Related papers: A Duality Based 2-Approximation Algorithm for Maxi…
In the Steiner Forest problem, we are given a graph with edge lengths, and a collection of demand pairs; the goal is to find a subgraph of least total length such that each demand pair is connected in this subgraph. For over twenty years,…
We give an algorithm that, given an $n$-vertex graph $G$ and an integer $k$, in time $2^{O(k)} n$ either outputs a tree decomposition of $G$ of width at most $2k + 1$ or determines that the treewidth of $G$ is larger than $k$. This is the…
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…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
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…
The matching distance is a computationally tractable topological measure to compare multi-filtered simplicial complexes. We design efficient algorithms for approximating the matching distance of two bi-filtered complexes to any desired…
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,…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
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,…
The Metric Traveling Salesman Problem (TSP) is a classical NP-hard optimization problem. The double-tree shortcutting method for Metric TSP yields an exponentially-sized space of TSP tours, each of which approximates the optimal solution…
Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…
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…
We describe a $\frac{3}{2}$-approximation algorithm for the Forest Augmentation Problem (\textsf{FAP}), which is a special case of the Weighted 2-Edge-Connected Spanning Subgraph Problem (\textsf{Weighted 2-ECSS}). This significantly…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
For an $m$-edge connected simple graph $G$, finding a spanning tree of $G$ with the maximum number of leaves is MAXSNP-complete. The problem remains NP-complete even if $G$ is planar and the maximal degree of $G$ is at most four. Lu and…
This paper revisits the 2-approximation algorithm for $k$-MST presented by Garg in light of a recent paper of Paul et al.. In the $k$-MST problem, the goal is to return a tree spanning $k$ vertices of minimum total edge cost. Paul et al.…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…