Related papers: Conspiracy in bacterial genomes
Bounds on the entropy of patterns of sequences generated by independently identically distributed (i.i.d.) sources are derived. A pattern is a sequence of indices that contains all consecutive integer indices in increasing order of first…
We introduce a new approach to functional causal modeling from observational data, called Causal Generative Neural Networks (CGNN). CGNN leverages the power of neural networks to learn a generative model of the joint distribution of the…
In this paper we have established relations of the genetic tables with magic and bimagic squares. Connections with Hamming distances, binomial coefficients are established. The idea of Gray code is applied. Shannon entropy of magic squares…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
In this paper, we introduce the general concept of coded power control (CPC) in a particular setting of the interference channel. Roughly, the idea of CPC consists in embedding information (about a random state) into the transmit power…
Complementarity relations between various characterizations of a probability distribution are at the core of information theory. In particular, lower and upper bounds for the entropic function are of great importance. In applied topics, we…
GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between…
We show that the essential properties of entropy (monotonicity, additivity and subadditivity) are consequences of entropy being a monoidal natural transformation from the under category functor $-/\mathsf{LProb}_{\rho}$ (where…
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…
We explore connections between homotopy type theory and information theory through homotopy cardinality. We define probability types and random variable types, prove that homotopy cardinality respects dependent sums under truncation and…
The lowest three moments of generalized parton distributions are calculated in full QCD and provide new insight into the behavior of nucleon electromagnetic form factors, the origin of the nucleon spin, and the transverse structure of the…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
We present a theory of particles, obeying intermediate statistics ("anyons"), interpolating between Bosons and Fermions, based on the principle of Detailed Balance. It is demonstrated that the scattering probabilities of identical particles…
Gamma distributions, which contain the exponential as a special case, have a distinguished place in the representation of near-Poisson randomness for statistical processes; typically, they represent distributions of spacings between events…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Considering vast amounts of genomic sequences of mostly unknown functionality, in-silico prediction of functional regions is an important enterprise. Many genomic browsers employ GC content, which was observed to be elevated in gene-rich…
Shannon's entropy is one of the building blocks of information theory and an essential aspect of Machine Learning methods (e.g., Random Forests). Yet, it is only finitely defined for distributions with fast decaying tails on a countable…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
We relate ordinary and skewed parton distributions to soft overlap contributions to elastic form factors and large angle Compton scattering, using light-cone wave functions in a Fock state expansion of the nucleon. With a simple ansatz for…