Related papers: Parametric Fermat-Weber and tropical supertrees
Tropical geometry is a degeneration of classical geometry which loose the property of unique factorization for polynomials. In this paper we explore a structure that is known to be a semi-degeneration between the classical algebra and the…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
In this paper, a supersymmetric extension of the polytropic gas dynamics equations is constructed through the use of a superspace involving two independent fermionic variables and two bosonic superfields. A superalgebra of symmetries of the…
The tropical semiring is an algebraic system with addition ``$\max$'' and multiplication ``$+$''. As well as in conventional algebra, linear programming in the tropical semiring has been developed. In this study, we introduce a new type of…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Finding a common factor of two multivariate polynomials with approximate coefficients is a problem in symbolic-numeric computing. Taking a tropical view on this problem leads to efficient preprocessing techniques, applying polyhedral…
Abstractly, tropical hyperelliptic curves are metric graphs that admit a two-to-one harmonic morphism to a tree. They also appear as embedded tropical curves in the plane arising from triangulations of polygons with all interior lattice…
We construct generating trees with one, two, and three labels for some classes of permutations avoiding generalized patterns of length 3 and 4. These trees are built by adding at each level an entry to the right end of the permutation,…
In teleparallel geometries the coframe and corresponding spin-connection are the principal geometric objects and consequently the appropriate definition of a symmetry is that of an affine symmetry. The set of invariant coframes and their…
The meander problem is a combinatorial problem which provides a toy model of the compact folding of polymer chains. In this paper we study various questions relating to the enumeration of meander diagrams, using diagrammatical methods. By…
We study infinite tree and ultrametric matrices, and their action on the boundary of the tree. For each tree matrix we show the existence of a symmetric random walk associated to it and we study its Green potential. We provide a…
We introduce a scheme-theoretic enrichment of the principal objects of tropical geometry. Using a category of semiring schemes, we construct tropical hypersurfaces as schemes over idempotent semirings such as $\mathbb{T} = (\mathbb{R}\cup…
We study the properties of ultrametric matrices aiming to design methods for fast ultrametric matrix-vector multiplication. We show how to encode such a matrix as a tree structure in quadratic time and demonstrate how to use the resulting…
We present a supersymmetric model of fermion masses, based on a non-Abelian family symmetry and the Froggatt-Nielsen mechanism, that can account for the solar and atmospheric neutrino problems via quasi-degenerate neutrinos. The model…
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…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
We study the tropicalization of intersections of plane curves, under the assumption that they have the same tropicalization. We show that the set of tropical divisors that arise in this manner is a pure dimensional balanced polyhedral…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Extreme value statistics is the max analogue of classical statistics, while tropical geometry is the max analogue of classical geometry. In this paper, we review recent work where insights from tropical geometry were used to develop new,…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…