Related papers: Classifying Tree Topologies along Tropical Line Se…

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…

We establish first parts of a tropical intersection theory. Namely, we define cycles, Cartier divisors and intersection products between these two (without passing to rational equivalence) and discuss push-forward and pull-back. We do this…

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…

We prove that every oriented tree on $n$ vertices with bounded maximum degree appears as a spanning subdigraph of every directed graph on $n$ vertices with minimum semidegree at least $n/2+o(n)$. This can be seen as a directed graph…

We consider Gaussian fields of real symmetric, complex Hermitian or quaternionic Hermitian matrices over an electrical network, and describe how the isomorphisms between these fields and random walks give rise to topological expansions…

We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…

The Tree Builder Random Walk is a special random walk that evolves on trees whose size increases with time, randomly and depending upon the walker. After every s steps of the walker, a random number of vertices are added to the tree and…

In 2004 Pachter and Speyer introduced the higher dissimilarity maps for phylogenetic trees and asked two important questions about their relation to the tropical Grassmannian. Multiple authors, using independent methods, answered…

Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…

Motivated by applications to low-rank matrix completion, we give a combinatorial characterization of the independent sets in the algebraic matroid associated to the collection of $m\times n$ rank-2 matrices and $n\times n$ skew-symmetric…

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…

While the positive Grassmannian is deeply understood through the rich combinatorics of plabic graphs and positroid cells, its tropical counterpart, the positive tropical Grassmannian Trop$_{>0}G(k,n)$, has lacked a comparable structural…

We show that every connected graph can be approximated by a normal tree, up to some arbitrarily small error phrased in terms of neighbourhoods around its ends. The existence of such approximate normal trees has consequences of both…

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…

We launch the study of the tropicalization of the symplectic Grassmannian, that is, the space of all linear subspaces that are isotropic with respect to a fixed symplectic form. We formulate tropical analogues of several equivalent…

There is an unproven duality theory hypothesizing that random discrete trees and their poissonized embeddings in continuous time share fundamental properties. We give additional evidence in favor of this theory by showing that several…

Since they became observable, neuron morphologies have been informally compared with biological trees but they are studied by distinct communities, neuroscientists, and ecologists. The apparent structural similarity suggests there may be…

We study tree metrics that can be realized as a mixture of two star tree metrics. We prove that the only trees admitting such a decomposition are the ones coming from a tree with at most one internal edge, and whose weight satisfies certain…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

We describe a technique to reorganize topologies of Steiner trees by exchanging neighbors of adjacent Steiner points. We explain how to use the systematic way of building trees, and therefore topologies, to find the correct topology after…