In this work, we present a plethora of results for the range longest increasing subsequence problem (Range-LIS) and its variants. The input to RLIS is a sequence $S$ of $n$ real numbers and a collection $Q$ of $m$ query ranges, and for each query in $Q$, the goal is to report the LIS of the sequence $S$ restricted to that query. Our two main results are for the following generalizations of the RLIS problem.
2D range queries: In this variant of the RLIS problem, each query is a pair of ranges, one of indices and the other of values, and we provide a randomized algorithm with running time $\tilde{O}(m n^{1/2} + n^{3/2}) + O(k)$, where $k$ is the cumulative length of the $m$ output subsequences. This improves on the elementary $O(mn)$-time algorithm when $m$ is at least $n^{1/2}$. Previously, the only known result breaking the quadratic barrier was due to Tiskin [SODA'10], which could only handle 1D range queries (i.e., each query was a range of indices) and also just outputted the length of the LIS (instead of reporting the subsequence achieving that length).
Colored sequences: In this variant of the RLIS problem, each element in $S$ is colored, and for each query in $Q$, the goal is to report a monochromatic LIS contained in the sequence $S$ restricted to that query. For 2D queries, we provide a randomized algorithm for this colored version with running time $\tilde{O}(m n^{2/3} + n^{5/3}) + O(k)$. Moreover, for 1D queries, we provide an improved algorithm with running time $\tilde{O}(m n^{1/2} + n^{3/2}) + O(k)$. Thus, we again improve on the elementary $O(mn)$-time algorithm. Additionally, assuming the well-known Combinatorial Boolean Matrix Multiplication Hypothesis, we prove that the running time for 1D queries is essentially tight for combinatorial algorithms.
Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $σ$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a subsequence in $O(n^3)$ time with $O(n)$ space, or online in $O(n^3 σ)$ space and time. Our first result can be extended to find the longest common Lyndon subsequence of two strings of length $n$ in $O(n^4 σ)$ time using $O(n^3)$ space.
We present an algorithm computing the longest periodic subsequence of a string of length $n$ in $O(n^7)$ time with $O(n^4)$ words of space. We obtain improvements when restricting the exponents or extending the search allowing the reported subsequence to be subperiodic down to $O(n^3)$ time and $O(n^2)$ words of space.
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n \log^{1.5} n}{2^{\sqrt{\log n}}}\right)$ bits of space.
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length $n$ can be computed using $O(n^2)$ time [Kosowski 2004], or with (model-dependent) polylogarithmic speed-ups using $O(n^2 (\log \log n)^2 / \log^2 n)$ time [Tiskin 2013]. We present the first algorithm for LSS whose running time depends on other parameters, i.e., we show that an LSS of $S$ can be computed in $O(r \min\{n, M\}\log \frac{n}{r} + n + M \log n)$ t…
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 consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm, therefore its performance improves if the string is not self similar. This occurs naturally on strings over large alphabets. Our algorithm relies on new results for data structures that support dynamic longest increasing sub-sequences. In the process we also obtain improved algorithms for the decremental string comparison problem.
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$ is the longest subsequence of $X$ and $Y$ such that $P$ is a subsequence of $Z$. Recently, Tsai \cite{Tsai} proposed an $O(n^2 \cdot m^2 \cdot r)$ time algorithm to solve this problem using dynamic programming technique, where $n$, $m$ and $r$ are the lengths of $X$, $Y$ and $P$, respectively. In this paper, we present a simple algorithm to solve the constra…
In this paper, we provide new approximation algorithms for dynamic variations of the longest increasing subsequence (\textsf{LIS}) problem, and the complementary distance to monotonicity (\textsf{DTM}) problem. In this setting, operations of the following form arrive sequentially: (i) add an element, (ii) remove an element, or (iii) substitute an element for another. At every point in time, the algorithm has an approximation to the longest increasing subsequence (or distance to monotonicity). We present a $(1+ε)$-approximation algorithm for \textsf{DTM} with polylogarithmic worst-case update t…
We study dynamic algorithms for the longest increasing subsequence (\textsf{LIS}) problem. A dynamic \textsf{LIS} algorithm maintains a sequence subject to operations of the following form arriving one by one: (i) insert an element, (ii) delete an element, or (iii) substitute an element for another. After performing each operation, the algorithm must report the length of the longest increasing subsequence of the current sequence. Our main contribution is the first exact dynamic \textsf{LIS} algorithm with sublinear update time. More precisely, we present a randomized algorithm that performs ea…
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…
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…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a generalization of the well-studied longest increasing subsequence problem and its complexity still remains open. An equivalent formulation of the longest heapable subsequence problem is that of finding a maximum-sized binary tree in a given permutation directed acyclic graph (permutation DAG). In this work, we study parameterized algorithms for both longest heapab…
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…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one run for each symbol (a run is a maximum substring of consecutive identical symbols). The problem has been shown to be NP-hard and to be fixed-parameter tractable when the parameter is the size of the alphabet on which the input string is defined. In this paper we further investigate the complexity of the problem and we show that it is fixed-parameter tracta…
Polynomial-Time Solutions for Longest Common Subsequence Related Problems Between a Sequence and a Pangenome Graph
College of Big Data Statistics, Guizhou University of Finance and Economics（贵州财经大学大数据统计学院）；Algorithm and Computational Complexity Laboratory of School of Information, Guizhou University of Finance and Economics（贵州财经大学信息学院算法与计算复杂性实验室）
String similarity, longest common subsequence and shortest edit scripts are the triplets of problem that related to each other. There are different algorithms exist to generate edit script by solving longest common subsequence problem. This paper proposes an algorithm that uses string similarity problem to generate shortest edit script. For this we use the famous Levenshtein distance algorithm, which computes a numerical value that represents similarity between the strings from 0 to n, where n is the length of longest input string, and produce the shortest edit script which contains instructio…
We consider the general problem of the Longest Common Subsequence (LCS) on weighted sequences. Weighted sequences are an extension of classical strings, where in each position every letter of the alphabet may occur with some probability. Previous results presented a PTAS and noticed that no FPTAS is possible unless P=NP. In this paper we essentially close the gap between upper and lower bounds by improving both. First of all, we provide an EPTAS for bounded alphabets (which is the most natural case), and prove that there does not exist any EPTAS for unbounded alphabets unless FPT=W[1]. Further…
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 Increasing Subsequence (LIS) is a fundamental statistic of a sequence, and has been studied for decades. While the LIS of a sequence of length $n$ can be computed exactly in time $O(n\log n)$, the complexity of estimating the (length of the) LIS in sublinear time, especially when LIS $\ll n$, is still open. We show that for any integer $n$ and any $λ= o(1)$, there exists a (randomized) non-adaptive algorithm that, given a sequence of length $n$ with LIS $\ge λn$, approximates the LIS up to a factor of $1/λ^{o(1)}$ in $n^{o(1)} / λ$ time. Our algorithm improves upon prior work substanti…
We consider the classic problem of computing the Longest Common Subsequence (LCS) of two strings of length $n$. While a simple quadratic algorithm has been known for the problem for more than 40 years, no faster algorithm has been found despite an extensive effort. The lack of progress on the problem has recently been explained by Abboud, Backurs, and Vassilevska Williams [FOCS'15] and Bringmann and Künnemann [FOCS'15] who proved that there is no subquadratic algorithm unless the Strong Exponential Time Hypothesis fails. This has led the community to look for subquadratic approximation algorit…
