Related papers: A 3-factor approximation algorithm for a Maximum A…
It follows from a classical result of Jordan that every tree with maximum degree at most $r$ containing a vertex set labeled by $[n]$, has a single-edge cut which separates two subsets $A,B \subset [n]$ for which $\min\{|A|,|B|\} \ge…
We present an approximation algorithm for Weighted Tree Augmentation with approximation factor $1+\ln 2 + \varepsilon < 1.7$. This is the first algorithm beating the longstanding factor of $2$, which can be achieved through many standard…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
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…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Random Forests (RF) are among the state-of-the-art in many machine learning applications. With the ongoing integration of ML models into everyday life, the deployment and continuous application of models becomes more and more an important…
We give an algorithm that, given an $n$-vertex graph $G$ and an integer $k$, in time $2^{O(k)} n$ either outputs a tree decomposition of $G$ of width at most $2k + 1$ or determines that the treewidth of $G$ is larger than $k$. This is the…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
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…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the…
Ancestral mixture model, proposed by Chen and Lindsay (2006), is an important model to build a hierarchical tree from high dimensional binary sequences. Mixture trees created from ancestral mixture models involve in the inferred…
Rotation distance between rooted binary 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. We give an efficient,…
We show that the cophylogenetic distance, k-interval cospeciation, is distinct from other metrics and accounts for global congruence between locally incongruent trees. The growth of the neighborhood of trees which satisfy the largest…