Related papers: Palindromic Decompositions with Gaps and Errors
We consider the problem of sorting $n$ elements subject to persistent random comparison errors. In this problem, each comparison between two elements can be wrong with some fixed (small) probability $p$, and comparing the same pair of…
We determine the maximal gap between the optimal values of an integer program and its linear programming relaxation, where the matrix and cost function are fixed but the right hand side is unspecified. Our formula involves irreducible…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
We use exponential start time clustering to design faster and more work-efficient parallel graph algorithms involving distances. Previous algorithms usually rely on graph decomposition routines with strict restrictions on the diameters of…
We study integer linear programs (ILP) of the form $\min\{c^\top x\ \vert\ Ax=b,l\le x\le u,x\in\mathbb Z^n\}$ and analyze their parameterized complexity with respect to their distance to the generalized matching problem, following the…
With distributed computing and mobile applications becoming ever more prevalent, synchronizing diverging replicas of the same data is a common problem. Reconciliation -- bringing two replicas of the same data structure as close as possible…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Optimal gap sequences in Shellsort, defined as gap sequences having the minimised maximum number of comparisons for a fixed number of pairwise distinct elements, are found by minimax search in reduced permutational spaces, namely Bad…
There are distributed graph algorithms for finding maximal matchings and maximal independent sets in $O(\Delta + \log^* n)$ communication rounds; here $n$ is the number of nodes and $\Delta$ is the maximum degree. The lower bound by Linial…
Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
The distinguishing result of this paper is a $\mathbf{P}$-time enumerable partition of all the potential perfect matchings in a bipartite graph. This partition is a set of equivalence classes induced by the missing edges in the potential…
A two-dimensional ($2$D) word is a $2$D palindrome if it is equal to its reverse and it is an HV-palindrome if all its columns and rows are $1$D palindromes. We study some combinatorial and structural properties of HV-palindromes and its…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…