Related papers: The Geometry of the Neighbor-Joining Algorithm for…
We describe a technique to reorganize topologies of Steiner trees by exchanging neighbors of adjacent Steiner points. We explain how to use the systematic way of building trees, and therefore topologies, to find the correct topology after…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
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…
Graph embeddings learn the structure of networks and represent it in low-dimensional vector spaces. Community structure is one of the features that are recognized and reproduced by embeddings. We show that an iterative procedure, in which a…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is a widely used clustering method. Here we show that UPGMA is a greedy heuristic for the normalized equidistant minimum evolution (NEME) problem, that is, finding a rooted tree that…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
Proximity graph-based methods have emerged as a leading paradigm for approximate nearest neighbor (ANN) search in the system community. This paper presents fresh insights into the theoretical foundation of these methods. We describe an…
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…
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…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
We consider in this paper the problem of discovering, via a traceroute algorithm, the topology of a network, whose graph is spanned by an infinite branching process. A subset of nodes is selected according to some criterion. As a measure of…
We propose a new architecture for difficult image processing operations, such as natural edge detection or thin object segmentation. The architecture is based on a simple combination of convolutional neural networks with the nearest…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
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…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
Network reconstruction consists in determining the unobserved pairwise couplings between $N$ nodes given only observational data on the resulting behavior that is conditioned on those couplings -- typically a time-series or independent…