The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized constrained LCS problem) were proposed by Chen and Chao [J. Comb. Optim, 2011]. In this paper, we consider the substring-excluding constrained LCS (STR-EC-LCS) problem. A string $Z$ is said to be an STR-EC-LCS of two given strings $A$ and $B$ excluding $P$ if, $Z$ is one of the longest common subsequences of $A$ and $B$ that does not contain $P$ as a substring. Wang et al. proposed a dynamic programming solution which computes an STR-EC-LCS in $O(mnr)$ time and space where $m = |A|, n = |B|, r = |P|$ [Inf. Process. Lett., 2013]. In this paper, we show a new solution for the STR-EC-LCS problem. Our algorithm computes an STR-EC-LCS in $O(n|Σ| + (L+1)(m-L+1)r)$ time where $|Σ| \leq \min\{m, n\}$ denotes the set of distinct characters occurring in both $A$ and $B$, and $L$ is the length of the STR-EC-LCS. This algorithm is faster than the $O(mnr)$-time algorithm for short/long STR-EC-LCS (namely, $L \in O(1)$ or $m-L \in O(1)$), and is at least as efficient as the $O(mnr)$-time algorithm for all cases.
The constrained LCS problem asks one to find a longest common subsequence of two input strings $A$ and $B$ with some constraints. The STR-IC-LCS problem is a variant of the constrained LCS problem, where the solution must include a given constraint string $C$ as a substring. Given two strings $A$ and $B$ of respective lengths $M$ and $N$, and a constraint string $C$ of length at most $\min\{M, N\}$, the best known algorithm for the STR-IC-LCS problem, proposed by Deorowicz~({\em Inf. Process. Lett.}, 11:423--426, 2012), runs in $O(MN)$ time. In this work, we present an $O(mN + nM)$-time soluti…
The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence problem. As the known algorithms for the STR-IC-LCS problem are cubic-time, the presented quadratic-time algorithm is significantly faster.
The Longest Common Increasing Subsequence (LCIS) is a variant of the classical Longest Common Subsequence (LCS), in which we additionally require the common subsequence to be strictly increasing. While the well-known "Four Russians" technique can be used to find LCS in subquadratic time, it does not seem applicable to LCIS. Recently, Duraj [STACS 2020] used a completely different method based on the combinatorial properties of LCIS to design an $\mathcal{O}(n^2(\log\log n)^2/\log^{1/6}n)$ time algorithm. We show that an approach based on exploiting tabulation can be used to construct an asympt…
The similarity between a pair of time series, i.e., sequences of indexed values in time order, is often estimated by the dynamic time warping (DTW) distance, instead of any in the well-studied family of measures including the longest common subsequence (LCS) length and the edit distance. Although it may seem as if the DTW and the LCS(-like) measures are essentially different, we reveal that the DTW distance can be represented by the longest increasing subsequence (LIS) length of a sequence of integers, which is the LCS length between the integer sequence and itself sorted. For a given pair of …
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is often too simplistic. Therefore, recent works introduce the variants of $LCS$ based on shared substrings of length exactly or at least $k$ ($LCS_k$ and $LCS_{k+}$ respectively). The main drawback of the state-of-the-art algorithms for computing $LCS_k$ and $LCS_{k+}$ is that they work well only in a limited setting: they either solve the average case well w…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants and animals, classic algorithms such as Longest Common Subsequence (LCS) fail due to demanding computational complexity. Recently, Benson et al. defined a similarity metric named $LCSk$. By relaxing the requirement that the $k$-length substrings should not overlap, we extend their definition into a new metric. An efficient algorithm is presented which computes…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|Σ|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a sketch size and streaming space usage of $\mathcal{O}(L^{|Σ| - 1} \log L)$. We also prove matching unconditional lower bounds. As an application, we study a variant of LCS where each alphabet symbol is equipped with a weight that is given as input, and the task is to compute a common subsequence of maximum total weight. Using our sketching algorithm, we obtain an $\…
Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly subquadratic time. A special case of $\mathsf{LCS}$ wherein each character appears at most once in every string is equivalent to the longest increasing subsequence problem ($\mathsf{LIS}$) which can be solved in quasilinear time. In this work, we present novel algorithms for approximating $\mathsf{LCS}$ in truly subquadratic time and $\mathsf{LIS}$ in truly …
