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In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…
We consider the problem of finding a spanning tree with maximum number of leaves (MaxLeaf). A 2-approximation algorithm is known for this problem, and a 3/2-approximation algorithm when restricted to graphs where every vertex has degree 3…
Online Contention Resolution Schemes (OCRS's) represent a modern tool for selecting a subset of elements, subject to resource constraints, when the elements are presented to the algorithm sequentially. OCRS's have led to some of the…
We consider the problem of exploring an unknown tree with a team of $k$ initially colocated mobile agents. Each agent has limited energy and cannot, as a result, traverse more than $B$ edges. The goal is to maximize the number of nodes…
There are many methods to find a maximum (or maximal) clique in large networks. Due to the nature of combinatorics, computation becomes exponentially expensive as the number of vertices in a graph increases. Thus, there is a need for…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
Providing an analytical solution for the problem of finding Fastest Distributed Consensus (FDC) is one of the challenging problems in the field of sensor networks. Here in this work we present analytical solution for the problem of fastest…
We introduce the problem of finding a spanning tree along with a partition of the tree edges into fewest number of feasible sets, where constraints on the edges define feasibility. The motivation comes from wireless networking, where we…
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…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
The graph retrieval problem is to search in a large corpus of graphs for ones that are most similar to a query graph. A common consideration for scoring similarity is the maximum common subgraph (MCS) between the query and corpus graphs,…
We study the Requirement Cut problem, a generalization of numerous classical graph partitioning problems including Multicut, Multiway Cut, $k$-Cut, and Steiner Multicut among others. Given a graph with edge costs, terminal groups $(S_1,…
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…
Red-black (RB) trees are one of the most efficient variants of balanced binary search trees. However, they have always been blamed for being too complicated, hard to explain, and not suitable for pedagogical purposes. In the pioneering work…
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…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
Many applications produce massive complex networks whose analysis would benefit from parallel processing. Parallel algorithms, in turn, often require a suitable network partition. For solving optimization tasks such as graph partitioning on…
Several important tasks in medical image analysis can be stated in the form of an optimization problem whose feasible solutions are connected subgraphs. Examples include the reconstruction of neural or vascular structures under…