Related papers: Terrace Aware Phylogenomic Inference from Supermat…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
A Bayesian treatment of latent directed graph structure for non-iid data is provided where each child datum is sampled with a directed conditional dependence on a single unknown parent datum. The latent graph structure is assumed to lie in…
High-dimensional time series phenotypic data is becoming increasingly common within plant breeding programmes. However, analysing and integrating such data for genetic analysis and genomic prediction remains difficult. Here we show how…
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
Probabilistic Regression Trees (PRTrees) generalize traditional decision trees by incorporating probability functions that associate each data point with different regions of the tree, providing smooth decisions and continuous responses.…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
In data analysis, latent variables play a central role because they help provide powerful insights into a wide variety of phenomena, ranging from biological to human sciences. The latent tree model, a particular type of probabilistic…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
Interpretability is crucial for doctors, hospitals, pharmaceutical companies and biotechnology corporations to analyze and make decisions for high stakes problems that involve human health. Tree-based methods have been widely adopted for…
Motivation: Single cell RNA sequencing (scRNA-seq) data makes studying the development of cells possible at unparalleled resolution. Given that many cellular differentiation processes are hierarchical, their scRNA-seq data is expected to be…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data,…
How can we effectively find the best structures in tree models? Tree models have been favored over complex black box models in domains where interpretability is crucial for making irreversible decisions. However, searching for a tree…
Positive selection drives the emergence of adaptive mutations in Mycobacterium tuberculosis, shaping drug resistance, transmissibility, and virulence. Phylogenetic trees capture evolutionary relationships among isolates and provide a…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…