Related papers: Point configurations, phylogenetic trees, and diss…
We study questions inspired by Erd\H os' celebrated distance problems with dot products in lieu of distances, and for more than a single pair of points. In particular, we study point configurations present in large finite point sets in the…
We give a complete description of Green's D relation for the multiplicative semigroup of all n-by-n tropical matrices. Our main tool is a new variant on the duality between the row and column space of a tropical matrix (studied by Cohen,…
Inferring the processes underlying the emergence of observed patterns is a key challenge in theoretical ecology. Much effort has been made in the past decades to collect extensive and detailed information about the spatial distribution of…
A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of size k subsets of X to the real numbers. Such maps naturally arise from edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is defined to be…
We solve a class of optimization problems for (phylogenetic) $X$-trees or their shapes. These problems have recently appeared in different contexts, e.g. in the context of the impact of tree shapes on the size of TBR neighborhoods, but so…
The overlap graphs of subtrees of a tree are equivalent to subtree filament graphs, the overlap graphs of subtrees of a star are cocomparability graphs, and the overlap graphs of subtrees of a caterpillar are interval filament graphs. In…
We investigate whether the Wigner semi-circle and Marcenko-Pastur distributions, often used for deep neural network theoretical analysis, match empirically observed spectral densities. We find that even allowing for outliers, the observed…
We consider special cases of the two tree degree sequences problem. We show that if two tree degree sequences do not have common leaves then they always have edge-disjoint caterpillar realizations. By using a probabilistic method, we prove…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
We study the statistics of height and balanced height in the binary search tree problem in computer science. The search tree problem is first mapped to a fragmentation problem which is then further mapped to a modified directed polymer…
The algebraic foundation of tropical polynomial algebra provides the framework for the geometric construction of the supplement and the reversal of tropical varieties, thereby inducing a duality of reduced tropical varieties; for classes of…
We undertake a combinatorial study of the piecewise linear map g : R^{2m+2n} --> R^{mn} which assigns to the four vectors a, A in R^m and b, B in R^n the m by n matrix given by g_{ij} = min (a_i + b_j, A_i+B_j). This map arises naturally in…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
Tree-like tableaux are objects in bijection with alternative or permutation tableaux. They have been the subject of a fruitful combinatorial study for the past few years. In the present work, we define and study a new subclass of tree-like…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
In this paper, we continue our study of blade arrangements and the positroidal subdivisions which are induced by them on $\Delta_{k,n}$. A blade is a tropical hypersurface which is generated by a system of $n$ affine simple roots of type…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
The enumeration of planar maps equipped with an Eulerian orientation has attracted attention in both combinatorics and theoretical physics since at least 2000. The case of 4-valent maps is particularly interesting: these orientations are in…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
Our objective in this project is three-fold, the first two covered in this paper. In tropical mathematics, as well as other mathematical theories involving semirings, when trying to formulate the tropical versions of classical algebraic…