Related papers: Infinite Mixture Models for Improved Modeling of A…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
For exchangeable data, mixture models are an extremely useful tool for density estimation due to their attractive balance between smoothness and flexibility. When additional covariate information is present, mixture models can be extended…
Prototyping robotic systems is a time consuming process. Computer aided design, however, might speed up the process significantly. Quality-diversity evolutionary approaches optimise for novelty as well as performance, and can be used to…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Researchers frequently wish to assess the equality or inequality of groups, but this poses the challenge of adequately adjusting for multiple comparisons. Statistically, all possible configurations of equality and inequality constraints can…
Statistical modelling in the presence of data organized in groups is a crucial task in Bayesian statistics. The present paper conceives a mixture model based on a novel family of Bayesian priors designed for multilevel data and obtained by…
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
Diffusion Models have become a cornerstone of modern generative AI for their exceptional generation quality and controllability. However, their inherent \textit{multi-step iterations} and \textit{complex backbone networks} lead to…
Stacking is a widely used model averaging technique that asymptotically yields optimal predictions among linear averages. We show that stacking is most effective when model predictive performance is heterogeneous in inputs, and we can…
We consider models for molecular sequence evolution in which the transition rates at each site depend on the local sequence context, giving rise to a time-inhomogeneous Markov process in which sites evolve under a complex dependency…
Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing…
The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…
Traditional methods for unsupervised learning of finite mixture models require to evaluate the likelihood of all components of the mixture. This becomes computationally prohibitive when the number of components is large, as it is, for…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account…
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
We develop two models for Bayesian estimation and selection in high-order, discrete-state Markov chains. Both are based on the mixture transition distribution, which constructs a transition probability tensor with additive mixing of…