Related papers: Representing Partitions on Trees
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Random forests are decision tree ensembles that can be used to solve a variety of machine learning problems. However, as the number of trees and their individual size can be large, their decision making process is often incomprehensible. In…
The need to harmonise apparently irreconcilable arrangements in an ecosystem --nestedness and segregation-- has triggered so far different strategies. Methodological refinements, or the inclusion of behavioural preferences to the network…
In this paper, we focus on families of bipartitions, i.e. set partitions consisting of at most two components. We say that a family of bipartitions is a separating family for a set $S$ if every two elements in $S$ can be separated by some…
We define an algorithm k which takes a connected graph G on a totally ordered vertex set and returns an increasing tree R (which is not necessarily a subtree of G). We characterize the set of graphs G such that k(G)=R. Because this set has…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
A \emph{set partition} of the set $[n]=\{1,...c,n\}$ is a collection of disjoint blocks $B_1,B_2,...c, B_d$ whose union is $[n]$. We choose the ordering of the blocks so that they satisfy $\min B_1<\min B_2<...b<\min B_d$. We represent such…
We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
We study completely independent spanning trees (CIST), \textit{i.e.}, trees that are both edge-disjoint and internally vertex-disjoint, in split graphs. We establish a correspondence between the existence of CIST in a split graph and some…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We study the complexity and expressive power of conjunctive queries over unranked labeled trees represented using a variety of structure relations such as ``child'', ``descendant'', and ``following'' as well as unary relations for node…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
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…
A Boolean ring and its Stone space (Boolean space) are primitive if the ring is disjointly generated by its pseudo-indecomposable (PI) elements. Hanf showed that a primitive PI Boolean algebra can be uniquely defined by a structure diagram.…
This paper investigates one of the most fundamental computer vision problems: image segmentation. We propose a supervised hierarchical approach to object-independent image segmentation. Starting with over-segmenting superpixels, we use a…