Related papers: Prefix Block-Interchanges on Binary and Ternary St…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
The block relocation problem (BRP) is a fundamental operational issue in modern warehouse and yard management, which, however, is very challenging to solve. In this paper, to advance our understanding on this problem and to provide a…
The main result here is a characterisation of binary $2$-neighbour-transitive codes with minimum distance at least $5$ via their minimal subcodes, which are found to be generated by certain designs. The motivation for studying this class of…
Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem. Length-limited Huffman coding, useful for many…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
We consider the problem of decomposing a higher-order tensor with binary entries. Such data problems arise frequently in applications such as neuroimaging, recommendation system, topic modeling, and sensor network localization. We propose a…
The Bandwidth Problem seeks for a simultaneous permutation of the rows and columns of the adjacency matrix of a graph such that all nonzero entries are as close as possible to the main diagonal. This work focuses on investigating novel…
A binary tanglegram is a pair <S,T> of binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example in phylogenetics or software engineering, it is required…
Sorting is a common and ubiquitous activity for computers. It is not surprising that there exist a plethora of sorting algorithms. For all the sorting algorithms, it is an accepted performance limit that sorting algorithms are linearithmic…
The paper describes a general glance to the use of element exchange techniques for optimization over permutations. A multi-level description of problems is proposed which is a fundamental to understand nature and complexity of optimization…
Non-overlapping codes are block codes that have arisen in diverse contexts of computer science and biology. Applications typically require finding non-overlapping codes with large cardinalities, but the maximum size of non-overlapping codes…
In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…
In the reordering buffer management problem, a sequence of requests must be executed by a service station, where a cost occurs for each pair of consecutive requests with different attributes. A reordering buffer management algorithm aims to…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
This paper studies the average complexity on the number of comparisons for sorting algorithms. Its information-theoretic lower bound is $n \lg n - 1.4427n + O(\log n)$. For many efficient algorithms, the first $n\lg n$ term is easy to…
Mathematically, ternary coding is more efficient than binary coding. It is little used in computation because technology for binary processing is already established and the implementation of ternary coding is more complicated, but remains…
We study a class of rearrangement problems under a novel pick-n-swap prehensile manipulation model, in which a robotic manipulator, capable of carrying an item and making item swaps, is tasked to sort items stored in lattices of variable…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
Recently, it was shown that any theory of strings containing the string-replace function (even the most restricted version where pattern/replacement strings are both constant strings) becomes undecidable if we do not impose some kind of…