Related papers: Additive Approximation for Near-Perfect Phylogeny …
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…
The dynamic optimality conjecture, postulating the existence of an $O(1)$-competitive online algorithm for binary search trees (BSTs), is among the most fundamental open problems in dynamic data structures. Despite extensive work and some…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
The Steiner tree enumeration problem is a well known problem that asks for enumerating Steiner trees. Numerous theoretical works proposed algorithms for the problem and analyzed their complexity, but there are no practical algorithms and…
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…
Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…
Suppose we are given a bipartite graph that admits a perfect matching and an adversary may delete any edge from the graph with the intention of destroying all perfect matchings. We consider the task of adding a minimum cost edge-set to the…
Decision tree optimization is fundamental to interpretable machine learning. The most popular approach is to greedily search for the best feature at every decision point, which is fast but provably suboptimal. Recent approaches find the…
The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
We give the first algorithm that maintains an approximate decision tree over an arbitrary sequence of insertions and deletions of labeled examples, with strong guarantees on the worst-case running time per update request. For instance, we…
In this article, we study the Euclidean minimum spanning tree problem in an imprecise setup. The problem is known as the \emph{Minimum Spanning Tree Problem with Neighborhoods} in the literature. We study the problem where the neighborhoods…
Phylogenetic Diversity(PD)is a well-regarded measure of the overall biodiversity of a set of present-day species(taxa)that indicates its ecological significance.In the Maximize Phylogenetic Diversity(Max-PD)problem one is asked to find a…
In this paper the minimum spanning tree problem with uncertain edge costs is discussed. In order to model the uncertainty a discrete scenario set is specified and a robust framework is adopted to choose a solution. The min-max, min-max…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
We consider the following generalization of binary search in sorted arrays to tree domains. In each step of the search, an algorithm is querying a vertex $q$, and as a reply, it receives an answer, which either states that $q$ is the…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…
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…