Related papers: The Hybrid k-Deck Problem: Reconstructing Sequence…
The recently introduced longest common substring with $k$-mismatches ($k$-LCF) problem is to find, given two sequences $S_1$ and $S_2$ of length $n$ each, a longest substring $A_1$ of $S_1$ and $A_2$ of $S_2$ such that the Hamming distance…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
Our aim is to develop dynamic data structures that support $k$-nearest neighbors ($k$-NN) queries for a set of $n$ point sites in the plane in $O(f(n) + k)$ time, where $f(n)$ is some polylogarithmic function of $n$. The key component is a…
The successor and predecessor problem consists of obtaining the closest value in a set of integers, greater/smaller than a given value. This problem has interesting applications, like the intersection of inverted lists. It can be easily…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…
Given \(k\) strings each of length at most $n$, computing the shortest common supersequence of them is a well-known NP-hard problem (when \(k\) is unbounded). On the other hand, when \(k=2\), such a shortest common supersequence can be…
This paper proposes an algorithmic framework for various reconfiguration problems using zero-suppressed binary decision diagrams (ZDDs), a data structure for families of sets. In general, a reconfiguration problem checks if there is a…
The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the…
The rooted tree is an important data structure, and the subtree size, height, and depth are naturally defined attributes of every node. We consider the problem of the existence of a k-ary tree given a list of attribute sequences. We give…
We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as…
Palindromes are non-empty strings that read the same forward and backward. The problem of recognizing strings that can be represented as the concatenation of even-length palindromes, the concatenation of palindromes of length at least two,…
The sequence reconstruction problem for insertion/deletion channels has attracted significant attention owing to their applications recently in some emerging data storage systems, such as racetrack memories, DNA-based data storage. Our goal…
A Dyck sequence is a sequence of opening and closing parentheses (of various types) that is balanced. The Dyck edit distance of a given sequence of parentheses $S$ is the smallest number of edit operations (insertions, deletions, and…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
We consider the problem of reconstructing compositions of an integer from their subcompositions, which was raised by Raykova (albeit disguised as a question about layered permutations). We show that every composition w of n\ge 3k+1 can be…
We consider the Minimum-$(k,\rho)$-$\mathrm{Shortcut}$ problem ($\min(k,\rho)\text{-}\mathrm{Shortcut}$), where the goal is to find the smallest set of shortcut edges such that every vertex in a given graph can reach its $\rho$ closest…
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…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
We consider the streaming complexity of a fundamental task in approximate pattern matching: the $k$-mismatch problem. It asks to compute Hamming distances between a pattern of length $n$ and all length-$n$ substrings of a text for which the…
We propose a recursive lattice reduction framework for finding short non-zero vectors or dense sublattices of a lattice. The framework works by recursively searching for dense sublattices of dense sublattices (or their duals) with…