scholarly journals Central Moments and Probability Distributions of Three Measures of Phylogenetic Tree Imbalance

1996 ◽  
Vol 45 (1) ◽  
pp. 99-110 ◽  
Author(s):  
James S. Rogers
Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1118
Author(s):  
Eivind Schneider

Due to the principle of minimal information gain, the measurement of points in an affine space V determines a Legendrian submanifold of V×V*×R. Such Legendrian submanifolds are equipped with additional geometric structures that come from the central moments of the underlying probability distributions and are invariant under the action of the group of affine transformations on V. We investigate the action of this group of affine transformations on Legendrian submanifolds of V×V*×R by giving a detailed overview of the structure of the algebra of scalar differential invariants, and we show how the scalar differential invariants can be constructed from the central moments. In the end, we view the results in the context of equilibrium thermodynamics of gases, and notice that the heat capacity is one of the differential invariants.


2021 ◽  
Author(s):  
Caleb P. Charpentier ◽  
April Wright

1: Phylogenetic methods are increasingly complex. Researchers need to make many choices about how to model different aspects of the data appropriately. It is increasingly common to deploy hierarchical Bayesian models in which different data types may be described by different processes. This necessitates tools to help users understand model assumptions more clearly.2: We describe the package \code{Revticulate}, which provides an R-based interface to the software RevBayes. RevBayes is a Bayesian phylogenetics program that implements an R-like computing language, but does not interface with R itself. Revticulate was designed to allow communication between an R session, and all of its associated capabilities, such as plotting and simulation, and a RevBayes session.3: Revticulate can be used to copy objects from RevBayes into R. We provide several usage examples demonstrating how objects, such as such as random variables drawn from probability distributions and phylogenetic trees, can be generated in RevBayes. We then show how these objects can be used with R's phylogenetic ecosystem to plot a phylogenetic tree, or with base R functions to simulate the behavior of a particular probability. 4: Revticulate is a broadly useful software. Revticulate can be used alongside popular document preparation packages, such as Knitr and pkgdown to generate attractive reports, tutorials, and websites. This means that researchers who are looking to communicate their work in RevBayes can do that very easily using Revticulate, enabling rapid generation of reproducible research outputs.


1997 ◽  
Vol 161 ◽  
pp. 197-201 ◽  
Author(s):  
Duncan Steel

AbstractWhilst lithopanspermia depends upon massive impacts occurring at a speed above some limit, the intact delivery of organic chemicals or other volatiles to a planet requires the impact speed to be below some other limit such that a significant fraction of that material escapes destruction. Thus the two opposite ends of the impact speed distributions are the regions of interest in the bioastronomical context, whereas much modelling work on impacts delivers, or makes use of, only the mean speed. Here the probability distributions of impact speeds upon Mars are calculated for (i) the orbital distribution of known asteroids; and (ii) the expected distribution of near-parabolic cometary orbits. It is found that cometary impacts are far more likely to eject rocks from Mars (over 99 percent of the cometary impacts are at speeds above 20 km/sec, but at most 5 percent of the asteroidal impacts); paradoxically, the objects impacting at speeds low enough to make organic/volatile survival possible (the asteroids) are those which are depleted in such species.


2020 ◽  
pp. 37-40

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.


2020 ◽  
Vol 3 (1) ◽  
pp. 10501-1-10501-9
Author(s):  
Christopher W. Tyler

Abstract For the visual world in which we operate, the core issue is to conceptualize how its three-dimensional structure is encoded through the neural computation of multiple depth cues and their integration to a unitary depth structure. One approach to this issue is the full Bayesian model of scene understanding, but this is shown to require selection from the implausibly large number of possible scenes. An alternative approach is to propagate the implied depth structure solution for the scene through the “belief propagation” algorithm on general probability distributions. However, a more efficient model of local slant propagation is developed as an alternative.The overall depth percept must be derived from the combination of all available depth cues, but a simple linear summation rule across, say, a dozen different depth cues, would massively overestimate the perceived depth in the scene in cases where each cue alone provides a close-to-veridical depth estimate. On the other hand, a Bayesian averaging or “modified weak fusion” model for depth cue combination does not provide for the observed enhancement of perceived depth from weak depth cues. Thus, the current models do not account for the empirical properties of perceived depth from multiple depth cues.The present analysis shows that these problems can be addressed by an asymptotic, or hyperbolic Minkowski, approach to cue combination. With appropriate parameters, this first-order rule gives strong summation for a few depth cues, but the effect of an increasing number of cues beyond that remains too weak to account for the available degree of perceived depth magnitude. Finally, an accelerated asymptotic rule is proposed to match the empirical strength of perceived depth as measured, with appropriate behavior for any number of depth cues.


2017 ◽  
Vol 9 (4) ◽  
pp. 59-66
Author(s):  
M. Forghani ◽  
P. Vasev ◽  
V. Averbukh

2009 ◽  
Vol 29 (3) ◽  
pp. 836-838
Author(s):  
Gang-cheng LI ◽  
Zan-bo LIU ◽  
Qing-guang ZENG

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