Related papers: Prefix Block-Interchanges on Binary and Ternary St…
In this paper we study several variations of the \emph{pancake flipping problem}, which is also well known as the problem of \emph{sorting by prefix reversals}. We consider the variations in the sorting process by adding with prefix…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…
We study a new generalization of palindromes and gapped palindromes called block palindromes. A block palindrome is a string that becomes a palindrome when identical substrings are replaced with a distinct character. We investigate several…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
Recent work has demonstrated that using a carefully designed dictionary instead of a predefined one, can improve the sparsity in jointly representing a class of signals. This has motivated the derivation of learning methods for designing a…
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…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
The discrepancy of a binary string is the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. In this note we determine the minimal discrepancy that a…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
The problem of designing bit-to-pattern mappings and power allocation schemes for orthogonal frequency-division multiplexing (OFDM) systems that employ subcarrier index modulation (IM) is considered. We assume the binary source conveys a…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length. The new algorithm uses two operations on binary strings,…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
A problem that arises in drawings of transportation networks is to minimize the number of crossings between different transportation lines. While this can be done efficiently under specific constraints, not all solutions are visually…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
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 the well-known Minimum Linear Arrangement problem (MinLA), the goal is to arrange the nodes of an undirected graph into a permutation so that the total stretch of the edges is minimized. This paper studies an online (learning) variant of…
In [4] we describe a variation of the classical permutation decoding algorithm that can be applied to any binary affine-invariant code; in particular, it can be applied to first-order Reed-Muller codes successfully. In this paper we study…
We consider the task of assigning unique integers to a group of processes in an asynchronous distributed system of a total of $n$ processes prone to crashes that communicate through shared read-write registers. In the Renaming problem, an…