Related papers: Minimum triplet covers of binary phylogenetic $X$-…

Motivated by the bijection between Schnyder labelings of a plane triangulation and partitions of its inner edges into three trees, we look for binary labelings for quadrangulations (whose edges can be partitioned into two trees). Our…

In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…

We study the extreme local structure of plane binary trees through the distribution of leaves at maximum depth. We first address two basic questions: (i) the asymptotic probability that exactly two leaves occur at the deepest level, and…

In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…

We study a partially ordered set of planar labeled rooted trees by use of combinatorial objects called Dyck tilings. A generating function of the poset is factorized when the minimum element of the poset is $312$-avoiding and satisfies some…

We consider the (precedence constrained) Minimum Feedback Arc Set problem with triangle inequalities on the weights, which finds important applications in problems of ranking with inconsistent information. We present a surprising structural…

We develop a combinatorial framework to study certain polyhedral maps which are higher-dimensional analogues of tropical covers between metric graphs. Under a mild combinatorial assumption, we show that a map satisfies the so-called…

We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…

We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…

We prove that for any two minimal models of an lc algebraically integrable foliated triple on potentially klt varieties, there exist small birational models that are connected by a sequence of flops. In particular, any two minimal models of…

Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…

For a branched cover between two closed orientable surfaces, the Riemann-Hurwitz formula relates the Euler characteristics of the surfaces, the total degree of the cover, and the total length of the partitions of the degree given by the…

Let $k$, $d$ be a positive integer, $G$ be a connected graph of order $n$, $T$ be a tree. The leaf distance of a tree is defined as the minimum distance between any two leaves. For $v\in V(T)$, the leaf degree of $v$ in $T$ is the number of…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…

While research on the geometry of planar graphs has been active in the past decades, many properties of planar metrics remain mysterious. This paper studies a fundamental aspect of the planar graph geometry: covering planar metrics by a…

We address the problem of finding nice labellings for event structures of degree 3. We develop a minimum theory by which we prove that the labelling number of an event structure of degree 3 is bounded by a linear function of the height. The…

A shelling of a graph, viewed as an abstract simplicial complex that is pure of dimension 1, is an ordering of its edges such that every edge is adjacent to some other edges appeared previously. In this paper, we focus on complete bipartite…

Trellises are crucial graphical representations of codes. While conventional trellises are well understood, the general theory of (tail-biting) trellises is still under development. Iterative decoding concretely motivates such theory. In…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…