Related papers: Codon Usage Bias Measured Through Entropy Approach
Entropy has emerged as a dynamic, interdisciplinary, and widely accepted quantitative measure of uncertainty across different disciplines. A unified understanding of entropy measures, supported by a detailed review of their theoretical…
Evaluating the performance of generative models in image synthesis is a challenging task. Although the Fr\'echet Inception Distance is a widely accepted evaluation metric, it integrates different aspects (e.g., fidelity and diversity) of…
A method for estimating the Shannon differential entropy of multidimensional random variables using independent samples is described. The method is based on decomposing the distribution into a product of the marginal distributions and the…
In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the…
In this perspective, the various measures of electron correlation used in wavefunction theory, density functional theory and quantum information theory are briefly reviewed. We then focus on a more traditional metric based on dominant…
Cosine similarity is an established similarity metric for computing associations on vectors, and it is commonly used to identify related samples from biological perturbational data. The distribution of cosine similarity changes with the…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Background Synonymous codon choice is mainly affected by mutation and selection. For the majority of genes within a genome, mutational pressure is the major driving force, but selective strength can be strong and dominant for specific set…
Quantifying coherence is a key task in both quantum mechanical theory and practical applications. Here, a reliable quantum coherence measure is presented by utilizing the quantum skew information of the state of interest subject to a…
Mixture distributions are extensively used as a modeling tool in diverse areas from machine learning to communications engineering to physics, and obtaining bounds on the entropy of probability distributions is of fundamental importance in…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
We explore the relation between entanglement entropy of quantum many body systems and the distribution of corresponding, properly selected, observables. Such a relation is necessary to actually measure the entanglement entropy. We show that…
The profile of a sample is the multiset of its symbol frequencies. We show that for samples of discrete distributions, profile entropy is a fundamental measure unifying the concepts of estimation, inference, and compression. Specifically,…
A mathematical description of heterodyne measurement of an optical frequency comb is presented. It is shown that for a signal beam containing many frequency teeth, the amplitude and phase of each tooth can be determined from the beatnote…
A frequency counter measures the input frequency $\bar{\nu}$ averaged over a suitable time $\tau$, versus the reference clock. High resolution is achieved by interpolating the clock signal. Further increased resolution is obtained by…
In this study, we employ purity benchmarking (PB) to explore the dynamics of gate noise in a superconducting qubit system. Over 1110 hours of observations on an Xmon qubit, we simultaneously measure the coherence noise budget across two…
We employ the time-dependent non-crossing approximation to study the time averaged conductance for a single electron transistor in the Kondo regime when the dot level is sinusoidally driven from its equilibrium position by means of a gate…
Bacteria meticulously regulate their intracellular ion concentrations and create ionic concentration gradients across the bacterial membrane. These ionic concentration gradients provide free energy for many cellular processes and are…
Inter-coder agreement measures, like Cohen's kappa, correct the relative frequency of agreement between coders to account for agreement which simply occurs by chance. However, in some situations these measures exhibit behavior which make…