Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We consider the two most fundamental string metrics: the Hamming distance and the edit distance. Under the Hamming distance, we search for substrings of $T$ that have at most $k$ mismatches with $P$, while under the edit distance, we search for substrings of $T$ that can be transformed to $P$ with at most $k$ edits.
Exact occurrences of $P$ in $T$ have a very simple structure: If we assume for simplicity that $|T| \le 3|P|/2$ and trim $T$ so that $P$ occurs both as a prefix and as a suffix of $T$, then both $P$ and $T$ are periodic with a common period. However, an analogous characterization for the structure of occurrences with up to $k$ mismatches was proved only recently by Bringmann et al. [SODA'19]: Either there are $O(k^2)$ $k$-mismatch occurrences of $P$ in $T$, or both $P$ and $T$ are at Hamming distance $O(k)$ from strings with a common period $O(m/k)$. We tighten this characterization by showing that there are $O(k)$ $k$-mismatch occurrences in the case when the pattern is not (approximately) periodic, and we lift it to the edit distance setting, where we tightly bound the number of $k$-edit occurrences by $O(k^2)$ in the non-periodic case. Our proofs are constructive and let us obtain a unified framework for approximate pattern matching for both considered distances. We showcase the generality of our framework with results for the fully-compressed setting (where $T$ and $P$ are given as a straight-line program) and for the dynamic setting (where we extend a data structure of Gawrychowski et al. [SODA'18]).
A maximum priority matching is a matching in an undirected graph that maximizes a priority score defined with respect to given vertex priorities. An earlier paper showed how to find maximum priority matchings in unweighted graphs. This paper describes an algorithm for bipartite graphs that is faster when the number of distinct priority classes is limited. For graphs with $k$ distinct priority classes it runs in $O(kmn^{1/2})$ time, where $n$ is the number of vertices in the graph and $m$ is the number of edges.
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper, we explore the opportunities for parallelization of the exact and inexact matches and present an efficient SIMD solution for the Occ portion of the algorithm. Our implementation computes all eight Occ values required for the inexact match algorithm step in a single pass. We showcase the algorithm performance in a multi-core genome aligner and discuss effects…
The Permutation Pattern Matching problem asks, given two permutations $σ$ on $n$ elements and $π$, whether $σ$ admits a subsequence with the same relative order as $π$ (or, in the counting version, how many such subsequences are there). This natural problem was shown by Bose, Buss and Lubiw [IPL 1998] to be NP-complete, and hence we should seek exact exponential time solutions. The asymptotically fastest such solution up to date, by Berendsohn, Kozma and Marx [IPEC 2019], works in $\mathcal{O}(1.6181^n)$ time. We design a simple and faster $\mathcal{O}(1.415^{n})$ time algorithm for both the d…
Faster fully compressed pattern matching by recompression
本文研究了一个完全压缩的模式匹配问题。压缩由直线程序（SLP）表示，即一种上下文无关文法，只生成一个字符串;该术语完全意味着模式和文本都以压缩形式给出。使用最近开发的局部再压缩技术来处理这个问题：重构SLP，使得模式和文本的子串以相同的方式在两个SLP中编码。为此，SLP被本地解压缩，然后以统一的方式重新压缩。该技术产生用于压缩模式匹配的O（（n+m）log M）算法，假设M适合O（1）机器字，其中n（m）是文本（模式）的压缩表示的大小，而M是解压缩模式的大小。如果只有m+n适合O（1）机器字，则运行时间增加到O（（n+m）log M log（n+m））。算法复杂度为O（n^2m）。
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that are at a distance at most k from x or from any of its rotations. In this article, we present a new algorithm for approximate circular string matching under the edit distance model with optimal average-case search time O(n(k + log m)/m). Optimal average-case search time can also be achieved by the algorithms for multiple approximate string matching (Fredriksson…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We present two fingerprinting methods, i.e., the parent-distance encoding and the binary encoding. By combining an efficient fingerprinting method and a conventional multiple string matching algorithm, we can efficiently solve multiple pattern Cartesian tree matching. We propose three practical algorithms for multiple pattern Cartesian tree matching based on the Wu-…
