Related papers: An Entropy-Based Technique for Classifying Bacteri…
Statistics of distinguishable particles has become relevant in systems of colloidal particles and in the context of applications of statistical mechanics to complex networks. When studying these type of systems with the standard textbook…
This work is an enquiry into the circumstances under which entropy methods can give an answer to the questions of both quantum separability and classical correlations of a composite state. Several entropy functionals are employed to examine…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…
Although several synonymous codons can encode the same aminoacid, this symmetry is generally broken in natural genetic systems. In this article, we show that the symmetry breaking can result from selective pressures due to the violation of…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
The similarity of local atomic environments is an important concept in many machine-learning techniques which find applications in computational chemistry and material science. Here, we present and discuss a connection between the…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Modelising the translation errors by suitable mathematical operators in the crystal basis model of the genetic code and requiring that codons prone to be misread encode the same amino-acid, the main features of the organisation in…
We introduce a novel approach, inspired from the theory of renewal processes, to determine the configurational entropy of ensembles of constrained configurations of particles on the one-dimensional lattice. The proposed method can deal with…
The entropy of network ensembles characterizes the amount of information encoded in the network structure, and can be used to quantify network complexity, and the relevance of given structural properties observed in real network datasets…
Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM…
There is a crescent use of enzymes in multiple industries and sciences, ranging from materials and fuel synthesis to pharmaceutical and food production. Their applicability in this variety of fields depends not only on their biochemical…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
Explanation-based generalization is used to extract a specialized grammar from the original one using a training corpus of parse trees. This allows very much faster parsing and gives a lower error rate, at the price of a small loss in…
Any continuous curve in a higher dimensional space can be considered a trajectory that can be parameterized by a single variable, usually taken as time. It is well known that a continuous curve can have a fractional dimensionality, which…
We introduce \emph{Term Coding}, a novel framework for analysing extremal problems in discrete mathematics by encoding them as finite systems of \emph{term equations} (and, optionally, \emph{non-equality constraints}). In its basic form,…
Automatic ICD coding is defined as assigning disease codes to electronic medical records (EMRs). Existing methods usually apply label attention with code representations to match related text snippets. Unlike these works that model the…
The discovery of nucleic acids and the structure of DNA have brought considerable advances in the understanding of life. The development of next-generation sequencing technologies has led to a large-scale generation of data, for which…