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We give almost-linear-time algorithms for approximating rooted minimum cut and maximum arborescence packing in directed graphs, two problems that are dual to each other [Edm73]. More specifically, for an $n$-vertex, $m$-edge directed graph…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
The goal for the Directed Steiner Tree problem is to find a minimum cost tree in a directed graph G=(V,E) that connects all terminals X to a given root r. It is well known that modulo a logarithmic factor it suffices to consider acyclic…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…
We give an O(sqrt n log n)-query quantum algorithm for evaluating size-n AND-OR formulas. Its running time is poly-logarithmically greater after efficient preprocessing. Unlike previous approaches, the algorithm is based on a quantum walk…
In this paper, we redesign and simplify an algorithm due to Remy et al. for the generation of rooted planar trees that satisfies a given partition of degrees. This new version is now optimal in terms of random bit complexity, up to a…
Tree search is a fundamental tool for planning, as many sequential decision-making problems can be framed as searching over tree-structured spaces. We propose an uncertainty-guided tree search algorithm for settings where the reward…
Optimal path planning requires finding a series of feasible states from the starting point to the goal to optimize objectives. Popular path planning algorithms, such as Effort Informed Trees (EIT*), employ effort heuristics to guide the…
In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…
Given a simple, unweighted, undirected graph $G=(V,E)$ with $|V|=n$ and $|E|=m$, and parameters $0 < \varepsilon, \delta <1$, along with \texttt{Degree}, \texttt{Neighbour}, \texttt{Edge} and \texttt{RandomEdge} query access to $G$, we…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
Constructing a Depth First Search (DFS) tree is a fundamental graph problem, whose parallel complexity is still not settled. Reif showed parallel intractability of lex-first DFS. In contrast, randomized parallel algorithms (and more…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
In this paper, we revisit the problem of sampling edges in an unknown graph $G = (V, E)$ from a distribution that is (pointwise) almost uniform over $E$. We consider the case where there is some a priori upper bound on the arboriciy of $G$.…
Given a set S of n \geq d points in general position in R^d, a random hyperplane split is obtained by sampling d points uniformly at random without replacement from S and splitting based on their affine hull. A random hyperplane search tree…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
In the context of tree-search stochastic planning algorithms where a generative model is available, we consider on-line planning algorithms building trees in order to recommend an action. We investigate the question of avoiding re-planning…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…