition Reasoning for Expected Runtimes of Randomized Algorithms","authors":"Benjamin Lucien Kaminski, J. Katoen, C. Matheja, Federico Olmedo","doi":"10.1145/3208102","DOIUrl":"https://doi.org/10.1145/3208102","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"45 1","pages":"1 - 68"},"PeriodicalIF":0.0,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90582667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Parameterized Complexity of the k-Biclique Problem","authors":"Bingkai Lin","doi":"10.1145/3212622","DOIUrl":"https://doi.org/10.1145/3212622","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"1 1","pages":"1 - 23"},"PeriodicalIF":0.0,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81814183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Cost of Unknown Diameter in Dynamic Networks","authors":"Haifeng Yu, Yuda Zhao, Irvan Jahja","doi":"10.1145/3209665","DOIUrl":"https://doi.org/10.1145/3209665","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"104 1","pages":"1 - 34"},"PeriodicalIF":0.0,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79222859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wojciech Czerwinski, W. Martens, Matthias Niewerth, P. Parys
{"title":"Minimization of Tree Patterns","authors":"Wojciech Czerwinski, W. Martens, Matthias Niewerth, P. Parys","doi":"10.1145/3180281","DOIUrl":"https://doi.org/10.1145/3180281","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"2674 1","pages":"1 - 46"},"PeriodicalIF":0.0,"publicationDate":"2018-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89485170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Optimal Multi-Way Number Partitioning","authors":"Ethan L. Schreiber","doi":"10.1145/3184400","DOIUrl":"https://doi.org/10.1145/3184400","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"90 1","pages":"1 - 61"},"PeriodicalIF":0.0,"publicationDate":"2018-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79739466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Invited Article Foreword","authors":"É. Tardos","doi":"10.1145/3231052","DOIUrl":"https://doi.org/10.1145/3231052","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"69 1","pages":"1 - 61"},"PeriodicalIF":0.0,"publicationDate":"2018-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72919292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Silence","authors":"G. Goren, Y. Moses","doi":"10.1145/3377883","DOIUrl":"https://doi.org/10.1145/3377883","url":null,"abstract":"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","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"12 1","pages":"1 - 26"},"PeriodicalIF":0.0,"publicationDate":"2018-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75189122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Tight Bounds for Undirected Graph Exploration with Pebbles and Multiple Agents","authors":"Y. Disser, J. Hackfeld, Max Klimm","doi":"10.1145/3356883","DOIUrl":"https://doi.org/10.1145/3356883","url":null,"abstract":"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.","PeriodicalId":17199,"journal":{"name":"Journal of the ACM (JACM)","volume":"454 1","pages":"1 - 41"},"PeriodicalIF":0.0,"publicationDate":"2018-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76769015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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