Related papers: The zero exemplar distance problem
The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
We revisit the algorithmic problem of reconstructing a graph from homomorphism counts that has first been studied in (B\"oker et al., STACS 2024): given graphs $F_1,\ldots,F_k$ and counts $m_1,\ldots,m_k$, decide if there is a graph $G$…
We consider the computational problem of finding short paths in the skeleton of the perfect matching polytope of a bipartite graph. We prove that unless $P=NP$, there is no polynomial-time algorithm that computes a path of constant length…
The authors and Fischer recently proved that any hereditary property of two-dimensional matrices (where the row and column order is not ignored) over a finite alphabet is testable with a constant number of queries, by establishing the…
We study decidability and complexity questions related to a continuous analogue of the Skolem-Pisot problem concerning the zeros and nonnegativity of a linear recurrent sequence. In particular, we show that the continuous version of the…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is sent through a probabilistic \emph{deletion channel} which independently deletes each bit with probability $\delta$ and concatenates the surviving…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
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…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
In the monotone integer dualization problem, we are given two sets of vectors in an integer box such that no vector in the first set is dominated by a vector in the second. The question is to check if the two sets of vectors cover the…
We adress the problem of the algebraic decoding of any cyclic code up to the true minimum distance. For this, we use the classical formulation of the problem, which is to find the error locator polynomial in terms of the syndroms of the…
We initiate the study of the shortest reconfiguration problem for independent sets under the adjacency relation derived from the independent set polytope. Given a graph and two independent sets, the problem asks for a shortest sequence…