Related papers: On the optimality of the standard genetic code: th…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
The choice of crossover and mutation strategies plays a crucial role in the searchability, convergence efficiency and precision of genetic algorithms. In this paper, a novel improved genetic algorithm is proposed by improving the crossover…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
Stopping sets, and in particular their numbers and sizes, play an important role in determining the performance of iterative decoders of linear codes over binary erasure channels. In the 2004 Shannon Lecture, McEliece presented an…
Cartesian Genetic Programming (CGP) suffers from a specific limitation: Positional bias, a phenomenon in which mostly genes at the start of the genome contribute to a program output, while genes at the end rarely do. This can lead to an…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
We approach index coding as a special case of rate-distortion with multiple receivers, each with some side information about the source. Specifically, using techniques developed for the rate-distortion problem, we provide two upper bounds…
While many optimization problems work with a fixed number of decision variables and thus a fixed-length representation of possible solutions, genetic programming (GP) works on variable-length representations. A naturally occurring problem…
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…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
In a certain way, this paper presents the continuation of the previous one which discussed the harmonic structure of the genetic code (Rakocevic, 2004). Several new harmonic structures presented in this paper, through specific unity and…
We propose a physical model to describe the mechanisms of two major scenarios of the genetic code evolution, the codon capture and ambiguous intermediate scenarios, in a consistent manner. We sketch the lowest dimensional version of our…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
The family of codeword stabilized codes encompasses the stabilizer codes as well as many of the best known nonadditive codes. However, constructing optimal $n$-qubit codeword stabilized codes is made difficult by two main factors. The first…
We consider the decoding of rank metric codes assuming the error matrix is symmetric. We prove two results. First, for rates $<1/2$ there exists a broad family of rank metric codes for which any symmetric error pattern, even of maximal rank…
This paper considers the problem of channel coding with a given (possibly suboptimal) maximum-metric decoding rule. A cost-constrained random-coding ensemble with multiple auxiliary costs is introduced, and is shown to achieve error…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
We introduce a purely graph-theoretical object, namely the coding clique, to construct quantum errorcorrecting codes. Almost all quantum codes constructed so far are stabilizer (additive) codes and the construction of nonadditive codes,…
Constant-dimension codes have recently received attention due to their significance to error control in noncoherent random linear network coding. What the maximal cardinality of any constant-dimension code with finite dimension and minimum…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…