相关论文: Species tree inference by the STAR method, and gen…

We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the…

Staged tree models are a discrete generalization of Bayesian networks. We show that these form curved exponential families and derive their natural parameters, sufficient statistic, and cumulant-generating function as functions of their…

The spanning tree heuristic is a commonly adopted procedure in network inference and estimation. It allows one to generalize an inference method developed for trees, which is usually based on a statistically rigorous approach, to a…

Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…

We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates…

Tree ensembles such as random forests and boosted trees are accurate but difficult to understand, debug and deploy. In this work, we provide the inTrees (interpretable trees) framework that extracts, measures, prunes and selects rules from…

Due to their accuracies, methods based on ensembles of regression trees are a popular approach for making predictions. Some common examples include Bayesian additive regression trees, boosting and random forests. This paper focuses on…

Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…

Knowing the causal structure of a system is of fundamental interest in many areas of science and can aid the design of prediction algorithms that work well under manipulations to the system. The causal structure becomes identifiable from…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Differential evolution possesses a multitude of various strategies for generating new trial solutions. Unfortunately, the best strategy is not known in advance. Moreover, this strategy usually depends on the problem to be solved. This paper…

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along…

Terraces are potentially large sets of trees with precisely the same likelihood or parsimony score, which can be induced by missing sequences in partitioned multi-locus phylogenetic data matrices. The set of trees on a terrace can be…

Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…

We study several enumeration problems connected to linear trees, a broad class which includes stars, paths, generalized stars, and caterpillars. We provide generating functions for counting the number of linear trees on $n$ vertices,…

Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…

Model performance is frequently reported only for the overall population under consideration. However, due to heterogeneity, overall performance measures often do not accurately represent model performance within specific subgroups. We…

An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…