Hagai Cohen, Ely Porat
In this paper we present a new problem, the fast set intersection problem, which is to preprocess a collection of sets in order to efficiently report the intersection of any two sets in the collection. In addition we suggest new solutions for the two-dimensional substring indexing problem and the document listing problem for two patterns by reduction to the fast set intersection problem.
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We study the budgeted versions of the well known matching and matroid intersection problems. While both problems admit a polynomial-time approximation scheme (PTAS) [Berger et al. (Math. Programming, 2011), Chekuri, Vondrak and Zenklusen (SODA 2011)], it has been an intriguing open question whether these problems admit a fully PTAS (FPTAS), or even an efficient PTAS (EPTAS). In this paper we answer the second part of this question affirmatively, by presenting an EPTAS for budgeted matching and budgeted matroid intersection. A main component of our scheme is a novel construction of representati…
While the basic greedy algorithm gives a semi-streaming algorithm with an approximation guarantee of $2$ for the \emph{unweighted} matching problem, it was only recently that Paz and Schwartzman obtained an analogous result for weighted instances. Their approach is based on the versatile local ratio technique and also applies to generalizations such as weighted hypergraph matchings. However, the framework for the analysis fails for the related problem of weighted matroid intersection and as a result the approximation guarantee for weighted instances did not match the factor $2$ achieved by the…
Maximum Matchings in Geometric Intersection Graphs
本文利用代数方法与几何交图的小分隔器性质，给出了一般几何交图最大匹配的高概率算法，并将多种常见几何对象情形归约为有界密度情形，从而获得更快的运行时间。
Efficient Hypergraph Pattern Matching via Match-and-Filter and Intersection Constraint
本文提出了一种高效的超图模式匹配算法，通过引入交集约束、候选超边空间和匹配与过滤框架，显著提升了查询处理效率。
Submodular Maximization over Bipartite Perfect Matchings and Matroid Intersection Bases
研究二分图完美匹配与拟阵交基上的单调子模最大化，证明其与有向图子模定向近似等价，并给出多项式时间双准则近似，目标值达到最优的1/2减epsilon。
In multistage perfect matching problems we are given a sequence of graphs on the same vertex set and asked to find a sequence of perfect matchings, corresponding to the sequence of graphs, such that consecutive matchings are as similar as possible. More precisely, we aim to maximize the intersections, or minimize the unions between consecutive matchings. We show that these problems are NP-hard even in very restricted scenarios. We propose new approximation algorithms and present methods to transfer results between different problem variants without loosing approximation guarantees.
A Faster Auction Algorithm for Weighted Matroid Intersection
提出一种确定性拍卖算法，在独立预言机模型下以近线性查询复杂度求解加权拟阵交的 $(1-\varepsilon)$-近似，为首个此类算法。
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how to improve the space and/or remove a dependency on the alphabet size for each problem using either an improved tabulation technique of an existing algorithm or by combining known algorithms in a new way.
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-…
Set intersection is a fundamental operation in information retrieval and database systems. This paper introduces linear space data structures to represent sets such that their intersection can be computed in a worst-case efficient way. In general, given k (preprocessed) sets, with totally n elements, we will show how to compute their intersection in expected time O(n/sqrt(w)+kr), where r is the intersection size and w is the number of bits in a machine-word. In addition,we introduce a very simple version of this algorithm that has weaker asymptotic guarantees but performs even better in practi…
Given a text $T$ and a pattern $P$, the order-preserving matching problem is to find all substrings in $T$ which have the same relative orders as $P$. Order-preserving matching has been an active research area since it was introduced by Kubica et al. \cite{kubica2013linear} and Kim et al. \cite{kim2014order}. In this paper we present two algorithms for the multiple order-preserving matching problem, one of which runs in sublinear time on average and the other in linear time on average. Both algorithms run much faster than the previous algorithms.
