Related papers: Identification of possible differences in coding a…
Recurrence quantification analysis is a widely used method for characterizing patterns in time series. This article presents a comprehensive survey for conducting a wide range of recurrence-based analyses to quantify the dynamical structure…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
Recurrence quantification analysis (RQA) is a widely used tool for studying complex dynamical systems, but its standard implementation requires computationally expensive calculations of recurrence plots (RPs) and line length histograms.…
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…
Recurrence quantification analysis (RQA) is a well established method of nonlinear data analysis. In this work we present a new strategy for an almost parameter-free RQA. The approach finally omits the choice of the threshold parameter by…
Test-time compute is central to large reasoning models, yet analysing their reasoning behaviour through generated text is increasingly impractical and unreliable. Response length is often used as a brute proxy for reasoning effort, but this…
In this work we explore the possibility of using Recurrence Quantification Analysis (RQA) in astronomical high-contrast imaging to statistically discriminate the signal of faint objects from speckle noise. To this end, we tested RQA on a…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Recurrence Quantification Analysis (RQA) defines a number of quantifiers, which base upon diagonal line structures in the recurrence plot (RP). Due to the finite size of an RP, these lines can be cut by the borders of the RP and, thus, bias…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
One challenge with the analysis of complex systems and the interaction between such systems is that they are composed of different numbers of components, or simply the fact that a different number of observables is available for each…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
Recurrence plots (RPs) are powerful tools for visualizing time series dynamics; however, traditional Recurrence Quantification Analysis (RQA) often relies on global metrics, such as line counting, that can overlook system-specific,…
Quantization has been an effective technology in ANN (approximate nearest neighbour) search due to its high accuracy and fast search speed. To meet the requirement of different applications, there is always a trade-off between retrieval…
Based on a model first studied in [Physical Review A, vol. 43, 5240-5260,1991] properties of correlation function for expansion-modification systems are developed. The existence of several characteristic exponents is proved. The…
Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
Recurrence plots were introduced to help aid the detection of signals in complicated data series. This effort was furthered by the quantification of recurrence plot elements. We now demonstrate the utility of combining recurrence…
Financial markets are systems with the complex behavior, that can be hardly analyzed by means of linear methods. Recurrence Quantification Analysis (RQA) is a nonlinear methodology, which is able to work with the nonstationary and short…
The nature of the quantitative distribution of the 64 DNA codons in the human genome has been an issue of debate for over a decade. Some groups have proposed that the quantitative distribution of the DNA codons ordered as a rank-frequency…