Related papers: Asymmetric Lee Distance Codes for DNA-Based Storag…
Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence…
Dihedral codes, particular cases of quasi-cyclic codes, have a nice algebraic structure which allows to store them efficiently. In this paper, we investigate it and prove some lower bounds on their dimension and minimum distance, in analogy…
We survey the emerging area of compression-based, parameter-free, similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a…
Let $\cal M$ denote the set ${\cal S}_{n, q}$ of $n \times n$ symmetric matrices with entries in ${\rm GF}(q)$ or the set ${\cal H}_{n, q^2}$ of $n \times n$ Hermitian matrices whose elements are in ${\rm GF}(q^2)$. Then $\cal M$ equipped…
Near maximum distance separable (NMDS) codes, where both the code and its dual are almost maximum distance separable, play pivotal roles in combinatorial design theory and cryptographic applications. Despite progress in fixed dimensions…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
A distance labeling scheme is an assignment of bit-labels to the vertices of an undirected, unweighted graph such that the distance between any pair of vertices can be decoded solely from their labels. We propose a series of new labeling…
Recently, the theory of quantum error control codes has been extended to subsystem codes over symmetric and asymmetric quantum channels -- qubit-flip and phase-shift errors may have equal or different probabilities. Previous work in…
Binary codes are widely used to represent the data due to their small storage and efficient computation. However, there exists an ambiguity problem that lots of binary codes share the same Hamming distance to a query. To alleviate the…
Maximum-distance separable (MDS) convolutional codes form an optimal family of convolutional codes, the study of which is of great importance. There are very few general algebraic constructions of MDS convolutional codes. In this paper, we…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
For $q,n,d \in \mathbb{N}$, let $A_q(n,d)$ be the maximum size of a code $C \subseteq [q]^n$ with minimum distance at least $d$. We give a divisibility argument resulting in the new upper bounds $A_5(8,6) \leq 65$, $A_4(11,8)\leq 60$ and…
In coded caching system we prefer to design a coded caching scheme with low subpacketization and small transmission rate (i.e., the low implementation complexity and the efficient transmission during the peak traffic times). Placement…
A new construction is proposed for low density parity check (LDPC) codes using quadratic permutation polynomials over finite integer rings. The associated graphs for the new codes have both algebraic and pseudo-random nature, and the new…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Separating codes have their applications in collusion-secure fingerprinting for generic digital data, while they are also related to the other structures including hash family, intersection code and group testing. In this paper we study…
We study the problem of coded information retrieval for block-structured data, motivated by DNA-based storage systems where a database is partitioned into multiple files that must each be recoverable as an atomic unit. We initiate and…
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 ($q=2$)…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…