We put forth a new string matching algorithm which matches the pattern from neither the left nor the right end, instead a special position. Comparing with the Knuth-Morris-Pratt algorithm and the Boyer-Moore algorithm, the new algorithm is more flexible to pick the position for starting comparisons. The option really brings it a saving in cost.
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP algorithm. We improve the running time of the previous solution by introducing new representations. We present the framework of a binary filtration method and an efficient verification technique for Cartesian tree matching. Any exact string matching algorithm can be used as a filtration for Cartesian tree matching on our framework. We also present a SIMD so…
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…
A fast implementation of the good-suffix array for the Boyer-Moore string matching algorithm
本文针对Boyer-Moore算法中好后缀表计算存在冗余操作的问题，基于对模式的精细分析提出一种快速实现，实验证明其两个版本在几乎所有测试场景中均为最快。
In this paper, we devise three deterministic algorithms for solving the $m$-set $k$-packing, $m$-dimensional $k$-matching, and $t$-dominating set problems in time $O^*(5.44^{mk})$, $O^*(5.44^{(m-1)k})$ and $O^*(5.44^{t})$, respectively. Although recently there has been remarkable progress on randomized solutions to those problems, our bounds make good improvements on the best known bounds for deterministic solutions to those problems.
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…
Basic path-matchings, introduced by Cunningham and Geelen (FOCS 1996), are a common generalization of matroid intersection and non-bipartite matching. The main results of this paper are a new algebraic characterization of basic path-matching problems and an algorithm for constructing basic path-matchings in O(n^w) time, where n is the number of vertices and w is the exponent for matrix multiplication. Our algorithms are randomized, and our approach assumes that the given matroids are linear and can be represented over the same field. Our main results have interesting consequences for several s…
We present an algorithm for evaluating a linear ``intersection transform'' of a function defined on the lattice of subsets of an $n$-element set. In particular, the algorithm constructs an arithmetic circuit for evaluating the transform in ``down-closure time'' relative to the support of the function and the evaluation domain. As an application, we develop an algorithm that, given as input a digraph with $n$ vertices and bounded integer weights at the edges, counts paths by weight and given length $0\leq\ell\leq n-1$ in time $O^*(\exp(n\cdot H(\ell/(2n))))$, where $H(p)=-p\log p-(1-p)\log(1-p)…
Polynomial Kernels with Reachability for Weighted $d$-Matroid Intersection
本文研究加权d-矩阵交集问题的随机多项式核化，提出当一个矩阵为任意而其他d-1个为划分矩阵时的多项式核，且适用于更广泛的矩阵类。
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is better than that of the fastest versions of the Boyer-Moore algorithm. The algorithm retains its efficiency advantages in a wide variety of sequence matching problems of practical interest, including traditional string matching; large-alphabet problems (as in Unicode strings); and small-alphabet, long-pattern problems (as in DNA searches). Since it is expresse…
We show that finding minimally intersecting $n$ paths from $s$ to $t$ in a directed graph or $n$ perfect matchings in a bipartite graph can be done in polynomial time. This holds more generally for unimodular set systems.
Fractional Linear Matroid Matching is in quasi-NC
针对线性拟阵匹配缺乏 quasi-NC 并行算法的问题，论文借助分数拟阵匹配与非交换 Edmonds 问题的联系，给出分数线性拟阵匹配的 quasi-NC 算法，并解决一类黑盒非交换 Edmonds 问题。
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of interest because of their prominence in virus DNA. Thus, given no restrictions on pre-processing time, how quickly all such circular rotation occurrences is of interest to many areas of study. We highlight, to the best of our knowledge, a novel approach to the ECPM problem and present four data structures that accompany this approach, each with their own time-spac…
A Faster Combinatorial Algorithm for Maximum Bipartite Matching
针对最大二分匹配快速算法是否必须依赖连续技术的问题，提出一种纯组合算法，在中等稠密图上性能优于现有经典算法，并拓展得到顶点容量一致的有向图最大顶点容量s-t流确定性算法。
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running times of the fastest available optimal matching algorithms are too costly. However, when the vertices of the graphs are point-sets in $R^d$ and edge weights correspond to the euclidean distances, the available optimal matching algorithms are substantially faster. In this paper, we propose a novel network embedding based heuristic algorithm to solve various match…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering the distance between two adjacent occurrences of the same $q$-gram contained in $P$. We also propose a theoretical improvement of it which runs in $O(n + m)$ time, though it is not necessarily faster in practice. We compare the execution times of our and existing algorithms on various kinds of real and artificial datasets such as an English text, a genome seq…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal values $q$ such that each $q$-grams of the pattern has a unique hash value. The new algorithms are fastest than algorithm of the HASH family for short patterns on large size alphabets.
