Related papers: Longest Common Subsequence with Gap Constraints
In the classical best approximation pair (BAP) problem, one is given two nonempty, closed, convex and disjoint subsets in a finite- or an infinite-dimensional Hilbert space, and the goal is to find a pair of points, each from each subset,…
Let $S_n$ denote the set of permutations of $[n]$ and let $\sigma=\sigma_1\cdots\sigma_n\in S_n$. For a subsequence $\{\sigma_{i_j}\}_{j=1}^k$ of $\{\sigma_i\}_{i=1}^n$ of length $k\ge2$, construct the ``up/down'' sequence $V_1\cdots…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
Frequent sequence mining methods often make use of constraints to control which subsequences should be mined. A variety of such subsequence constraints has been studied in the literature, including length, gap, span, regular-expression, and…
The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,...,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently…
This paper proves the minimum size of a supersequence over a set of eight elements is 52. This disproves a conjecture that the lower bound of the supersequence is the partial sum of the geometric Connell sequence. By studying the internal…
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…
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,…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
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…
We are interested in the statistics of the length of the longest increasing subsequence of 2-rowed lexicographically sorted arrays chosen according to distinct families of distributions D = (D_n)_n, and when n goes to infinity. This…
Sequence representations supporting queries $access$, $select$ and $rank$ are at the core of many data structures. There is a considerable gap between the various upper bounds and the few lower bounds known for such representations, and how…
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can…
Recently, generalizations of the classical Three Gap Theorem to higher dimensions attracted a lot of attention. In particular, upper bounds for the number of nearest neighbor distances have been established for the Euclidean and the maximum…
The following geometric vehicle scheduling problem has been considered: given continuous curves $f_1, \ldots, f_n : \mathbb{R} \rightarrow \mathbb{R}^2$, find non-negative delays $t_1, \ldots, t_n$ minimizing $\max \{ t_1, \ldots, t_n \}$…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…