Related papers: Algorithms for Maximum Agreement Forest of Multipl…

A common subgraph of two graphs $G_1$ and $G_2$ is a graph that is isomorphic to subgraphs of $G_1$ and $G_2$. In the largest common subgraph problem the task is to determine a common subgraph for two given graphs $G_1$ and $G_2$ that is of…

In this short note we prove that, given two (not necessarily binary) rooted phylogenetic trees T_1, T_2 on the same set of taxa X, where |X|=n, the hybridization number of T_1 and T_2 can be computed in time O^{*}(2^n) i.e. O(2^{n}…

In the Multiagent Path Finding problem (MAPF for short), we focus on efficiently finding non-colliding paths for a set of $k$ agents on a given graph $G$, where each agent seeks a path from its source vertex to a target. An important…

Random Forests (RF) is a popular machine learning method for classification and regression problems. It involves a bagging application to decision tree models. One of the primary advantages of the Random Forests model is the reduction in…

Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…

The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…

Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…

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…

We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…

The minimal number of rooted subtree prune and regraft (rSPR) operations needed to transform one phylogenetic tree into another one induces a metric on phylogenetic trees - the rSPR-distance. The rSPR-distance between two phylogenetic trees…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…

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…

Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…

Graph isomorphism, subgraph isomorphism, and maximum common subgraphs are classical well-investigated objects. Their (parameterized) complexity and efficiently tractable cases have been studied. In the present paper, for a given set of…

We study the Maximum Cardinality Matching (MCM) and the Maximum Weight Matching (MWM) problems, on trees and on some special classes of graphs, in the Online Preemptive and the Incremental Dynamic Graph models. In the {\em Online…

The Matching Augmentation Problem (MAP) has recently received significant attention as an important step towards better approximation algorithms for finding cheap $2$-edge connected subgraphs. This has culminated in a…

It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…