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower average time complexity by the cost of space. The algorithms of this family perform well for short patterns and middle size alphabets. In such case the shift of the window by several pattern lengths at once is quite probable, which is the main factor of algorithm success. Our algorithms outperform the Boyer-Moore-Horspool algorithm, either in the original ve…
For two matroids $\mathcal{M}_1$ and $\mathcal{M}_2$ defined on the same ground set $E$, the online matroid intersection problem is to design an algorithm that constructs a large common independent set in an online fashion. The algorithm is presented with the ground set elements one-by-one in a uniformly random order. At each step, the algorithm must irrevocably decide whether to pick the element, while always maintaining a common independent set. While the natural greedy algorithm---pick an element whenever possible---is half competitive, nothing better was previously known; even for the spec…
We show how to represent sets in a linear space data structure such that expressions involving unions and intersections of sets can be computed in a worst-case efficient way. This problem has applications in e.g. information retrieval and database systems. We mainly consider the RAM model of computation, and sets of machine words, but also state our results in the I/O model. On a RAM with word size $w$, a special case of our result is that the intersection of $m$ (preprocessed) sets, containing $n$ elements in total, can be computed in expected time $O(n (\log w)^2 / w + km)$, where $k$ is the…
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…
Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method for computing the limit of the expected speed of pattern matching algorithms, with regard to $w$, over iid texts. Next, we show how to determine the greatest speed which can be achieved among a large class of algorithms, altogether with an algorithm running this speed. Since the complexity of this determination make it impossible to deal with patterns of len…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $Δ$, the {\em exact string matching} problem consists of finding all occurrences of $P$ in $T$. For this problem, we present algorithms that in $O(nΔ^2)$ time pre-process $P$ to essentially identify $sparse(P)$, a rarely occurring substring of $P$, and then use it to find occurrences of $P$ in $T$ efficiently. Our algorithms require a worst case search time of $O(m)$, and expected search time of $O(m/min(|sparse(P)|, Δ))$, where $|sparse(P)|$ is …
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression methods: given an uncompressed pattern s[1..m] and a Lempel-Ziv representation of a string t[1..N], does s occur in t? Farach and Thorup gave a randomized O(nlog^2(N/n)+m) time solution for this problem, where n is the size of the compressed representation of t. We improve their result by developing a faster and fully deterministic O(nlog(N/n)+m) time algorith…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have lengths $m$ and $n$, respectively. On a standard unit-cost word RAM with word size $w \geq \log n$ we present an algorithm using time $$ O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n) $$ When $P$ is short, namely, $m = 2^{o(\sqrt{\log n})}$ or $m = 2^{o(\sqrt{w/\log w})}$ this improves the previously best known time bounds for the problem. …
Identifying intersections among a set of d-dimensional rectangular regions (d-rectangles) is a common problem in many simulation and modeling applications. Since algorithms for computing intersections over a large number of regions can be computationally demanding, an obvious solution is to take advantage of the multiprocessing capabilities of modern multicore processors. Unfortunately, many solutions employed for the Data Distribution Management service of the High Level Architecture are either inefficient, or can only partially be parallelized. In this paper we propose the Interval Tree Matc…
