Related papers: L-infinity optimization to linear spaces and phylo…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
We introduce an efficient and scalable method for density-based multi-material topology optimization, integrating classical mirror descent techniques with point-wise polytopal design constraints. Such constraints arise naturally in this…
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$.…
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…
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 develop a unified spectral framework for finite ultrametric phylogenetic trees, grounding the analysis of phylogenetic structure in operator theory and stochastic dynamics in the finite setting. For a given finite ultrametric measure…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
Let $T$ be a tree, we show that the null space of the adjacency matrix of $T$ has relevant information about the structure of $T$. We introduce the Null Decomposition of trees, and use it in order to get formulas for independence number and…