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We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…
Let $P$ and $S$ be two disjoint sets of $n$ and $m$ points in the plane, respectively. We consider the problem of computing a Steiner tree whose Steiner vertices belong to $S$, in which each point of $P$ is a leaf, and whose longest edge…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
Rectangular layouts, subdivisions of an outer rectangle into smaller rectangles, have many applications in visualizing spatial information, for instance in rectangular cartograms in which the rectangles represent geographic or political…
A tree tensor network variational method is proposed to simulate quantum many-body systems with global symmetries where the optimization is reduced to individual charge configurations. A computational scheme is presented, how to extract the…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
In this paper we consider the enumeration of binary trees avoiding non-contiguous binary tree patterns. We begin by computing closed formulas for the number of trees avoiding a single binary tree pattern with 4 or fewer leaves and compare…
Topological drawings are natural representations of graphs in the plane, where vertices are represented by points, and edges by curves connecting the points. Topological drawings of complete graphs and of complete bipartite graphs have been…
For an arbitrary tree we investigate the problems of constructing a maximum matching which minimizes or maximizes the cardinality of a maximum matching of the graph obtained from original one by its removal and present corresponding…
We formulate learning of a binary autoencoder as a biconvex optimization problem which learns from the pairwise correlations between encoded and decoded bits. Among all possible algorithms that use this information, ours finds the…
Given a finite planar graph, a grove is a spanning forest in which every component tree contains one or more of a specified set of vertices (called nodes) on the outer face. For the uniform measure on groves, we compute the probabilities of…
We apply a recent duality theorem for tangles in abstract separation systems to derive tangle-type duality theorems for width-parameters in graphs and matroids. We further derive a duality theorem for the existence of clusters in large data…
Classification and Regression Trees (CARTs) are off-the-shelf techniques in modern Statistics and Machine Learning. CARTs are traditionally built by means of a greedy procedure, sequentially deciding the splitting predictor variable(s) and…
Given a 2-edge connected, unweighted, and undirected graph $G$ with $n$ vertices and $m$ edges, a $\sigma$-tree spanner is a spanning tree $T$ of $G$ in which the ratio between the distance in $T$ of any pair of vertices and the…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
This article focuses on a combinatorial structure specific to triangulated plane graphs with quadrangular outer face and no separating triangle, which are called irreducible triangulations. The structure has been introduced by Xin He under…