We present a new algorithm which detects the maximal possible number of matched disjoint pairs satisfying a given caliper when a bipartite matching is done with respect to a scalar index (e.g., propensity score), and constructs a corresponding matching. Variable width calipers are compatible with the technique, provided that the width of the caliper is a Lipschitz function of the index. If the observations are ordered with respect to the index then the matching needs $O(N)$ operations, where $N$ is the total number of subjects to be matched. The case of 1-to-$n$ matching is also considered. We…
A Better-Than-$3$ Approximation Algorithm for Demand Matching via Knapsack Intersection LP and Contention Resolution
针对需求匹配问题，通过背包交集线性规划松弛和冲突消解方案，首次给出优于3的随机近似算法，达到约2.914的近似比，二分图情形可达2+ε。
We consider Bayesian online selection problem of a matching in bipartite graphs, i.e., online weighted matching problem with edge arrivals where online algorithm knows distributions of weights, that corresponds to the intersection of two matroids in [Kleinberg and Wienberg STOC 12] model. We consider a simple class of non adaptive vertex-additive policies that assign static prices to all vertices in the graph and accept each edge only if its weight exceeds the sum of the prices of the edge's endpoints. We show existence of a vertex-additive policy with the expected payoff of at least one third…
Reconfigurable optical topologies promise to improve the performance in datacenters by dynamically optimizing the physical network in a demand-aware manner. State-of-the-art optical technologies allow to establish and update direct connectivity (in the form of edge-disjoint matchings) between top-of-rack switches within microseconds or less. However, to fully exploit temporal structure in the demand, such fine-grained reconfigurations also require fast algorithms for optimizing the interconnecting matchings. Motivated by the desire to offload a maximum amount of demand to the reconfigurable ne…
Graphs are widely used to model complicated data semantics in many application domains. In this paper, two novel and efficient algorithms Fast-ON and Fast-P are proposed for solving the subgraph isomorphism problem. The two algorithms are based on Ullman algorithm [Ullmann 1976], apply vertex-at-a-time matching manner and path-at-a-time matching manner respectively, and use effective heuristics to cut the search space. Comparing to the well-known algorithms, Fast-ON and Fast-P achieve up to 1-4 orders of magnitude speed-up for both dense and sparse graph data.
In this paper we consider the classic matroid intersection problem: given two matroids $\M_{1}=(V,\I_{1})$ and $\M_{2}=(V,\I_{2})$ defined over a common ground set $V$, compute a set $S\in\I_{1}\cap\I_{2}$ of largest possible cardinality, denoted by $r$. We consider this problem both in the setting where each $\M_{i}$ is accessed through an independence oracle, i.e. a routine which returns whether or not a set $S\in\I_{i}$ in $\indep$ time, and the setting where each $\M_{i}$ is accessed through a rank oracle, i.e. a routine which returns the size of the largest independent subset of $S$ in $\…
Exact substring matching is a common task in many software applications. Despite the existence of several algorithms for finding whether or not a pattern string is present in a target string, the most common implementation is a naïve, brute force approach. Alternative approaches either do not provide enough of a benefit for the added complexity, or are impractical for modern character sets, e.g., Unicode. We present a new algorithm, Scout, that is straightforward, quick and appropriate for all applications. We also compare the performance characteristics of the Scout algorithm with several oth…
The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image processing, among other application areas. This work describes a quantum algorithm which solves the pattern matching problem for random patterns and texts in time $\widetilde{O}((n/m)^{d/2} 2^{O(d^{3/2}\sqrt{\log m})})$. For large $m$ this is super-polynomially faster than the best possible classical algorithm, which requires time $\widetildeΩ( (n/m)^d + n^{d/…