There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..σ]^n$ to $T\in[1..σ]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over strings of respective lengths $n$ and $m$ (which is likely to be optimal), and in time within $O(n{+}m)$ in some special cases (e.g. disjoint alphabets). We describe how indexing the strings (in linear time), and using such an index to refine the recurrence formulas underlying the dynamic programs, yield faster algorithms in a variety of models, on a continuum of clas…
In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the problem is to find a common subsequence $Z$ of $X$ and $Y$ excluding $P$ as a substring and the length of $Z$ is maximized. The problem and its solution were first proposed by Chen and Chao\cite{1}, but we found that their algorithm can not solve the problem correctly. A new dynamic programming solution for the STR-EC-LCS problem is then presented in this paper. T…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the LCS of a set of query strings $Q$ with the strings of $I$ can be computed faster. Since the problem is NP-hard for arbitrary $k$, we allow an error that allows some characters to be replaced by other characters. We define the approximation version of the problem with an extra input $m$, which is the length of the regular expression (regex) that describes the…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent, no $O(n^{2-\varepsilon})$-time algorithm is known. Recent work indeed shows that such an algorithm would refute the Strong Exponential Time Hypothesis (SETH) [Abboud, Backurs, Vassilevska Williams + Bringmann, Künnemann FOCS'15]. Despite the quadratic-time barrier, for over 40 years an enduring scientific interest continued to produce fast algorithms for LCS …
This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input sequence, all longest common subsequences (LCSs) of $p$ and $q$ can be generated in time proportional to the output size, once the all-prefixes-LCSs-graph has been constructed. The problem can be solved in the context of generating all the distinct character strings that represent an LCS or in the context of generating all ways of embedding an LCS in the two input …
The edit distance (ED) and longest common subsequence (LCS) are two fundamental problems which quantify how similar two strings are to one another. In this paper, we consider these problems in the asymmetric streaming model introduced by Andoni et al. (FOCS'10) and Saks and Seshadhri (SODA'13). In this model we have random access to one string and streaming access the other string. Our main contribution is a constant factor approximation algorithm for ED with the memory of $\tilde O(n^δ)$ for any constant $δ> 0$. In addition to this, we present an upper bound of $\tilde O_ε(\sqrt{n})$ on the m…
The problem of aligning two strings A,B in order to determine their similarity is fundamental in the field of pattern matching. An important concept in this domain is the "all scores matrix" that encodes the local alignment comparison of two strings. Namely, let K denote the all scores matrix containing the alignment score of every substring of B with A, and let J denote the all scores matrix containing the alignment score of every suffix of B with every prefix of A. In this paper we consider the problem of maintaining an all scores matrix where the scoring function is the LCS score, while sup…
In this paper, we consider a generalized longest common subsequence problem, in which a constraining sequence of length $s$ must be included as a substring and the other constraining sequence of length $t$ must be excluded as a subsequence of two main sequences and the length of the result must be maximal. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and the given two constraining sequences of length $s$ and $t$, we present an $O(nmst)$ time dynamic programming algorithm for solving the new generalized longest common subsequence problem. The time complexity can be reduced fu…
A noticeable fraction of Algorithms papers in the last few decades improve the running time of well-known algorithms for fundamental problems by logarithmic factors. For example, the $O(n^2)$ dynamic programming solution to the Longest Common Subsequence problem (LCS) was improved to $O(n^2/\log^2 n)$ in several ways and using a variety of ingenious tricks. This line of research, also known as "the art of shaving log factors", lacks a tool for proving negative results. Specifically, how can we show that it is unlikely that LCS can be solved in time $O(n^2/\log^3 n)$? Perhaps the only approach …
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are equivalent; the state of the art running time is (almost) quadratic and this is tight under plausible fine-grained complexity assumptions. But for approximation algorithms the picture is different: there is a long line of works with improved approximation factors for Edit Distance, but for LCS (with binary strings) only a trivial $1/2$-approximation was known. In…
