Related papers: Maximum parsimony distance on phylogenetictrees: a…
This paper relates parameter distance to gradient breakdown for a broad class of nonlinear compositional functions. The analysis leads to a new distance function called deep relative trust and a descent lemma for neural networks. Since the…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Finding an optimal assignment between two sets of objects is a fundamental problem arising in many applications, including the matching of `bag-of-words' representations in natural language processing and computer vision. Solving the…
Extending some properties from the Euclidean plane to any normed plane, we show the validity of the Monma-Paterson-Suri-Yao algorithm for finding the maximum-weighted spanning tree of a set of $n$ points, where the weight of an edge is the…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
Gromov-Hausdorff (GH) distance is a natural way to measure the distortion between two metric spaces. However, there has been only limited algorithmic development to compute or approximate this distance. We focus on computing the…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
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.…
Given a graph $G=(V,E)$ with non-negative real edge lengths and an integer parameter $k$, the Min-Max k-Tree Cover problem seeks to find a set of at most $k$ subtrees of $G$, such that the union of the trees is the vertex set $V$. The…
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…
Given two sets of points in the plane, $P$ of $n$ terminals and $S$ of $m$ Steiner points, a Steiner tree of $P$ is a tree spanning all points of $P$ and some (or none or all) points of $S$. A Steiner tree with length of longest edge…
Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
Phylogenetic networks are notoriously difficult to reconstruct. Here we suggest that it can be useful to view unknown genetic distance along edges in phylogenetic networks as analogous to unknown resistance in electric circuits. This…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
The minimum height of vertex and edge partition trees are well-studied graph parameters known as, for instance, vertex and edge ranking number. While they are NP-hard to determine in general, linear-time algorithms exist for trees.…
Cubicity of a graph $G$ is the smallest dimension $d$, for which $G$ is a unit disc graph in ${\mathbb{R}}^d$, under the $l^\infty$ metric, i.e. $G$ can be represented as an intersection graph of $d$-dimensional (axis-parallel) unit…