Related papers: An Entropy-Based Technique for Classifying Bacteri…
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
Motivation: Entropy measurements on hierarchical structures have been used in methods for information retrieval and natural language modeling. Here we explore its application to semantic similarity. By finding shared ontology terms,…
A simple method for categorizing texts into predetermined text genre categories using the statistical standard technique of discriminant analysis is demonstrated with application to the Brown corpus. Discriminant analysis makes it possible…
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 derive the amino acid assignment to one codon representation (typical 64-dimensional irreducible representation) of the basic classical Lie superalgebra osp(5|2) from biochemical arguments. We motivate the approach of mathematical…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
We propose an additional category of dimensionless groups based on the principle of {\it entropic similarity}, defined by ratios of (i) entropy production terms; (ii) entropy flow rates or fluxes; or (iii) information flow rates or fluxes.…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes is one of the crucial steps in the process and can be accomplished…
Comparison-based algorithms are algorithms for which the execution of each operation is solely based on the outcome of a series of comparisons between elements. Comparison-based computations can be naturally represented via the following…
This paper is devoted to change-point detection using only the ordinal structure of a time series. A statistic based on the conditional entropy of ordinal patterns characterizing the local up and down in a time series is introduced and…
It has been argued that the sum of usage probabilities for codons, belonging to quartets, that have as third nucleotide C or A, is independent of the biological species for vertebrates. The comparison between the theoretical correlation…
Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with quality criteria. There exists a bunch of…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
Encodings or the proof of their absence are the main way to compare process calculi. To analyse the quality of encodings and to rule out trivial or meaningless encodings, they are augmented with encodability criteria. There exists a bunch…
This article concerns testing for equality of distribution between groups. We focus on screening variables with shared distributional features such as common support, modes and patterns of skewness. We propose a Bayesian testing method…
The density classification task is to determine which of the symbols appearing in an array has the majority. A cellular automaton solving this task is required to converge to a uniform configuration with the majority symbol at each site. It…
International Classification of Diseases (ICD) are the de facto codes used globally for clinical coding. These codes enable healthcare providers to claim reimbursement and facilitate efficient storage and retrieval of diagnostic…
Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual…