相关论文: Polyhedral Combinatorics of UPGMA Cones

Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…

Arithmetic combinatorics is often concerned with the problem of bounding the behaviour of arbitrary finite sets in a group or ring with respect to arithmetic operations such as addition or multiplication. Similarly, combinatorial geometry…

We study sets of univariate hyperbolic polynomials that share the same first few coefficients and show that they have a natural combinatorial description akin to that of polytopes. We define a stratification of such sets in terms of root…

In 2019, Yoshida et al. introduced a notion of tropical principal component analysis (PCA). The output is a tropical polytope with a fixed number of vertices that best fits the data. We here apply tropical PCA to dimension reduction and…

In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…

We consider a family of parallel methods for constrained optimization based on projected gradient descents along individual coordinate directions. In the case of polyhedral feasible sets, local convergence towards a regular solution occurs…

This paper introduces a discrete relaxation for the class of combinatorial optimization problems which can be described by a set partitioning formulation under packing constraints. We present two combinatorial relaxations based on computing…

Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Deciding whether the union of two convex polyhedra is itself a convex polyhedron is a basic problem in polyhedral computations; having important applications in the field of constrained control and in the synthesis, analysis, verification…

Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In…

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 maximal clades in random phylogenetic trees with the Yule-Harding model or, equivalently, in binary search trees. We use probabilistic methods to reprove and extend earlier results on moment asymptotics and asymptotic normality. In…

We use the differential algebra of polytopes to explain the known remarkable relation of the combinatorics of the associahedra and permutohedra with the universal compositional and multiplicative inversion formulas for the formal power…

This is a survey on tropical polytopes from the combinatorial point of view and with a focus on algorithms. Tropical convexity is interesting because it relates a number of combinatorial concepts including ordinary convexity, monomial…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

In this paper we propose a method that uses Lagrange multipliers and numerical algebraic geometry to find all critical points, and therefore globally solve, polynomial optimization problems. We design a polyhedral homotopy algorithm that…

Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…

We study the interaction between two structures on the group of polynomial automorphisms of the affine plane: its structure as an amalgamated free product and as an infinite-dimensional algebraic variety. We introduce a new conjecture, and…

We use the characteristic polynomial of the Coxeter matrix of an algebra to complete the combinatorial classification of piecewise hereditary algebras which Happel gave in terms of the trace of the Coxeter matrix. We also give a…