Related papers: The Longest Run Subsequence Problem: Further Compl…
The all-pairs suffix-prefix (APSP) problem is a classical problem in string processing which has important applications in bioinformatics. Given a set $\mathcal{S} = \{S_1, \ldots, S_k\}$ of $k$ strings, the APSP problem asks one to compute…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
In the Palindrome Problem one tries to find all palindromes (palindromic substrings) in a given string. A palindrome is defined as a string which reads forwards the same as backwards, e.g., the string "racecar". A related problem is the…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
In this paper, we consider the parameterized complexity of the following scheduling problem. We must schedule a number of jobs on $m$ machines, where each job has unit length, and the graph of precedence constraints consists of a set of…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
A generalized Davenport-Schinzel sequence is one over a finite alphabet that contains no subsequences isomorphic to a fixed forbidden subsequence. One of the fundamental problems in this area is bounding (asymptotically) the maximum length…
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…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
The maximum labelled clique problem is a variant of the maximum clique problem where edges in the graph are given labels, and we are not allowed to use more than a certain number of distinct labels in a solution. We introduce a new…
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…
A polynomial Turing kernel for some parameterized problem $P$ is a polynomial-time algorithm that solves $P$ using queries to an oracle of $P$ whose sizes are upper-bounded by some polynomial in the parameter. Here the term "polynomial"…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Inferring the exact parameters of a neural network with only query access is an NP-Hard problem, with few practical existing algorithms. Solutions would have major implications for security, verification, interpretability, and understanding…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
We study the existence of polynomial kernels for the problem of deciding feasibility of integer linear programs (ILPs), and for finding good solutions for covering and packing ILPs. Our main results are as follows: First, we show that the…