In this paper we present linear time approximation schemes for several generalized matching problems on nonbipartite graphs. Our results include $O_ε(m)$-time algorithms for $(1-ε)$-maximum weight $f$-factor and $(1+ε)$-approximate minimum weight $f$-edge cover. As a byproduct, we also obtain direct algorithms for the exact cardinality versions of these problems running in $O(m\sqrt{f(V)})$ time. The technical contributions of this work include an efficient method for maintaining {\em relaxed complementary slackness} in generalized matching problems and approximation-preserving reductions betw…
We present a randomized algorithm to maintain a maximal matching without 3 length augmenting paths in the fully dynamic setting. Consequently, we maintain a $3/2$ approximate maximum cardinality matching. Our algorithm takes expected amortized $O(\sqrt{n})$ time where $n$ is the number of vertices in the graph when the update sequence is generated by an oblivious adversary. Over any sequence of $t$ edge insertions and deletions presented by an oblivious adversary, the total update time of our algorithm is $O(t\sqrt{n})$ in expectation and $O(t\sqrt{n} + n \log n)$ with high probability. To the…
We give an $\tilde{O}(n^{7/5} \log (nC))$-time algorithm to compute a minimum-cost maximum cardinality matching (optimal matching) in $K_h$-minor free graphs with $h=O(1)$ and integer edge weights having magnitude at most $C$. This improves upon the $\tilde{O}(n^{10/7}\log{C})$ algorithm of Cohen et al. [SODA 2017] and the $O(n^{3/2}\log (nC))$ algorithm of Gabow and Tarjan [SIAM J. Comput. 1989]. For a graph with $m$ edges and $n$ vertices, the well-known Hungarian Algorithm computes a shortest augmenting path in each phase in $O(m)$ time, yielding an optimal matching in $O(mn)$ time. The Hop…
A Faster Deterministic Algorithm for Fully Dynamic Maximal Matching
Toyota Technological Institute at Chicago（芝加哥丰田技术研究所）；Courant Institute School of Mathematics, Computing, and Data Science, New York University（纽约大学库朗数学科学与技术学院）
本文提出了一种新的确定性框架，用于完全动态最大匹配的验证与维护，实现了 amortized update time 为 n^{1/2+o(1)} 的高效算法。
Expander graphs play a central role in graph theory and algorithms. With a number of powerful algorithmic tools developed around them, such as the Cut-Matching game, expander pruning, expander decomposition, and algorithms for decremental All-Pairs Shortest Paths (APSP) in expanders, to name just a few, the use of expanders in the design of graph algorithms has become ubiquitous. Specific applications of interest to us are fast deterministic algorithms for cut problems in static graphs, and algorithms for dynamic distance-based graph problems, such as APSP. Unfortunately, the use of expanders …
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be transformed to $P$ with at most $k$ edits. More than 20 years ago, Cole and Hariharan [SODA'98, J. Comput.'02] gave an $\mathcal{O}(n+k^4 \cdot n/ m)$-time algorithm for this classic problem, and this runtime has not been improved since. Here, we present an algorithm that runs in time $\mathcal{O}(n+k^{3.5} \sqrt{\log m \log k} \cdot n/m)$, thus breaking thr…
Hash tables are ubiquitous in computer science for efficient access to large datasets. However, there is always a need for approaches that offer compact memory utilisation without substantial degradation of lookup performance. Cuckoo hashing is an efficient technique of creating hash tables with high space utilisation and offer a guaranteed constant access time. We are given $n$ locations and $m$ items. Each item has to be placed in one of the $k\ge2$ locations chosen by $k$ random hash functions. By allowing more than one choice for a single item, cuckoo hashing resembles multiple choice allo…
In a recent breakthrough, Paz and Schwartzman (SODA'17) presented a single-pass ($2+ε$)-approximation algorithm for the maximum weight matching problem in the semi-streaming model. Their algorithm uses $O(n\log^2 n)$ bits of space, for any constant $ε>0$. We present two simplified and more intuitive analyses, for essentially the same algorithm, which also improve the space complexity to the optimal bound of $O(n\log n)$ bits --- this is optimal as the output matching requires $Ω(n\log n)$ bits. Our analyses rely on a simple use of the primal-dual method and a simple accounting method.
