Related papers: Parametric Fermat-Weber and tropical supertrees
Metrics in Grassmannians, or distances between subspaces of same dimension, have many uses, and extending them to the Total Grassmannian of subspaces of different dimensions is an important problem, as usual extensions lack good properties…
We consider a model of random tree growth, where at each time unit a new vertex is added and attached to an already existing vertex chosen at random. The probability with which a vertex with degree $k$ is chosen is proportional to $w(k)$,…
We discuss the connection between supersymmetric field theories and topological field theories and show how this connection may be used to construct local lattice field theories which maintain an exact supersymmetry. It is shown how metric…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
In this paper, we explore a new type of global symmetries$-$the fermionic higher-form symmetries. They are generated by topological operators with fermionic parameter, which act on fermionic extended objects. We present a set of field…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
In this paper we present two intrinsic algebraic definitions of tropical variety motivated by the classical Zariski correspondence, one utilizing the algebraic structure of the coordinate semiring of an affine supertropical algebraic set,…
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…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
Merge trees are a common topological descriptor for data with a hierarchical component, such as terrains and scalar fields. The interleaving distance, in turn, is a common distance for comparing merge trees. However, the interleaving…
Mandelbrot and Frame studied the geometry of self-contracting symmetric binary trees in which they stated that the height of such trees occurred at the branch tip of the path consisting of branches that alternate left and right. Taylor…
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)…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
The problem of how to estimate diffusion on a graph effectively is of importance both theoretically and practically. In this paper, we make use of two widely studied indices, geodesic distance and mean first-passage time ($MFPT$) for random…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Teminal Wiener index is one of the commonly used topological index in mathematical chemistry. If two or more chemical compounds have the same terminal Wiener index then they will have similar physico-chemical properties. In this work we…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…