In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides suffix array only held approximately 20%~30% of the space relative to suffix tree, the coalesced binary search and tile optimization make suffix array clearly outperform suffix tree using GPU. Consequently, the experimental results show that multiple genome sequence matching based on suffix array is more than 99 times speedup than that of CPU serial implemen…
Spanning trees are a representative example of linear matroid bases that are efficiently countable. Perfect matchings of Pfaffian bipartite graphs are a countable example of common bases of two matrices. Generalizing these two examples, Webb (2004) introduced the notion of Pfaffian pairs as a pair of matrices for which counting of their common bases is tractable via the Cauchy-Binet formula. This paper studies counting on linear matroid problems extending Webb's work. We first introduce "Pfaffian parities" as an extension of Pfaffian pairs to the linear matroid parity problem, which is a commo…
Finding maximum matchings in RDV graphs efficiently
本文针对RDV图最大匹配问题，提出通过正交射线射击查询和动态线段相交测试的归约方法，实现O(n log n)时间的高效求解。
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two special kinds, namely, uniformly labeled trees (i.e., trees with all their nodes labeled by the same symbol) and evolutionary trees (i.e., leaf-labeled trees with distinct symbols for distinct leaves). This paper presents an algorithm for comparing trees that are labeled in an arbitrary manner. In addition to this generality, this algorithm is faster than the pr…
We design a fully polynomial time approximation scheme (FPTAS) for counting the number of matchings (packings) in arbitrary 3-uniform hypergraphs of maximum degree three, referred to as $(3,3)$-hypergraphs. It is the first polynomial time approximation scheme for that problem, which includes also, as a special case, the 3D Matching counting problem for 3-partite $(3,3)$-hypergraphs. The proof technique of this paper uses the general correlation decay technique and a new combinatorial analysis of the underlying structures of the intersection graphs. The proof method could be also of independent…
It is well-known that the intersection of the matching polytope with a cardinality constraint is integral [8]. We prove a similar result for the polytope corresponding to the transportation problem with market choice (TPMC) (introduced in [4]) when the demands are in the set $\{1,2\}$. This result generalizes the result regarding the matching polytope and also implies that some special classes of minimum weight perfect matching problem with a cardinality constraint on a subset of edges can be solved in polynomial time.
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined with pruning strategy. However, the computation cost of those methods is easily dominated by the size of signal N instead of that of template K. This paper proposes a probabilistic and fast matching scheme, which computation costs requires O(N) additions and O(K \log K) multiplications, based on cross-correlation. The nuclear idea is to first downsample signa…
Asymptotically Optimal Hardness for $k$-Set Packing and $k$-Matroid Intersection
本文证明了 $k$-Dimensional Matching 及相关独立系统优化问题的近似硬度下界，将其从 $\Omega(k/\log k)$ 提升至常数级别，缩小了与 $O(k)$ 近似算法的差距，并基于新颖的保近似 gadget 归约提供了理论解释。
Small Independent Sets versus Small Separator in Geometric Intersection Graphs
研究发现某些几何交图中存在亚指数算法，但不满足平方根现象，引入弱平方根现象概念及新的图参数α-调制数。
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two decades a general trend has appeared trying to exploit the power of the word RAM model to speed-up the performances of classical string matching algorithms. In this model an algorithm operates on words of length w, grouping blocks of characters, and arithmetic and logic operations on the words take one unit of time. In this paper we use specialized word-size pa…
Optimality of Fast Matching Algorithms for Random Networks with Applications to Structural Controllability
研究快速可扩展算法在随机网络中寻找最大匹配的最优性，分析Karp和Sipser的启发式方法及其简化版本的渐近最优性，探讨最大匹配大小的渐近结果。
Hardness of Regular Expression Matching with Extensions
本文研究了带有回溯、平方、交集和补集等扩展的正则表达式匹配问题，证明了在不同假设下这些扩展无法在特定时间内解决，揭示了ERE匹配算法的最优性。
Fast Approximation Algorithms for Euclidean Minimum Weight Perfect Matching
本文提出了一种在$O(n \log n)$时间内求解欧几里得最小权重完美匹配问题的算法，其近似比为$O(n^{0.206})$，并扩展到高维空间，近似比为$O(n^{0.412})$。
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