Related papers: On the optimality of the standard genetic code: th…
Stopping criteria automatically determine when to stop an evolutionary algorithm, so as not to waste function evaluations on a stagnant population. Although stopping criteria play an important role in real-world applications, they have…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
We investigate a family of $(\mu+\lambda)$ Genetic Algorithms (GAs) which creates offspring either from mutation or by recombining two randomly chosen parents. By scaling the crossover probability, we can thus interpolate from a fully…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
Efficient protein synthesis depends on the availability of charged tRNA molecules. With 61 different codons, shifting the balance among the tRNA abundances can lead to large changes in the protein synthesis rate. Previous theoretical work…
Mutation is one of the most important stages of the genetic algorithm because of its impact on the exploration of global optima, and to overcome premature convergence. There are many types of mutation, and the problem lies in selection of…
Codes for rank modulation have been recently proposed as a means of protecting flash memory devices from errors. We study basic coding theoretic problems for such codes, representing them as subsets of the set of permutations of $n$…
A random-key genetic algorithm is an evolutionary metaheuristic for discrete and global optimization. Each solution is encoded as a vector of N random keys, where a random key is a real number randomly generated in the continuous interval…
Batch codes are a useful notion of locality for error correcting codes, originally introduced in the context of distributed storage and cryptography. Many constructions of batch codes have been given, but few lower bound (limitation)…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
Explaining to what extent the real power of genetic algorithms lies in the ability of crossover to recombine individuals into higher quality solutions is an important problem in evolutionary computation. In this paper we show how the…
In Index coding there is a single sender with multiple messages and multiple receivers each wanting a different set of messages and knowing a different set of messages a priori. The Index Coding problem is to identify the minimum number of…
This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable…
This paper presents encoding and decoding algorithms for several families of optimal rank metric codes whose codes are in restricted forms of symmetric, alternating and Hermitian matrices. First, we show the evaluation encoding is the right…
DNA storage systems face significant challenges, including insertion, deletion, and substitution (IDS) errors. Therefore, designing effective synchronization codes, i.e., codes capable of correcting IDS errors, is essential for DNA storage…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…