Related papers: Cavity Matchings, Label Compressions, and Unrooted…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Finding a maximum-cardinality or maximum-weight matching in (edge-weighted) undirected graphs is among the most prominent problems of algorithmic graph theory. For $n$-vertex and $m$-edge graphs, the best known algorithms run in…
Straight-line (linear) context-free tree (SLT) grammars have been used to compactly represent ordered trees. It is well known that equivalence of SLT grammars is decidable in polynomial time. Here we extend this result and show that…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
We study budget constrained network upgradeable problems. We are given an undirected edge weighted graph $G=(V,E)$ where the weight an edge $e \in E$ can be upgraded for a cost $c(e)$. Given a budget $B$ for improvement, the goal is to find…
We design a deterministic algorithm for the $(1+\epsilon)$-approximate maximum matching problem. Our primary result demonstrates that this problem can be solved in $O(\epsilon^{-6})$ semi-streaming passes, improving upon the…
Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…
We prove a square-root space simulation for deterministic multitape Turing machines, showing $\mathrm{TIME}[t]\subseteq \mathrm{SPACE}[O(\sqrt{t})]$ \emph{measured in tape cells over a fixed finite alphabet}. The key step is a Height…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
An {\em ancestry labeling scheme} labels the nodes of any tree in such a way that ancestry queries between any two nodes in a tree can be answered just by looking at their corresponding labels. The common measure to evaluate the quality of…
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…
The hierarchical and recursive expressive capability of rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. On the other hand, such hierarchical…
Given a graph and a root, the Maximum Bounded Rooted-Tree Packing (MBRTP) problem aims at finding K rooted-trees that span the largest subset of vertices, when each vertex has a limited outdegree. This problem is motivated by peer-to-peer…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…
Counterfactual explanations are usually generated through heuristics that are sensitive to the search's initial conditions. The absence of guarantees of performance and robustness hinders trustworthiness. In this paper, we take 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…
Let $\T_{n}$ be the set of rooted labeled trees on $\set{0,...,n}$. A maximal decreasing subtree of a rooted labeled tree is defined by the maximal subtree from the root with all edges being decreasing. In this paper, we study a new…
We consider problems in which we are given a rooted tree as input, and must find a subtree with the same root, optimizing some objective function of the nodes in the subtree. When this function is the sum of constant node weights, the…