Related papers: The genetic code, 8-dimensional hypercomplex numbe…
We introduce the gonosomal algebra. Gonosomal algebra extend the evolution algebra of the bisexual population (EABP) defined by Ladra and Rozikov. We show that gonosomal algebras can represent algebraically a wide variety of sex…
The mitosis process of an eukaryotic cell can be represented by the structure constants of an evolution algebra. Any isotopism of the latter corresponds to a mutation of genotypes of the former. This paper uses Computational Algebraic…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
The string theory landscape may include a multitude of ultraviolet embeddings of the Standard Model, but identifying these has proven difficult due to the enormous number of available string compactifications. Genetic Algorithms (GAs)…
This paper studies the properties of two kinds of matroids: (a) algebraic matroids and (b) finite and infinite matroids whose ground set have some canonical symmetry, for example row and column symmetry and transposition symmetry. For (a)…
The tree based representation described in this paper, hereditarily binary numbers, applies recursively a run-length compression mechanism that enables computations limited by the structural complexity of their operands rather than by their…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases…
Motivated by the Hadamard product of matrices we define the Hadamard product of multivariate polynomials and study its arithmetic circuit and branching program complexity. We also give applications and connections to polynomial identity…
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…
The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of a presentation of each sequence in a form of three digital binary sequences. This method uses biochemical attributes of nucleotides…
Graphs and hypergraphs combine expressive modeling power with algorithmic efficiency for a wide range of applications. Hedgegraphs generalize hypergraphs further by grouping hyperedges under a color/hedge. This allows hedgegraphs to model…
Hypergraphs provide a natural framework to model higher-order interactions in scientific, social, and biological systems. Hypergraph neural networks (HGNNs) aim to learn from such data, yet it remains unclear which higher-order structures…
We propose a way of characterizing the algorithms computing a Walsh-Hadamard transform that consist of a sequence of arrays of butterflies ($I_{2^{n-1}}\otimes \text{DFT}_2$) interleaved by linear permutations. Linear permutations are those…
There has been significant recent interest towards achieving highly efficient deep neural network architectures. A promising paradigm for achieving this is the concept of evolutionary deep intelligence, which attempts to mimic biological…
Application of Genetic Algorithm (GA) for determination of parameters of an analytical representation of diatomic molecule potential is presented. GA can be used for finding potential characteristics of an electronic energy state which can…
Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…
We study a random code ensemble with a hierarchical structure, which is closely related to the generalized random energy model with discrete energy values. Based on this correspondence, we analyze the hierarchical random code ensemble by…
An iterative decoding algorithm for convolutional codes is presented. It successively processes $N$ consecutive blocks of the received word in order to decode the first block. A bound is presented showing which error configurations can be…
Bialgebras and Hopf (bi)modules are typical algebraic structures with several interacting operations. Their structural and homological study is therefore quite involved. We develop the machinery of braided systems, tailored for handling…