The Longest Common Subsequence Problem (LCS) deals with finding the longest subsequence among a given set of strings. The LCS problem is an NP-hard problem which makes it a target for lots of effort to find a better solution with heuristics methods. The baseline for most famous heuristics functions is a tabular random, probabilistic approach. This approach approximates the length of the LCS in each iteration. The combination of beam search and tabular probabilistic-based heuristics has led to a large number of proposals and achievements in algorithms for solving the LCS problem. In this work, …
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the alignment distance (AD)). Multiple sequence alignment is a well-studied problem in bioinformatics and is used to identify regions of similarity among DNA, RNA, or protein sequences to detect functional, structural, or evolutionary relationships among them. It is known that exact computation of LCS or AD of $m$ sequences each of length $n$ requires $Θ(n^m)$ time unle…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model, this model allows one to have streaming access to one string and random access to the other string. Our first main contribution is a systematic study of space lower bounds for ED and LCS in the asymmetric streaming model. Previously, there are no explicitly stated results in this context, although some lower bounds about LCS can be inferred from the lower boun…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of total length $r$, the problem is to find a common subsequence $Z$ of $X$ and $Y$ excluding each of constrain string in $P$ as a substring and the length of $Z$ is maximized. The problem was declared to be NP-hard\cite{1}, but we finally found that this is not true. A new dynamic programming solution for this problem is presented in this paper. The correctness o…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$ of total length $r$, the problem is to find a common subsequence $Z$ of $X$ and $Y$ including each of constraint string in $P$ as a substring and the length of $Z$ is maximized. A new dynamic programming solution to this problem is presented in this paper. The correctness of the new algorithm is proved. The time complexity of our algorithm is $O(d2^dnmr)$. In…
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co from A to N, the DC-LCS problem consists in finding the longest subsequence s of s1 and s2 such that s is a supersequence of all the strings in Cs and such that the number of occurrences in s of each symbol a in A is upper bounded by Co(a). The DC-LCS problem provides a clear mathematical formulation of a sequence comparison problem in Computational Biology a…
Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of applications. Simple dynamic programming algorithms solve these tasks in $O(n^2)$ time, and despite an extensive amount of research, no algorithms with significantly better worst case upper bounds are known. In this paper, we show that an $O(n^{2-ε})$ time algorithm, for some $ε>0$, for computing the LCS or the DTWD of two sequences of length $n$ over a constant siz…
We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution dating back to the discovery of suffix trees (Weiner, 1973) and their efficient construction for integer alphabets (Farach-Colton, 1997). However, these solutions require $Θ(n)$ space, which is prohibitive in many applications. To address this issue, Starikovskaya and Vildhøj (CPM 2013) showed that for $n^{2/3} \le s \le n^{1-o(1)}$, the LCS problem can be s…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and this is essentially best possible under plausible fine-grained complexity assumptions, so a natural problem is to find faster approximation algorithms. When the inputs are two binary strings, there is a simple $\frac{1}{2}$-approximation in linear time: compute the longest common all-0s or all-1s subsequence. It has been open whether a better approximation …
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related problems. The semi-local LCS problem asks for the LCS scores for each of the input strings against every substring of the other input string, and for every prefix of each input string against every suffix of the other input string. Such a comparison pattern provides a much more detailed picture of string similarity than a single LCS score; it also arises naturally …
