相关论文: Approximation algorithms for nonbinary agreement f…

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…

Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…

A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…

Algorithms for binary classification based on adaptive tree partitioning are formulated and analyzed for both their risk performance and their friendliness to numerical implementation. The algorithms can be viewed as generating a set…

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…

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…

Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…

Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…

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…

Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…

We consider the following generalization of the binary search problem. A search strategy is required to locate an unknown target node $t$ in a given tree $T$. Upon querying a node $v$ of the tree, the strategy receives as a reply an…

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…

Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. Even for…

Assuming Zipf's Law to be accurate, we show that existing techniques for partially optimizing binary trees produce results that are approximately 10% worse than true optimal. We present a new approximate optimization technique that runs in…

We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…

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,…

Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…

Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…

We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…

The Forest Augmentation Problem (FAP) asks for a minimum set of additional edges (links) that make a given forest 2-edge-connected while spanning all vertices. A key special case is the Path Augmentation Problem (PAP), where the input…