Related papers: Additive Approximation for Near-Perfect Phylogeny …
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
The Euclidean Steiner tree problem, normally posed in two dimensions, seeks to connect a set of prescribed terminal nodes by placing additional nodes, known as Steiner points, with edges connecting such nodes either to another Steiner point…
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…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
For a given graph $G=(V,\, E)$ with a terminal set $S$ and a selected root $r\in S$, a positive integer cost and a delay on every edge and a delay constraint $D\in Z^{+}$, the shallow-light Steiner tree (\emph{SLST}) problem is to compute a…
We study the query complexity of the metric Steiner Tree problem, where we are given an $n \times n$ metric on a set $V$ of vertices along with a set $T \subseteq V$ of $k$ terminals, and the goal is to find a tree of minimum cost that…
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…
The best algorithm for approximating Steiner tree has performance ratio $\ln(4)+\epsilon \approx 1.386$ [J. Byrka et al., \textit{Proceedings of the 42th Annual ACM Symposium on Theory of Computing (STOC)}, 2010, pp. 583-592], whereas the…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present LvD, (Likelihood via Decomposition), an alternative to…
We present four novel approximation algorithms for finding triangulation of minimum treewidth. Two of the algorithms improve on the running times of algorithms by Robertson and Seymour, and Becker and Geiger that approximate the optimum by…
Given a metric space on n points, an {\alpha}-approximate universal algorithm for the Steiner tree problem outputs a distribution over rooted spanning trees such that for any subset X of vertices containing the root, the expected cost of…
This paper addresses a graph optimization problem, called the Witness Tree problem, which seeks a spanning tree of a graph minimizing a certain non-linear objective function. This problem is of interest because it plays a crucial role in…
Search trees on trees (STTs) generalize the fundamental binary search tree (BST) data structure: in STTs the underlying search space is an arbitrary tree, whereas in BSTs it is a path. An optimal BST of size $n$ can be computed for a given…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Boosted decision trees enjoy popularity in a variety of applications; however, for large-scale datasets, the cost of training a decision tree in each round can be prohibitively expensive. Inspired by ideas from the multi-arm bandit…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…