Dynamic time warping distance (DTW) is a widely used distance measure between time series. The best known algorithms for computing DTW run in near quadratic time, and conditional lower bounds prohibit the existence of significantly faster algorithms. The lower bounds do not prevent a faster algorithm for the special case in which the DTW is small, however. For an arbitrary metric space $Σ$ with distances normalized so that the smallest non-zero distance is one, we present an algorithm which computes $\operatorname{dtw}(x, y)$ for two strings $x$ and $y$ over $Σ$ in time $O(n \cdot \operatornam…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological sequence comparison. However, in numerous contexts, words represent cyclic sequences of symbols and LCS must be generalized to consider all circular shifts of the strings. This occurs especially in computational biology when genetic material is sequenced form circular DNA or RNA molecules. This initiates the problem of {\em longest common cyclic subsequence (LC…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$ space and $O(n)$ time solution (Weiner [FOCS'73], Hui [CPM'92]). However, the use of linear space is impractical in many applications. In this paper we show that for any trade-off parameter $1 \leq τ\leq n$, the LCS problem can be solved in $O(τ)$ space and $O(n^2/τ)$ time, thus providing the first smooth deterministic time-space trade-off from constant to …
The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS problem is at least as hard as the well-studied longest common subsequence problem for four strings (the 4-LCS problem). Then, we present a new algorithm which solves the 2-LCPS problem in $O(σM^2 + n)$ time, where $n$ denotes the length of $A$ and $B$, $M$ denotes the number of matching positions between $A$ and $B$, and $σ$ denotes the number of distinct cha…
The Longest Common Subsequence (LCS) of two strings is a fundamental string similarity measure with a classical dynamic programming solution taking quadratic time. Despite significant efforts, little progress was made in improving the runtime. Even in the realm of approximation, not much was known for linear time algorithms beyond the trivial $\sqrt{n}$-approximation. Recent breakthrough result provided a $n^{0.497}$-factor approximation algorithm [HSSS19], which was more recently improved to a $n^{0.4}$-factor one [BCD21]. The latter paper also showed a $n^{2-2.5α}$ time algorithm which outpu…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under the Strong Exponential Time Hypothesis the quadratic running time cannot be beaten. There are no such limitations for the approximate computation of the LCS however, except in some limited scenarios. There is also a scarcity of approximation algorithms. When the two given strings are over an alphabet of size $k$, returning the subsequence formed by the most…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied problem in computer science with a known $\mathcal{O}(n)$-time solution. In the fully dynamic version of the problem, edit operations are allowed in either of the two strings, and we are asked to report an LCS after each such operation. We present the first solution to this problem that requires sublinear time per edit operation. In particular, we show how to r…
Joint Graduate School of Mathematics for Innovation, Kyushu University（九州大学数学创新联合研究生院）；Department of Information Science and Technology, Kyushu University（九州大学信息科学技术系）；Graduate School of Informatics and Engineering, University of Electro-Communications（电波大学信息与工程学院）；Department of Informatics, Kyushu University（九州大学信息学系）
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input strings have a common substring of length $d$. The two extreme cases, $d=1$ and $d=n$, correspond respectively to Element Distinctness and Unstructured Search, two fundamental problems in quantum query complexity. However, the intermediate case $1\ll d\ll n$ was not fully understood. We show that the complexity of LCS with threshold $d$ smoothly interpolates betw…
For graph learning tasks, many existing methods utilize a message-passing mechanism where vertex features are updated iteratively by aggregation of neighbor information. This strategy provides an efficient means for graph features extraction, but obtained features after many iterations might contain too much information from other vertices, and tend to be similar to each other. This makes their representations less expressive. Learning graphs using paths, on the other hand, can be less adversely affected by this problem because it does not involve all vertex neighbors. However, most of them ca…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. Palindrome is a word which reads the same forward as it does backward. The {\em longest common palindromic subsequence (LCPS)} problem is an interesting variant of the classic LCS problem which finds the longest common subsequence between two given strings such that the computed subsequence is also a palindrome. In this paper, we study the LCPS problem and give efficient algorithms to solve this problem. To the best of our knowledge, this is the first attempt to study and solve this in…
Nokia Bell Labs（诺基亚贝尔实验室）；Rutgers University（罗格斯大学）
Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS) for $L$ strings is NP-hard, e.g., the computational complexity is exponential in $L$. In this paper, we develop a randomized algorithm, referred to as {\em Random-MCS}, for finding a random instance of Maximal Common Subsequence ($MCS$) of multiple strings. A common subsequence is {\em maximal} if inserting any character into the subsequence no longer yields a…
