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In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

For years, recursive neural networks (RvNNs) have been shown to be suitable for representing text into fixed-length vectors and achieved good performance on several natural language processing tasks. However, the main drawback of RvNNs is…

We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…

Automated analysis of imaged phenotypes enables fast and reproducible quantification of biologically relevant features. Despite recent developments, recordings of complex, networked structures, such as: leaf venation patterns, cytoskeletal…

Recent advances in generative models, such as diffusion models, have made generating high-quality synthetic images widely accessible. Prior works have shown that training on synthetic images improves many perception tasks, such as image…

PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out…

The generative modeling landscape has experienced tremendous growth in recent years, particularly in generating natural images and art. Recent techniques have shown impressive potential in creating complex visual compositions while…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…

The design of complex engineering systems is an often long and articulated process that highly relies on engineers' expertise and professional judgment. As such, the typical pitfalls of activities involving the human factor often manifest…

Natural language definitions of terms can serve as a rich source of knowledge, but structuring them into a comprehensible semantic model is essential to enable them to be used in semantic interpretation tasks. We propose a method and…

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…

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer…

UniFrac is a family of distance metrics over microbial abundances, that take taxonomic relatedness into account. Current tools and libraries for calculating UniFrac have specific requirements regarding the user's technical expertise,…

This paper offers a new authentication algorithm based on image matching of nano-resolution visual identifiers with tree-shaped patterns. The algorithm includes image-to-tree conversion by greedy extraction of the fractal pattern skeleton…

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…

Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…

Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…