Related papers: The genetic code Via Godel encoding
This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
A new kind of Convolutional Codes generalizing Goppa Codes is proposed. This provides a systematic method for constructing convolutional codes with prefixed properties. In particular, examples of Maximum-Distance Separable (MDS)…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
A quantitative theory on the construction and the evolution of the genetic code is proposed. Through introducing the concept of mutational deterioration (MD) and developing a theoretical formalism on MD minimization we have proved: 1, the…
Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Regular expression is important for many natural language processing tasks especially when used to deal with unstructured and semi-structured data. This work focuses on automatically generating regular expressions and proposes a novel…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution…
Program code serves as a bridge linking vision and logic, providing a feasible supervisory approach for enhancing the multimodal reasoning capability of large models through geometric operations such as auxiliary line construction and…
In this paper, we construct new families of convolutional codes. Such codes are obtained by means of algebraic geometry codes. Additionally, more families of convolutional codes are constructed by means of puncturing, extending, expanding…
The number of atoms in the four ribonucleotides uridine monophosphate, cytidine monophosphate, adenine monophosphate and guanine monophosphate is taken as a key parameter. A mathematical relation describing the condensation of the three…
There has been much research on codes over $\mathbb{Z}_4$, sometimes called quaternary codes, for over a decade. Yet, no database is available for best known quaternary codes. This work introduces a new database for quaternary codes. It…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens that properties of the degeneracy pattern…
We study the problem of building generative models of natural source code (NSC); that is, source code written and understood by humans. Our primary contribution is to describe a family of generative models for NSC that have three key…
In this paper, we present a framework for generic decoding of convolutional codes, which allows us to do cryptanalysis of code-based systems that use convolutional codes. We then apply this framework to information set decoding, study…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…