Related papers: Imputing phylogenetic trees using tropical polytop…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
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…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
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…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…
Given a tree $T$, its path polytope is the convex hull of the edge indicator vectors for the paths between any two distinct leaves in $T$. These polytopes arise naturally in polyhedral geometry and applications, such as phylogenetics,…
In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming…