Related papers: Three phases in the evolution of the standard gene…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We present a simple and effective approach to incorporating syntactic structure into neural attention-based encoder-decoder models for machine translation. We rely on graph-convolutional networks (GCNs), a recent class of neural networks…
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
Present day data allow significant reconsideration of ideas on mechanisms underlying the degeneracy in the genetic code. Here a hypothesis is presented which links the degeneracy to possible conformational alterations in the codon-anticodon…
We present new techniques for synthesizing programs through sequences of mutations. Among these are (1) a method of local scoring assigning a score to each expression in a program, allowing us to more precisely identify buggy code, (2)…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
Artificial intelligence generated content (AIGC), a rapidly advancing technology, is transforming content creation across domains, such as text, images, audio, and video. Its growing potential has attracted more and more researchers and…
Universal coding of integers~(UCI) is a class of variable-length code, such that the ratio of the expected codeword length to $\max\{1,H(P)\}$ is within a constant factor, where $H(P)$ is the Shannon entropy of the decreasing probability…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share…
This paper presents a novel design framework for protograph-based LDPC codes that simultaneously achieves full diversity in block-fading channels (BFCs) and nearcapacity performance in additive white Gaussian noise channels (AWGNCs). By…
We introduce the star cluster evolution code Evolve Me A Cluster of StarS (EMACSS), a simple yet physically motivated computational model that describes the evolution of some fundamental properties of star clusters in static tidal fields.…
The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
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…
The standard genetic code is well known to be optimized for minimizing the phenotypic effects of single nucleotide substitutions, a property that was likely selected for during the emergence of a universal code. Given the fitness advantage…
We introduce version two of the fast star cluster evolution code Evolve Me A Cluster of StarS (EMACSS). The first version (Alexander & Gieles) assumed that cluster evolution is balanced for the majority of the life-cycle, meaning that the…