Related papers: Maximum parsimony distance on phylogenetictrees: a…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
We discuss the computational complexity of approximating maximum a posteriori inference in sum-product networks. We first show NP-hardness in trees of height two by a reduction from maximum independent set; this implies non-approximability…
In the $L_0$ Fitting Tree Metrics problem, we are given all pairwise distances among the elements of a set $V$ and our output is a tree metric on $V$. The goal is to minimize the number of pairwise distance disagreements between the input…
In this paper, we present a factor 16 approximation algorithm for the following NP-hard distance fitting problem: given a finite set X and a distance d on X, find a Robinsonian distance dR on X minimizing the l\infty-error ||d - dR||\infty…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
Rotation distance between trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. In the case of ordered rooted trees, we…
Uniform cost-distance Steiner trees minimize the sum of the total length and weighted path lengths from a dedicated root to the other terminals. They are applied when the tree is intended for signal transmission, e.g. in chip design or…
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…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
This work briefly explores the possibility of approximating spatial distance (alternatively, similarity) between data points using the Isolation Forest method envisioned for outlier detection. The logic is similar to that of isolation: the…
Inference is typically intractable in high-treewidth undirected graphical models, making maximum likelihood learning a challenge. One way to overcome this is to restrict parameters to a tractable set, most typically the set of…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
The emergence of massive graph data sets requires fast mining algorithms. Centrality measures to identify important vertices belong to the most popular analysis methods in graph mining. A measure that is gaining attention is forest…