Related papers: A Simple 4-Approximation Algorithm for Maximum Agr…
Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species trees. In this article we introduce an Integer Linear…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
For an arbitrary tree we investigate the problems of constructing a maximum matching which minimizes or maximizes the cardinality of a maximum matching of the graph obtained from original one by its removal and present corresponding…
The Forest Augmentation Problem (FAP) asks for a minimum set of additional edges (links) that make a given forest 2-edge-connected while spanning all vertices. A key special case is the Path Augmentation Problem (PAP), where the input…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
In Part II, we study the unweighted Tree Augmentation Problem (TAP) via the Lasserre (Sum~of~Squares) system. We prove that the integrality ratio of an SDP relaxation (the Lasserre tightening of an LP relaxation) is $\leq…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
The Weighted Tree Augmentation Problem (WTAP) is a fundamental network design problem where the goal is to find a minimum-cost set of additional edges (links) to make an input tree 2-edge-connected. While a 2-approximation is standard and…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
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…
This paper focuses on finding a spanning tree of a graph to maximize the number of its internal vertices. We present an approximation algorithm for this problem which can achieve a performance ratio $\frac{4}{3}$ on undirected simple…
This paper is concerned with near-optimal approximation of a given function $f \in L_2([0,1])$ with elements of a polynomially enriched wavelet frame, a so-called quarklet frame. Inspired by $hp$-approximation techniques of Binev, we use…
Until recently, LP relaxations have played a limited role in the design of approximation algorithms for the Steiner tree problem. In 2010, Byrka et al. presented a ln(4)+epsilon approximation based on a hypergraphic LP relaxation, but…
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…
Asadpour, Feige, and Saberi proved that the integrality gap of the configuration LP for the restricted max-min allocation problem is at most $4$. However, their proof does not give a polynomial-time approximation algorithm. A lot of efforts…
Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
We present a class of linear programming approximations for constrained optimization problems. In the case of mixed-integer polynomial optimization problems, if the intersection graph of the constraints has bounded tree-width our…
We develop and analyze methods for computing provably optimal {\em maximum a posteriori} (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex…