Related papers: Representing Partitions on Trees
Bipartite networks provide an effective resource for representing, characterizing, and modeling several abstract and real-world systems and structures involving binary relations, which include food webs, social interactions, and…
We prove that the complement of a $\sigma$-compact subset of a topological space that has a $\pi$-tree also has a $\pi$-tree. To do this, we construct the foliage hybrid operation, which deals with foliage trees (that is, set-theoretic…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
We study the problem of decomposing (clustering) a tree with respect to costs attributed to pairs of nodes, so as to minimize the sum of costs for those pairs of nodes that are in the same component (cluster). For the general case and for…
Phylogenomics commonly aims to construct evolutionary trees from genomic sequence information. One way to approach this problem is to first estimate event-labeled gene trees (i.e., rooted trees whose non-leaf vertices are labeled by…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
We look for partition theorems for large subtrees for suitable uncountable trees and colourings. We concentrate on sub-trees of $^{\kappa \ge} 2$ expanded by a well ordering of each level. Unlike earlier works, we do not ask the embedding…
We consider the problem of computing matrix polynomials $p(X)$, where $X$ is a large dense matrix, with as few matrix-matrix multiplications as possible. More precisely, let $\Pi_{2^{m}}^*$ represent the set of polynomials computable with…
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…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
One of the important features of an interconnection network is its ability to efficiently simulate programs or parallel algorithms written for other architectures. Such a simulation problem can be mathematically formulated as a graph…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We introduce two definitions of $G$-equivariant partitions of a finite $G$-set, both of which yield $G$-equivariant partition complexes. By considering suitable notions of equivariant trees, we show that $G$-equivariant partitions and…
We study the problem to find a partition of \textcolor{black}{a} graph $G$ with maximum social welfare based on social distance between vertices in $G$, called MaxSWP. This problem is known to be NP-hard in general. In this paper, we first…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…