Related papers: Clades and clans: a comparison study of two evolut…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge…
Recently several authors have proposed stochastic evolutionary models for the growth of complex networks that give rise to power-law distributions. These models are based on the notion of preferential attachment leading to the ``rich get…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
The problem of categorical data analysis in high dimensions is considered. A discussion of the fundamental difficulties of probability modeling is provided, and a solution to the derivation of high dimensional probability distributions…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
Credible intervals and credible sets, such as highest posterior density (HPD) intervals, form an integral statistical tool in Bayesian phylogenetics, both for phylogenetic analyses and for development. Readily available for continuous…
In the density estimation model, the question of adaptive inference using P\'olya tree-type prior distributions is considered. A class of prior densities having a tree structure, called spike-and-slab P\'olya trees, is introduced. For this…
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where…
We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with…
Probabilistic programming languages and other machine learning applications often require samples to be generated from a categorical distribution where the probability of each one of $n$ categories is specified as a parameter. If the…
We consider a model of aggregation, both diffusion-limited and ballistic, based on the Cayley tree. Growth is from the leaves of the tree towards the root, leading to non-trivial screening and branch competition effects. The model exhibits…
We introduce Exponential Family Discriminant Analysis (EFDA), a unified generative framework that extends classical Linear Discriminant Analysis (LDA) beyond the Gaussian setting to any member of the exponential family. Under the assumption…
When using machine learning for imbalanced binary classification problems, it is common to subsample the majority class to create a (more) balanced training dataset. This biases the model's predictions because the model learns from data…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
We propose a phylogenetic approach (PA) as a novel and robust tool to detect galaxy populations (GPs) based on their chemical composition. The branches of the tree are interpreted as different GPs and the length between nodes as the…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are…
Using graphical methods based on a `lookdown' and pruned version of the {\em ancestral selection graph}, we obtain a representation of the type distribution of the ancestor in a two-type Wright-Fisher population with mutation and selection,…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…