Related papers: A tight kernel for computing the tree bisection an…

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…

We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…

We study restricted computation models related to the Tree Evaluation Problem}. The TEP was introduced in earlier work as a simple candidate for the (*very*) long term goal of separating L and LogDCFL. The input to the problem is a rooted,…

In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at…

Let $\mathcal{T}$ be an unrooted binary tree with $n$ distinctly labelled leaves. Deriving its name from the field of phylogenetics, a convex character on $\mathcal{T}$ is simply a partition of the leaves such that the minimal spanning…

We combine two methods for the lossless compression of unlabeled graphs - entropy compressing adjacency lists and computing canonical names for vertices - and solve an ensuing novel optimisation problem: Minimum-Entropy Tree-Extraction…

Over the last few years Explainable Clustering has gathered a lot of attention. Dasgupta et al. [ICML'20] initiated the study of explainable $k$-means and $k$-median clustering problems where the explanation is captured by a threshold…

The tree reconstruction problem is to collect and analyze massive data at the $n$th level of the tree, to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. Its connection to the clustering problem in…

This paper presents a gentle tutorial and a structured reformulation of Bock's 1971 Algol procedure for constructing minimum directed spanning trees. Our aim is to make the original algorithm readable and reproducible for modern readers,…

Network design problems aim to compute low-cost structures such as routes, trees and subgraphs. Often, it is natural and desirable to require that these structures have small hop length or hop diameter. Unfortunately, optimization problems…

Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…

We extend the notion of lossy kernelization, introduced by Lokshtanov et al. [STOC 2017], to approximate Turing kernelization. An $\alpha$-approximate Turing kernel for a parameterized optimization problem is a polynomial-time algorithm…

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree…

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…

We give almost-linear-time algorithms for approximating rooted minimum cut and maximum arborescence packing in directed graphs, two problems that are dual to each other [Edm73]. More specifically, for an $n$-vertex, $m$-edge directed graph…

Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…

For a family of graphs $\cal F$, the $\mathcal{F}$-Contraction problem takes as an input a graph $G$ and an integer $k$, and the goal is to decide if there exists $S \subseteq E(G)$ of size at most $k$ such that $G/S$ belongs to $\cal F$.…

The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…