A phylogenetic tree can reflect the evolutionary relationships between species or gene
families, and they play a critical role in modern biological research. In this review, we …

Biological tree analysis serves as a pivotal tool in uncovering the evolutionary and
differentiation relationships among organisms, genes, and cells. Its applications span …

Phylogenetic trees provide a framework for organizing evolutionary histories across the tree
of life and aid downstream comparative analyses such as metagenomic identification …

Structural information of phylogenetic tree topologies plays an important role in phylogenetic
inference. However, finding appropriate topological structures for specific phylogenetic …

Motivation Phylogenetic placement of a query sequence on a backbone tree is increasingly
used across biomedical sciences to identify the content of a sample from its DNA content …

Principal Component Analysis (PCA) is a workhorse of modern data science. While PCA
assumes the data conforms to Euclidean geometry, for specific data types, such as …

Phylogenetic regression is a type of generalised least squares (GLS) method that
incorporates a modelled covariance matrix based on the evolutionary relationships between …

Hierarchical and tree-like data sets arise in many applications, including language
processing, graph data mining, phylogeny and genomics. It is known that tree-like data …

In this article, we study the distance matrix as a representation of a phylogeny by way of
hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the …

Hyperbolic geometry is gaining traction in machine learning for its effectiveness at capturing
hierarchical structures in real-world data. Hyperbolic spaces, where neighborhoods grow …