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet $Σ$, let $q$ be a query defined also on $Σ$, and let $k$ be a positive integer. We want to build a data structure on $D$ capable of answering the following query: find all words in $D$ that are at most different from the query word $q$ with $k$ errors. In this thesis, we study the approximate string matching methods in dictionaries, texts, and indexes, to propose pr…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on the Strong Exponential Time Hypothesis (SETH) implies an algorithm significantly faster than $O(|E|m)$ time is unlikely [Equi et al., ICALP 2019]. However, for many special graphs, such as de Bruijn graphs, the problem can be solved in linear time [Bowe et al., WABI 2012]. For approximate matching, the picture is more complex. When edits (substitutions, ins…
We consider the communication complexity of finding an approximate maximum matching in a graph in a multi-party message-passing communication model. The maximum matching problem is one of the most fundamental graph combinatorial problems, with a variety of applications. The input to the problem is a graph $G$ that has $n$ vertices and the set of edges partitioned over $k$ sites, and an approximation ratio parameter $α$. The output is required to be a matching in $G$ that has to be reported by one of the sites, whose size is at least factor $α$ of the size of a maximum matching in $G$. We show …
We aim to speed up approximate keyword matching by storing a lightweight, fixed-size block of data for each string, called a fingerprint. These work in a similar way to hash values; however, they can be also used for matching with errors. They store information regarding symbol occurrences using individual bits, and they can be compared against each other with a constant number of bitwise operations. In this way, certain strings can be deduced to be at least within the distance $k$ from each other (using Hamming or Levenshtein distance) without performing an explicit verification. We show expe…
Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a surprisingly simple solution called a split index, which is based on the Dirichlet principle, for matching a keyword with few mismatches, and experimentally show that it offers competitive space-time tradeoffs. Our implementation in the C++ language is focused mostly on data compaction, which is beneficial for the search speed (e.g., by being cache friendly). W…
The problem of finding \emph{distance} between \emph{pattern} of length $m$ and \emph{text} of length $n$ is a typical way of generalizing pattern matching to incorporate dissimilarity score. For both Hamming and $L_1$ distances only a super linear upper bound $\widetilde{O}(n\sqrt{m})$ are known, which prompts the question of relaxing the problem: either by asking for $(1 \pm \varepsilon)$ approximate distance (every distance is reported up to a multiplicative factor), or $k$-approximated distance (distances exceeding $k$ are reported as $\infty$). We focus on $L_1$ distance, for which we sho…
The approximate period recovery problem asks to compute all $\textit{approximate word-periods}$ of a given word $S$ of length $n$: all primitive words $P$ ($|P|=p$) which have a periodic extension at edit distance smaller than $τ_p$ from $S$, where $τ_p = \lfloor \frac{n}{(3.75+ε)\cdot p} \rfloor$ for some $ε>0$. Here, the set of periodic extensions of $P$ consists of all finite prefixes of $P^\infty$. We improve the time complexity of the fastest known algorithm for this problem of Amir et al. [Theor. Comput. Sci., 2018] from $O(n^{4/3})$ to $O(n \log n)$. Our tool is a fast algorithm for App…
A temporal graph is a sequence of graphs (called layers) over the same vertex set -- describing a graph topology which is subject to discrete changes over time. A $Δ$-temporal matching $M$ is a set of time edges $(e,t)$ (an edge $e$ paired up with a point in time $t$) such that for all distinct time edges $(e,t),(e',t') \in M$ we have that $e$ and $e'$ do not share an endpoint, or the time-labels $t$ and $t'$ are at least $Δ$ time units apart. Mertzios et al. [STACS '20] provided a $2^{O(Δν)}\cdot |{\mathcal G}|^{O(1)}$-time algorithm to compute the maximum size of a $Δ$-temporal matching in a…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the approximate pattern matching problem asks for computation of a particular \emph{distance} function between $P$ and every $m$-substring of $T$. We consider a $(1\pm\varepsilon)$ multiplicative approximation variant of this problem, for $\ell_p$ distance function. In this paper, we describe two $(1+\varepsilon)$-approximate algorithms with a runtime of $\widetilde{O}(\frac{n}{\varepsilon})$ for all (constant) non-negative values of $p$. For constant $p \ge 1$ we show a deterministic $(1+\varepsilon)$-approximation algorithm. Pre…
The maximum matching problem in dynamic graphs subject to edge updates (insertions and deletions) has received much attention over the last few years; a multitude of approximation/time tradeoffs were obtained, improving upon the folklore algorithm, which maintains a maximal (and hence $2$-approximate) matching in $O(n)$ worst-case update time in $n$-node graphs. We present the first deterministic algorithm which outperforms the folklore algorithm in terms of {\em both} approximation ratio and worst-case update time. Specifically, we give a $(2-Ω(1))$-approximate algorithm with $O(m^{3/8})=O(n^…
A recent line of research investigates how algorithms can be augmented with machine-learned predictions to overcome worst case lower bounds. This area has revealed interesting algorithmic insights into problems, with particular success in the design of competitive online algorithms. However, the question of improving algorithm running times with predictions has largely been unexplored. We take a first step in this direction by combining the idea of machine-learned predictions with the idea of "warm-starting" primal-dual algorithms. We consider one of the most important primitives in combinator…
Faster Directed Hopsets, Distance Preservers, and Deterministic Shortcut Sets
CWI, Amsterdam, The Netherlands（荷兰阿姆斯特丹CWI）；Vrije Universiteit Amsterdam, The Netherlands（荷兰阿姆斯特丹自由大学）；TTIC, Chicago, United States（美国芝加哥陶尔森理论计算机科学研究所）
Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can be an exact or as an approximate (inexact). Exact matching is to search for the pattern without allowing for mismatches (or insertions and deletions) of one or more characters in the pattern), while approximate matching is the opposite. For exact matching, several data structures that can be built in linear time and space are used and in practice nowadays. Fo…
We consider the problems of maintaining an approximate maximum matching and an approximate minimum vertex cover in a dynamic graph undergoing a sequence of edge insertions/deletions. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized dynamic algorithm for this problem that has an approximation ratio of $2$ and an amortised update time of $O(1)$ with high probability. This algorithm requires the assump…
