Related papers: Additive Approximation for Near-Perfect Phylogeny …
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
We consider a variant of the prize collecting Steiner tree problem in which we are given a \emph{directed graph} $D=(V,A)$, a monotone submodular prize function $p:2^V \rightarrow \mathbb{R}^+ \cup \{0\}$, a cost function $c:V \rightarrow…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
In the \emph{budgeted rooted node-weighted Steiner tree} problem, we are given a graph $G$ with $n$ nodes, a predefined node $r$, two weights associated to each node modelling costs and prizes. The aim is to find a tree in $G$ rooted at $r$…
The cost-distance Steiner tree problem seeks a Steiner tree that minimizes the total congestion cost plus the weighted sum of source-sink delays. This problem arises as a subroutine in timing-constrained global routing with a linear delay…
In this paper we design and prove correct a fully dynamic distributed algorithm for maintaining an approximate Steiner tree that connects via a minimum-weight spanning tree a subset of nodes of a network (referred as Steiner members or…
In the Steiner Tree Augmentation Problem (STAP), we are given a graph $G = (V,E)$, a set of terminals $R \subseteq V$, and a Steiner tree $T$ spanning $R$. The edges $L := E \setminus E(T)$ are called links and have non-negative costs. The…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Let $P$ and $S$ be two disjoint sets of $n$ and $m$ points in the plane, respectively. We consider the problem of computing a Steiner tree whose Steiner vertices belong to $S$, in which each point of $P$ is a leaf, and whose longest edge…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Motivated by a phylogeny reconstruction problem in evolutionary biology, we study the minimum Steiner arborescence problem on directed hypercubes (MSA-DH). Given $m$, representing the directed hypercube $\vec{Q}_m$, and a set of terminals…
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…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
We present a quantum algorithm in bioinformatics for solving the Binary Near-Perfect Phylogeny Problem (BNPP) with a complexity bound of $O(8.926^q + 8^q nm2)$, where n is the number of input taxa and m is the sequence length for each taxon…
The Steiner tree problem is one of the classic and most fundamental $\mathcal{NP}$-hard problems: given an arbitrary weighted graph, seek a minimum-cost tree spanning a given subset of the vertices (terminals). Byrka \emph{et al}. proposed…