相关论文: Combinatorial properties of phylogenetic diversity…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
Since the debut of Evolution Strategies (ES) as a tool for Reinforcement Learning by Salimans et al. 2017, there has been interest in determining the exact relationship between the Evolution Strategies gradient and the gradient of a similar…
An interactive stochastics, evaluated by an entropy functional (EF) of a random field and informational process' path functional (IPF), allows us modeling the evolutionary information processes and revealing regularities of evolution…
We are facing a real challenge when coping with the continuous acceleration of scientific production and the increasingly changing nature of science. In this article, we extend the classical framework of co-word analysis to the study of…
A self-similar growth-fragmentation describes the evolution of particles that grow and split as time passes. Its genealogy yields a self-similar continuum tree endowed with an intrinsic measure. Extending results of Haas for pure…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
In abstract terms, ecosystem ecology is about determining when two ecosystems, superficially different, are alike in some deeper way. An external observer can choose any ecosystem property as being important. In contrast, two ecosystems are…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Staged trees are a recently-developed, powerful family of probabilistic graphical models. An equivalence class of staged trees has now been characterised, and two fundamental statistical operators have been defined to traverse the…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Tree balance plays an important role in phylogenetics and other research areas, which is why several indices to measure tree balance have been introduced over the years. Nevertheless, a formal definition of what a balance index actually is…
Cohort Shapley value is a model-free method of variable importance grounded in game theory that does not use any unobserved and potentially impossible feature combinations. We use it to evaluate algorithmic fairness, using the well known…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
Ordered leaf attachment, Phylo2Vec, and HOP are three recently introduced vector representations for rooted phylogenetic trees where the representation is determined by an ordering of the underlying leaf set X. Comparing the vectors of two…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…