相关论文: Simplified amino acid alphabets based on deviation…
The problem of characterizing trees with minimal atom-bond-connectivity index (minimal-ABC trees) has a reputation as one of the most demanding recent open optimization problems in mathematical chemistry. Here firstly, we give an…
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…
Automatic phylogenetic inference plays an increasingly important role in computational historical linguistics. Most pertinent work is currently based on expert cognate judgments. This limits the scope of this approach to a small number of…
The mathematical concept of q-deformations, in particular the one of qnumbers, is used to study the genetic code(s). After considering two kinds of q-numbers, for comparison, a phenomenological classification scheme of the genetic code…
In this paper, we quantify weak protein protein interactions in solution using Cross-Interaction Chromatography (CIC) and Surface Plasmon Resonance (SPR) and demonstrate that they can be modulated by the addition of free amino acids. With…
In a recent paper, Klaere et al. modeled the impact of substitutions on arbitrary branches of a phylogenetic tree on an alignment site by the so-called One Step Mutation (OSM) matrix. By utilizing the concept of the OSM matrix for the…
This work is focused on improving the character recognition capability of feed-forward back-propagation neural network by using one, two and three hidden layers and the modified additional momentum term. 182 English letters were collected…
In multi-level systems, the commonly used adiabatic elimination is a method for approximating the dynamics of the system by eliminating irrelevant, non-resonantly coupled levels. This procedure is, however, somewhat ambiguous and it is not…
We reformulated the string formalism given by Aoyama, using an adjacent matrix of a network and introduced a series of generalized clustering coefficients based on it. Furthermore we numerically evaluated Milgram condition proposed by their…
Proteins are the essential drivers of biological processes. At the molecular level, they are chains of amino acids that can be viewed through a linguistic lens where the twenty standard residues serve as an alphabet combining to form a…
In prefix coding over an infinite alphabet, methods that consider specific distributions generally consider those that decline more quickly than a power law (e.g., Golomb coding). Particular power-law distributions, however, model many…
Contextual biasing improves rare word recognition of ASR models by prioritizing the output of rare words during decoding. A common approach is Trie-based biasing, which gives "bonus scores" to partial hypothesis (e.g. "Bon") that may lead…
Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever) explanation of why living organisms have 4…
Kolmogorov complexity of a finite binary word reflects both algorithmic structure and the empirical distribution of symbols appearing in the word. Words with symbol frequencies far from one half have smaller combinatorial richness and…
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results…
Given two sequences over a finite alphabet $\mathcal{L}$, the $D_2$ statistic is the number of $m$-letter word matches between the two sequences. This statistic is used in bioinformatics for expressed sequence tag database searches. Here we…
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of residue substitutions from amino acid sequences is also…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
We consider polar codes for memoryless sources with side information and show that the blocklength, construction, encoding and decoding complexities are bounded by a polynomial of the reciprocal of the gap between the compression rate and…
We describe a novel algorithm for random sampling of freely reduced words equal to the identity in a finitely presented group. The algorithm is based on Metropolis Monte Carlo sampling. The algorithm samples from a stretched Boltzmann…