Related papers: Halfspace Representations of Path Polytopes of Tre…
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
This article provides an overview of our joint work on binary polynomial optimization over the past decade. We define the multilinear polytope as the convex hull of the feasible region of a linearized binary polynomial optimization problem.…
We further the study of local profiles of trees. Bubeck and Linial showed that the set of 5-profiles contains a certain polytope, namely the convex hull of d-millipedes, and they proved that the segment [0-millipede, 1-millipede]…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
Tropical polytopes are images of polytopes in an affine space over the Puiseux series field under the degree map. This viewpoint gives rise to a family of cellular resolutions of monomial ideals which generalize the hull complex of Bayer…
The map which takes a square matrix $A$ to its polytrope is piecewise linear. We show that cones of linearity of this map form a polytopal fan partition of $\{R}^{n \times n}$, whose face lattice is anti-isomorphic to the lattice of…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
The Chow polytope of an algebraic cycle in a torus depends only on its tropicalisation. Generalising this, we associate a Chow polytope to any abstract tropical variety in a tropicalised toric variety. Several significant polyhedra…
An $S$-hypersimplex for $S \subseteq \{0,1, \dots,d\}$ is the convex hull of all $0/1$-vectors of length $d$ with coordinate sum in $S$. These polytopes generalize the classical hypersimplices as well as cubes, crosspolytopes, and…
Periodic trees are combinatorial structures which are in bijection with cluster tilting objects in cluster categories of affine type $\tilde{A}_{n-1}$. The internal edges of the tree encode the $c$-vectors corresponding to the cluster…
A dot-product representation of a graph is a mapping of its vertices to vectors of length $k$ so that vertices are adjacent if and only if the inner product (a.k.a. dot product) of their corresponding vertices exceeds some threshold.…
We introduce topological notions of polytopes and simplexes, the latter being expected to play in p-adically closed fields the role played by real simplexes in the classical results of triangulation of semi-algebraic sets over real closed…
A polytrope is a tropical polyhedron that is also classically convex. We study the tropical combinatorial types of polytropes associated to weighted directed acyclic graphs (DAGs). This family of polytropes arises in algebraic statistics…
Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure -- a barrier tree -- the leaves and internal nodes of which represent, respectively, the local minima and the…
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…
The space of phylogenetic trees arises naturally in tropical geometry as the tropical Grassmannian. Tropical geometry therefore suggests a natural notion of a tropical path between two trees, given by a tropical line segment in the tropical…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
This note wants to explain how to obtain meaningful pictures of (possibly high-dimensional) convex polytopes, triangulated manifolds, and other objects from the realm of geometric combinatorics such as tight spans of finite metric spaces…