相关论文: Combinatorial properties of phylogenetic diversity…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Federated Learning (FL) wherein multiple institutions collaboratively train a machine learning model without sharing data is becoming popular. Participating institutions might not contribute equally, some contribute more data, some better…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
To determine if two lists of numbers are the same set, we sort both lists and see if we get the same result. The sorted list is a canonical form for the equivalence relation of set equality. Other canonical forms arise in graph isomorphism…
Natural selection has produced an extraordinary diversity of life histories spanning many orders of magnitude in body size, vital rates, and biological times. In general, big and cold organisms grow and reproduce slowly and live long lives;…
Difficulties identifying appropriate biodiversity impact metrics remain a major barrier to inclusion of biodiversity considerations in environmentally responsible investment. We propose and analyse a simple science-based local metric: the…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian…
Estimating the effective sample size (ESS) is fundamental in Bayesian phylogenetic inference to properly account for autocorrelation in MCMC samples. While methods for continuous parameters are well established, the discrete and…
Random forest (RF) stands out as a highly favored machine learning approach for classification problems. The effectiveness of RF hinges on two key factors: the accuracy of individual trees and the diversity among them. In this study, we…
Despite their ubiquitous use, Shapley value feature attributions can be misleading due to feature interaction in both model and data. We propose an alternative attribution approach, Shapley Sets, which awards value to sets of features.…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
An Allee effect occurs when the per-capita growth rate increases at low densities. Here, we investigate the evolutionary stability of a partial migration population with migrant population experiencing Allee effects. Partial migration is a…
Variation and selection are the core principles of Darwinian evolution, yet quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
In this paper we at first consider plane trees with the root vertex and a marked directed edge, outgoing from the root vertex. For such trees we introduce a new characteristic --- the \emph{parity}, using the bracket code. It turns out that…
We argue that relative importance and its equitable attribution in terms of Shapley-Owen effects is an appropriate one, and, if we accept a small number of reasonable imperatives for equitable attribution, the only way to measure fairness.…