Related papers: A Duality Based 2-Approximation Algorithm for Maxi…
This article presents two novel algorithms for generating random increasing trees. The first algorithm efficiently generates strictly increasing binary trees using an ad hoc method. The second algorithm improves the recursive method for…
Given a directed graph $G=(V,A)$, the Directed Maximum Leaf Spanning Tree problem asks to compute a directed spanning tree (i.e., an out-branching) with as many leaves as possible. By designing a Branch-and-Reduced algorithm combined with…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
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…
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…
We consider the $k$-prize-collecting Steiner tree problem. An instance is composed of an integer $k$ and a graph $G$ with costs on edges and penalties on vertices. The objective is to find a tree spanning at least $k$ vertices which…
We present several modifications to the previously proposed MSPP algorithm that can speed-up its execution considerably. The MSPP algorithm leverages a multiscale representation of the environment in $n$ dimensions. The information of the…
The personnel rostering problem is the problem of finding an optimal way to assign employees to shifts, subject to a set of hard constraints which all valid solutions must follow, and a set of soft constraints which define the relative…
This paper derives a unifying theorem establishing consistency results for a broad class of tree-based algorithms. It improves current results in two aspects. First of all, it can be applied to algorithms that vary from traditional Random…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
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…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
In the Steiner Forest problem, we are given a graph with edge lengths, and a collection of demand pairs; the goal is to find a subgraph of least total length such that each demand pair is connected in this subgraph. For over twenty years,…
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}…
For complexity of the heterogeneous minimum spanning forest problem has not been determined, we reduce 3-SAT which is NP-complete to 2-heterogeneous minimum spanning forest problem to prove this problem is NP-hard and spread result to…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
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…
We achieve a (randomized) polynomial-time approximation scheme (PTAS) for the Steiner Forest Problem in doubling metrics. Before our work, a PTAS is given only for the Euclidean plane in [FOCS 2008: Borradaile, Klein and Mathieu]. Our PTAS…
We present a class of linear programming approximations for constrained optimization problems. In the case of mixed-integer polynomial optimization problems, if the intersection graph of the constraints has bounded tree-width our…
We propose a new modified primal-dual proximal best approximation method for solving convex not necessarily differentiable optimization problems. The novelty of the method relies on introducing memory by taking into account iterates…