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The reconstruction of phylogenetic trees from discrete character data typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate $\lambda$. When $\lambda$ is too high…
We introduce an efficient and scalable method for density-based multi-material topology optimization, integrating classical mirror descent techniques with point-wise polytopal design constraints. Such constraints arise naturally in this…
We study the Bergman complex B(M) of a matroid M: a polyhedral complex which arises in algebraic geometry, but which we describe purely combinatorially. We prove that a natural subdivision of the Bergman complex of M is a geometric…
We develop a tropical analogue of the classical double description method allowing one to compute an internal representation (in terms of vertices) of a polyhedron defined externally (by inequalities). The heart of the tropical algorithm is…
There is a well known correspondence between the triangle inequality for a distance function on a finite set, and idempotency of an associated matrix over the tropical semiring. Recent research has shed new light on the structure…
The set of ultrametrics on $[n]$ nodes that are $\ell^\infty$-nearest to a given dissimilarity map forms a $(\max,+)$ tropical polytope. Previous work of Bernstein has given a superset of the set containing all the phylogenetic trees that…
We obtain structure theorems for graphs excluding a fan (a path with a universal vertex) or a dipole ($K_{2,k}$) as a topological minor. The corresponding decompositions can be computed in FPT linear time. This is motivated by the study of…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
We extend the tropical intersection theory to tropicalizations of germs of analytic sets. In particular, we construct a (not entirely obvious) local version of the ring of tropical fans with a nondegenerate intersection pairing. As an…
The motivic nearby fiber is an invariant obtained from degenerating a complex variety over a disc. It specializes to the Euler characteristic of the original variety but also contains information on the variation of Hodge structure…
Polytropes are both ordinary and tropical polytopes. We show that tropical types of polytropes in $\mathbb{TP}^{n-1}$ are in bijection with cones of a certain Gr\"{o}bner fan $\mathcal{GF}_n$ in $\mathbb{R}^{n^2 - n}$ restricted to a small…
This work studies the combinatorial optimization problem of finding an optimal core tensor shape, also called multilinear rank, for a size-constrained Tucker decomposition. We give an algorithm with provable approximation guarantees for its…
We compute an $L_\infty$-algebroid structure on a projective resolution of some classes of singular foliations on a vector space $V$ induced by the linear action of some Lie subalgebra of $\mathfrak {gl}(V)$. This $L_\infty$-algebroid…
In this paper, a link between polymatroid theory and locally repairable codes (LRCs) is established. The codes considered here are completely general in that they are subsets of $A^n$, where $A$ is an arbitrary finite set. Three classes of…
We extend reconstruction methods for phylogenetic trees to ultrametrics of arbitrary matroids and study the stability of these data analysis methods in the combinatorial spirit of Andreas Dress. In particular, we generalize Atteson's work…
The tropical variety of a $d$-dimensional prime ideal in a polynomial ring with complex coefficients is a pure $d$-dimensional polyhedral fan. This fan is shown to be connected in codimension one. We present algorithmic tools for computing…
We study a parametric version of the Fermat-Weber problem with respect to an asymmetric distance function, which occurs naturally in tropical geometry. Our results yield a method for constructing phylogenetic supertrees.
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…
We give an overview of recently implemented polymake features for computations in tropical geometry. The main focus is on explicit examples rather than technical explanations. Our computations employ tropical hypersurfaces, moduli of…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…