Related papers: A 3-approximation algorithm for computing a parsim…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
The paper presents complexity results and performance guaranties for a family of approximation algorithms for an optimisation problem arising in software testing and manufacturing. The problem is formulated as a partitioning of a set where…
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 reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
In 1996, Guigo et al. [Mol. Phylogenet. Evol., 6 (1996), 189-203] posed the following problem: for a given species tree and a number of gene trees, what is the minimum number of duplication episodes, where several genes could have undergone…
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…
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 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 rooted Subtree…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
Exponential-time approximation has recently gained attention as a practical way to deal with the bitter NP-hardness of well-known optimization problems. We study for the first time the $(1 + \varepsilon)$-approximate min-sum subset…
In the Maximum Duo-Preservation String Mapping problem we are given two strings and wish to map the letters of the former to the letters of the latter so as to maximise the number of duos. A duo is a pair of consecutive letters that is…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We propose a simple and natural approximation algorithm for the problem of finding a 2-edge-connected spanning subgraph of minimum total edge cost in a graph. The algorithm maintains a spanning forest starting with an empty edge set. In…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Given a graph $G = (V, E)$, the $3$-path partition problem is to find a minimum collection of vertex-disjoint paths each of order at most $3$ to cover all the vertices of $V$. It is different from but closely related to the well-known…
The (non-uniform) sparsest cut problem is the following graph-partitioning problem: given a "supply" graph, and demands on pairs of vertices, delete some subset of supply edges to minimize the ratio of the supply edges cut to the total…
We study the classical scheduling problem on parallel machines %with precedence constraints where the precedence graph has the bounded depth $h$. Our goal is to minimize the maximum completion time. We focus on developing approximation…
In this paper, we consider an NP-hard problem of scheduling a set of jobs of equal processing time on two machines, given a partial precedence order on the set of jobs, with an objective to minimize the makespan. An approximation algorithm…
The submodular partitioning problem asks to minimize, over all partitions $P$ of a ground set $V$, the sum of a given submodular function $f$ over the parts of $P$. The problem has seen considerable work in approximability, as it…
We consider the problem of computing first-passage time distributions for reaction processes modelled by master equations. We show that this generally intractable class of problems is equivalent to a sequential Bayesian inference problem…