Related papers: Representing Partitions on Trees
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
An independent edge set of graph $G$ is a matching, and is maximal if it is not a proper subset of any other matching of $G$. The number of all the maximal matchings of $G$ is denoted by $\Psi(G)$. In this paper, an algorithm to count…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
An open partition \pi{} [Cod09a, Cod09b] of a tree T is a partition of the vertices of T with the property that, for each block B of \pi, the upset of B is a union of blocks of \pi. This paper deals with the number, NP(n), of open…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Convolution trees, loopy belief propagation, and fast numerical p-convolution are combined for the first time to efficiently solve networks with several additive constraints between random variables. An implementation of this "convolution…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
The paper presents complexity results and performance guaranties for a family of approximation algorithms for an optimisation problem arising in software testing and manufacturing. The problem is formulated as a partitioning of a set where…
A graph $G$ is {\it weakly semiregular} if there are two numbers $a,b$, such that the degree of every vertex is $a$ or $b$. The {\it weakly semiregular number} of a graph $G$, denoted by $wr(G)$, is the minimum number of subsets into which…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
We introduce several axioms which may or may not hold for any given subgraph of the directed graph of all organisms (past, present and future) where edges represent biological parenthood, with the simplifying background assumption that life…
This paper considers the problem of matching fragment to organism using its complete genome. Our method is based on the probability measure representation of a genome. We first demonstrate that these probability measures can be modelled as…
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
We study the problems of covering or partitioning a polygon $P$ (possibly with holes) using a minimum number of small pieces, where a small piece is a connected sub-polygon contained in an axis-aligned unit square. For covering, we seek to…
Formal XAI (explainable AI) is a growing area that focuses on computing explanations with mathematical guarantees for the decisions made by ML models. Inside formal XAI, one of the most studied cases is that of explaining the choices taken…
We propose Partition Tree, a novel tree-based framework for conditional density estimation over general outcome spaces that supports both continuous and categorical variables within a unified formulation. Our approach models conditional…
Property $(P)$, introduced in recent work and rooted in the classical theory of Parter vertices, concerns the existence of a nonsingular matrix $A\in S(G)$ for which every vertex of $G$ is a $P$-vertex. Previous investigations have fully…