Related papers: On the existence of a cherry-picking sequence
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…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
A binary matrix satisfies the consecutive ones property (COP) if its columns can be permuted such that the ones in each row of the resulting matrix are consecutive. Equivalently, a family of sets F = {Q_1,..,Q_m}, where Q_i is subset of R…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
The election is a classical problem in distributed algorithmic. It aims to design and to analyze a distributed algorithm choosing a node in a graph, here, in a tree. In this paper, a class of randomized algorithms for the election is…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Recent work has shown that not only decision trees (DTs) may not be interpretable but also proposed a polynomial-time algorithm for computing one PI-explanation of a DT. This paper shows that for a wide range of classifiers, globally…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
The method for analyzing algorithmic runtime complexity using decision trees is discussed using the sorting algorithm. This method is then extended to optimal algorithms which may find all cliques of size q in network N, or simply the first…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
We study the problem of sampling a uniformly random directed rooted spanning tree, also known as an arborescence, from a possibly weighted directed graph. Classically, this problem has long been known to be polynomial-time solvable; the…
Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of species), it is possible to determine in polynomial time whether there exists a level-1…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
We examine a discrete random recursive tree growth process that, at each time step, either adds or deletes a node from the tree with probability $p$ and $1-p$, respectively. Node addition follows the usual uniform attachment model. For node…
A rectilinear Steiner tree for a set $P$ of points in $\mathbb{R}^2$ is a tree that connects the points in $P$ using horizontal and vertical line segments. The goal of Minimal Rectilinear Steiner Tree is to find a rectilinear Steiner tree…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…