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This paper addresses a theory of R(p,q)-deformed combinatorics in discrete probability. It mainly focuses on R(p,q)-deformed factorials, binomial coefficients, Vandermonde's formula, Cauchy's formula, binomial and negative binomial…
Gaussian binomial coefficients are q-analogues of the binomial coefficients of integers. On the other hand, binomial coefficients have been extended to finite words, i.e., elements of the finitely generated free monoids. In this paper we…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
In the framework of the crystal basis model of the genetic code, where each codon is assigned to an irreducible representation of $U_{q \to 0}(sl(2) \oplus sl(2))$, single base mutation matrices are introduced. The strength of the mutation…
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function…
In the second paper of this series we extend our Bayesian reanalysis of the evidence for a cosmic variation of the fine structure constant to the semi-parametric modelling regime. By adopting a mixture of Dirichlet processes prior for the…
In this article, after introducing a kind of q-deformation in quantum mechanics, first, q-deformed form of Dirac equation in relativistic quantum mechanics is derived. Then three important scat erring problem in physics are studied. All…
We prove the well-definedness of some deformations of the fibred biset category in characteristic zero. The method is to realize the fibred biset category and the deformations as the invariant parts of some categories whose compositions are…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
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…
By exploiting the connection between scattered $\mathbb{F}_q$-subspaces of $\mathbb{F}_{q^m}^3$ and minimal non degenerate $3$-dimensional rank metric codes of $\mathbb{F}_{q^m}^{n}$, $n \geq m+2$, described in [2], we will exhibit a new…
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…
This paper is a continuation of our first paper [10] in which we showed how deformation theory of representation varieties can be used to study finite simple quotients of triangle groups. While in Part I, we mainly used deformations of the…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
In this work, we study a class of generalized quasi-cyclic (GQC) codes called skew GQC codes. By the factorization theory of ideals, we give the Chinese Remainder Theorem over the skew polynomial ring, which leads to a canonical…
The case-control design is often used to test associations between the case-control status and genetic variants. In addition to this primary phenotype a number of additional traits, known as secondary phenotypes, are routinely recorded and…
We present a novel approach to semi-supervised learning which is based on statistical physics. Most of the former work in the field of semi-supervised learning classifies the points by minimizing a certain energy function, which corresponds…
We use semi--classical and perturbation methods to establish the quantum theory of the Neumann model, and explain the features observed in previous numerical computations.
A many variable $q$-calculus is introduced using the formalism of braided covector algebras. Its properties when certain of its deformation parameters are roots of unity are discussed in detail, and related to fractional supersymmetry. The…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…