Related papers: Deterministic Polynomial-Time Algorithms for Desig…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
In the Shortest Superstring problem we are given a set of strings $S=\{s_1, \ldots, s_n\}$ and integer $\ell$ and the question is to decide whether there is a superstring $s$ of length at most $\ell$ containing all strings of $S$ as…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
Word Break is a prototypical factorization problem in string processing: Given a word $w$ of length $N$ and a dictionary $\mathcal{D} = \{d_1, d_2, \ldots, d_{K}\}$ of $K$ strings, determine whether we can partition $w$ into words from…
We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
Pseudo-deterministic algorithms are randomized algorithms that, with high constant probability, output a fixed canonical solution. The study of pseudo-deterministic algorithms for the global minimum cut problem was recently initiated by…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
In this paper we give a detailed analysis of deterministic and randomized algorithms that enumerate any number of irreducible polynomials of degree $n$ over a finite field and their roots in the extension field in quasilinear where $N=n^2$…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
In this paper, we explore applications of combinatorics on words across various domains, including data compression, error detection, cryptographic protocols, and pseudorandom number generation. The examination of the theoretical…
We give a deterministic O(log n)^n algorithm for the {\em Shortest Vector Problem (SVP)} of a lattice under {\em any} norm, improving on the previous best deterministic bound of n^O(n) for general norms and nearly matching the bound of…
The random access problem for compressed strings is to build a data structure that efficiently supports accessing the character in position $i$ of a string given in compressed form. Given a grammar of size $n$ compressing a string of size…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
In real-time trajectory planning for unmanned vehicles, on-board sensors, radars and other instruments are used to collect information on possible obstacles to be avoided and pathways to be followed. Since, in practice, observations of the…
Until recently, techniques for obtaining lower bounds for kernelization were one of the most sought after tools in the field of parameterized complexity. Now, after a strong influx of techniques, we are in the fortunate situation of having…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
We present two deterministic dynamic algorithms for the maximum matching problem. (1) An algorithm that maintains a $(2+\epsilon)$-approximate maximum matching in general graphs with $O(\text{poly}(\log n, 1/\epsilon))$ update time. (2) An…