Related papers: An Entropy-Based Technique for Classifying Bacteri…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…
The one-class classification problem is a well-known research endeavor in pattern recognition. The problem is also known under different names, such as outlier and novelty/anomaly detection. The core of the problem consists in modeling and…
New developments are presented in the framework of the model introduced by the authors in refs. [1,2] and in which nucleotides as well as codons are classified in crystal bases of the quantum group U_q(sl(2)+sl(2)) in the limit q -> 0. An…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
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…
In a recent paper, the authors proposed a general methodology for probabilistic learning on manifolds. The method was used to generate numerical samples that are statistically consistent with an existing dataset construed as a realization…
We use Topological Data Analysis tools for studying the inner organization of cells in segmented images of epithelial tissues. More specifically, for each segmented image, we compute different persistence barcodes, which codify lifetime of…
The spread of microbial infections is governed by the self-organization of bacteria on surfaces. Limitations of live imaging techniques make collective behaviors in clinically relevant systems challenging to quantify. Here, novel…
Shannon entropy is widely used to measure the complexity of DNA sequences but suffers from saturation effects that limit its discriminative power for long uniform segments. We introduce a novel metric, the entropy rank ratio R, which…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Diatoms, a major group of microalgae, play a critical role in global carbon cycling and primary production. Despite their ecological significance, comprehensive genomic resources for diatoms are limited. To address this, we have annotated…
This paper is a follow up to the authors' recent work on barcode entropy. We study the growth of the barcode of the Floer complex for the iterates of a compactly supported Hamiltonian diffeomorphism. In particular, we introduce sequential…
The determination of block-entropies is a well established method for the investigation of discrete data, also called symbols (7). There is a large variety of such symbolic sequences, ranging from texts written in natural languages,…
The Contextuality-by-Default approach to determining and measuring the (non)contextuality of a system of random variables requires that every random variable in the system be represented by an equivalent set of dichotomous random variables.…
Polyphonic music files were analyzed using the set of symbols that produced the Minimal Entropy Description which we call the Fundamental Scale. This allowed us to create a novel space to represent music pieces by developing: a) a method to…
The mean length and the variability of coding sequences for 48 genomes of bacteria and archaea were analyzed. It was found that the plotted data can be described by an angular area. This suggests the followings: a) The variability of a…
In this paper will be presented new approach to entropy coding: family of generalizations of standard numeral systems which are optimal for encoding sequence of equiprobable symbols, into asymmetric numeral systems - optimal for freely…