Related papers: When Do Phylogenetic Mixture Models Mimic Other Ph…

Despite the flexibility and popularity of mixture models, their associated parameter spaces are often difficult to represent due to fundamental identification problems. This paper looks at a novel way of representing such a space for…

Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the…

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…

Mixtures of regression are a powerful class of models for regression learning with respect to a highly uncertain and heterogeneous response variable of interest. In addition to being a rich predictive model for the response given some…

The widespread use of generative models has created a feedback loop, in which each generation of models is trained on data partially produced by its predecessors. This process has raised concerns about model collapse: A critical degradation…

Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…

Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…

Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…

Complex networks, modeled as large graphs, received much attention during these last years. However, data on such networks is only available through intricate measurement procedures. Until recently, most studies assumed that these…

Growth mixture models are an important tool for detecting group structure in repeated measures data. Unlike traditional clustering methods, they explicitly model the repeat measurements on observations, and the statistical framework they…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Mixture models combine multiple components into a single probability density function. They are a natural statistical model for many situations in astronomy, such as surveys containing multiple types of objects, cluster analysis in various…

Tree-shaped graphical models are widely used for their tractability. However, they unfortunately lack expressive power as they require committing to a particular sparse dependency structure. We propose a novel class of generative models…

Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…

Diversification models describe the random growth of evolutionary trees, modeling the historical relationships of species through speciation and extinction events. One class of such models allows for independently changing traits, or types,…

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…