This research is supported by Academy of Finland through grant 319454 and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 690941
发表信息：
SOFSEM 2020: Theory and Practice of Computer Science
We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on the distance allowed between subpatterns. VLG patterns have numerous applications in computational biology (motif search), information retrieval (e.g., for language models, snippet generation, machine translation) and capture a useful subclass of the regular expressions commonly used in practice for searching source code. Our best approach provides search speeds several times faster than prior art across a broad range of patterns and texts.
The dictionary matching with gaps problem is to preprocess a dictionary $D$ of $d$ gapped patterns $P_1,\ldots,P_d$ over alphabet $Σ$, where each gapped pattern $P_i$ is a sequence of subpatterns separated by bounded sequences of don't cares. Then, given a query text $T$ of length $n$ over alphabet $Σ$, the goal is to output all locations in $T$ in which a pattern $P_i\in D$, $1\leq i\leq d$, ends. There is a renewed current interest in the gapped matching problem stemming from cyber security. In this paper we solve the problem where all patterns in the dictionary have one gap with at least $α…
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al. We introduce a formalism, called search schemes, to specify search strategies of this type, then develop a probabilistic measure for the efficiency of a search scheme, prove several combinatorial results on efficient search schemes, and finally, provide experimental computations supporting the superiority of our strategies.
For the first time we provide a succinct pattern matching index for arbitrary graphs that can be built in polynomial time, which requires less space and answers queries more efficiently than the one in [SODA 2021]. We show that, given an edge-labeled graph $ G = (V, E) $, there exists a data structures of $|E /_{\le_G}|(\lceil \log|Σ|\rceil + \lceil\log q\rceil + 2)\cdot (1+o(1)) + |V /_{\le_G}|\cdot (1+o(1))$ bits which can be built in $ O(|E|^2 + |V /_{\le_G}|^{5 / 2}) $ time and supports pattern matching on $ G $ in $O(|P| \cdot q^2 \cdot \log(q\cdot |Σ|))$ time, where $ G /_{\le_G} = (V /_…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting queries (return all positions where the pattern occurs), and counting queries (return the number of occurrences of the pattern). In this paper we consider a variant of string indexing, where the goal is to compactly represent the string such that given two patterns P1 and P2 and a gap range [α,β] we can quickly find the consecutive occurrences of P1 and P2 with d…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same relative order as the pattern elements. For this problem we consider the offline version in which we build an index for the reference sequence so that subsequent searches can be completed very efficiently. We propose a space-efficient index that works well in practice despite its lack of good worst-case time bounds. Our solution is based on the new approach of deco…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such that each elastic-degenerate symbol corresponds to a set of two or more variable length strings. Here, we present an algorithm for solving the pattern matching problem with (solid) pattern and elastic-degenerate text, running in O(N+αγnm) time; where m is the length of the given pattern; n and N are the length and total size of the given elastic-degenerate t…
U-index: A Universal Indexing Framework for Matching Long Patterns
Brunel University London（布鲁内尔伦敦大学）；Università di Palermo（巴勒莫大学）；ETH Zurich（苏黎世联邦理工学院）；King’s College London（伦敦国王学院）；University of Maryland, College Park（马里兰大学帕克分校）；Ca’ Foscari University of Venice（威尼斯卡福斯卡里大学）；ISTI-CNR（意大利国家研究委员会信息科学技术研究所）；CWI（荷兰数学和计算机科学研究学会）；Vrije Universiteit, Amsterdam（阿姆斯特丹自由大学）
An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of indexing arbitrary finite automata. Our solution consists in finding a partial co-lexicographic order of the states and proving, as in the total order case, that states reached by a given string form one interval on the partial order, thus enabling indexing. We provide a lower bound stating that such an interval requires $O(p)$ words to be represented, $p$ be…
Document listing on string collections is the task of finding all documents where a pattern appears. It is regarded as the most fundamental document retrieval problem, and is useful in various applications. Many of the fastest-growing string collections are composed of very similar documents, such as versioned code and document collections, genome repositories, etc. Plain pattern-matching indexes designed for repetitive text collections achieve orders-of-magnitude reductions in space. Instead, there are not many analogous indexes for document retrieval. In this paper we present a simple docume…
