Related papers: CVTree for 16S rRNA: Constructing Taxonomy-Compati…
In this paper, we propose DeepTree, a novel method for modeling trees based on learning developmental rules for branching structures instead of manually defining them. We call our deep neural model situated latent because its behavior is…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
Decision trees are a commonly used class of machine learning models valued for their interpretability and versatility, capable of both classification and regression. We propose ZTree, a novel decision tree learning framework that replaces…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
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…
In image classification, Convolutional Neural Network(CNN) models have achieved high performance with the rapid development in deep learning. However, some categories in the image datasets are more difficult to distinguished than others.…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
A decision tree is commonly restricted to use a single hyperplane to split the covariate space at each of its internal nodes. It often requires a large number of nodes to achieve high accuracy, hurting its interpretability. In this paper,…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
While Vision-Language Models (VLMs) excel at visual understanding, they often fail to grasp hierarchical knowledge. This leads to common errors where VLMs misclassify coarser taxonomic levels even when correctly identifying the most…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…