Related papers: Additive Approximation for Near-Perfect Phylogeny …
We consider the problem of designing sublinear time algorithms for estimating the cost of a minimum metric traveling salesman (TSP) tour. Specifically, given access to a $n \times n$ distance matrix $D$ that specifies pairwise distances…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new…
The goal for the Directed Steiner Tree problem is to find a minimum cost tree in a directed graph G=(V,E) that connects all terminals X to a given root r. It is well known that modulo a logarithmic factor it suffices to consider acyclic…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
Given point sets $A$ and $B$ in $\mathbb{R}^d$ where $A$ and $B$ have equal size $n$ for some constant dimension $d$ and a parameter $\varepsilon>0$, we present the first deterministic algorithm that computes, in $n\cdot(\varepsilon^{-1}…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
In the classical (min-cost) Steiner tree problem, we are given an edge-weighted undirected graph and a set of terminal nodes. The goal is to compute a min-cost tree S which spans all terminals. In this paper we consider the min-power…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
The Euclidean Steiner Minimal Tree problem takes as input a set $\mathcal P$ of points in the Euclidean plane and finds the minimum length network interconnecting all the points of $\mathcal P$. In this paper, in continuation to the works…
We consider the single-source (or single-sink) buy-at-bulk problem with an unknown concave cost function. We want to route a set of demands along a graph to or from a designated root node, and the cost of routing x units of flow along an…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Given a directed graph $G=(V,A)$, the Directed Maximum Leaf Spanning Tree problem asks to compute a directed spanning tree (i.e., an out-branching) with as many leaves as possible. By designing a Branch-and-Reduced algorithm combined with…