Related papers: On the optimality of the standard genetic code: th…
Block codes, which correct asymmetric errors with limited-magnitude, are studied. These codes have been applied recently for error correction in flash memories. The codes will be represented by lattices and the constructions will be based…
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…
The homogeneous metric can be viewed as a natural extension of the Hamming metric to finite chain rings. It distinguishes between three types of elements: zero, non-zero elements in the socle, and elements outside the socle. Since the…
We consider stopping criteria that balance algebraic and discretization errors for the conjugate gradient algorithm applied to high-order finite element discretizations of Poisson problems. Firstly, we introduce a new stopping criterion…
This paper explores the design of convolutional codes for varying constraint lengths, focusing on their role in error correction in digital communication systems. Convolutional codes are essential in achieving reliable data transmission…
This article is interested in the origin of the genetic code, it puts forward a scenario of a simultaneous selection of the bases and amino acids and setting up of a correlation between them. Each amino acid is associated with a pair of its…
We revisit the notion of gene regulatory code in embryonic development in the light of recent findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the…
Finding the best configuration of algorithms' hyperparameters for a given optimization problem is an important task in evolutionary computation. We compare in this work the results of four different hyperparameter tuning approaches for a…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Life relies on the efficient performance of molecular codes, which relate symbols and meanings via error-prone molecular recognition. We describe how optimizing a code to withstand the impact of molecular recognition noise may be…
The color code is both an interesting example of an exactly solved topologically ordered phase of matter and also among the most promising candidate models to realize fault-tolerant quantum computation with minimal resource overhead. The…
Rank modulation is a way of encoding information to correct errors in flash memory devices as well as impulse noise in transmission lines. Modeling rank modulation involves construction of packings of the space of permutations equipped with…
Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set…
An index coding problem arises when there is a single source with a number of messages and multiple receivers each wanting a subset of messages and knowing a different set of messages a priori. The noiseless Index Coding Problem is to…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
A flag is a sequence of nested subspaces of a given ambient space F_q^n over a finite field F_q. In network coding, a flag code is a set of flags, all of them with the same sequence of dimensions, the type vector. In this paper, we…
Conflict-avoiding codes are used in the multiple-access collision channel without feedback. The number of codewords in a conflict-avoiding code is the number of potential users that can be supported in the system. In this paper, a new upper…