Related papers: A Duality Based 2-Approximation Algorithm for Maxi…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
In the node-weighted prize-collecting Steiner tree problem (NW-PCST) we are given an undirected graph $G=(V,E)$, non-negative costs $c(v)$ and penalties $\pi(v)$ for each $v \in V$. The goal is to find a tree $T$ that minimizes the total…
The Steiner Forest problem is among the fundamental network design problems. Finding tight linear programming bounds for the problem is the key for both fast Branch-and-Bound algorithms and good primal-dual approximations. On the…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
We consider the tree consensus problem, an important problem in bioinformatics. Given a rooted tree $t$ and another tree $T$, one would like to incorporate compatible information from $T$ to $t$. This problem is a subproblem in the tree…
The emergence of massive graph data sets requires fast mining algorithms. Centrality measures to identify important vertices belong to the most popular analysis methods in graph mining. A measure that is gaining attention is forest…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
In this paper, we are concerned with the weighted backup 2-center problem on a tree. The backup 2-center problem is a kind of center facility location problem, in which one is asked to deploy two facilities, with a given probability to…
We present a $2$-approximation algorithm for the Flexible Graph Connectivity problem [AHM20] via a reduction to the minimum cost $r$-out $2$-arborescence problem.
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
Moss and Rabani[12] study constrained node-weighted Steiner tree problems with two independent weight values associated with each node, namely, cost and prize (or penalty). They give an O(log n)-approximation algorithm for the…
Given two phylogenetic trees with the $\{1, \ldots, n\}$ leaf-set the maximum agreement subtree problem asks what is the maximum size of the subset $A \subseteq \{1, \ldots, n\}$ such that the two trees are equivalent when restricted to…
We study the following two maximization problems related to spanning trees in the Euclidean plane. It is not known whether or not these problems are NP-hard. We present approximation algorithms with better approximation ratios for both…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
The paper deals with optimality issues in connection with updating beliefs in networks. We address two processes: triangulation and construction of junction trees. In the first part, we give a simple algorithm for constructing an optimal…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
In the Priority Steiner Tree (PST) problem, we are given an undirected graph $G=(V,E)$ with a source $s \in V$ and terminals $T \subseteq V \setminus \{s\}$, where each terminal $v \in T$ requires a nonnegative priority $P(v)$. The goal is…
We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…