Related papers: Reconstructing Metric Trees from Order Information…

Trees are partial orderings where every element has a linearly ordered set of smaller elements. We define and study several natural notions of completeness of trees, extending Dedekind completeness of linear orders and Dedekind-MacNeille…

In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…

An arborescence, which is a directed analogue of a spanning tree in an undirected graph, is one of the most fundamental combinatorial objects in a digraph. In this paper, we study arborescences in digraphs from the viewpoint of…

We consider the problem of finding a subgraph of a given graph which maximizes a given function evaluated at its degree sequence. While the problem is intractable already for convex functions, we show that it can be solved in polynomial…

We study the problem of learning hypergraphs with shortest-path queries (SP-queries), and present the first provably optimal online algorithm for a broad and natural class of hypertrees that we call orderly hypertrees. Our online algorithm…

It is a well-known result that bilevel linear optimization is NP-hard. In many publications, reformulations as mixed-integer linear optimization problems are proposed, which suggests that the decision version of the problem belongs to NP.…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

Computing the similarity between two data points plays a vital role in many machine learning algorithms. Metric learning has the aim of learning a good metric automatically from data. Most existing studies on metric learning for…

The quadratic minimum spanning tree problem and its variations such as the quadratic bottleneck spanning tree problem, the minimum spanning tree problem with conflict pair constraints, and the bottleneck spanning tree problem with conflict…

Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…

We show that any infinite matroid can be reconstructed from the torsos of a tree-decomposition over its 2-separations, together with local information at the ends of the tree. We show that if the matroid is tame then this local information…

We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…

Given a graph G and an integer k, the objective of the $\Pi$-Contraction problem is to check whether there exists at most k edges in G such that contracting them in G results in a graph satisfying the property $\Pi$. We investigate the…

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 introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…

A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…

Query evaluation in an XML database requires reconstructing XML subtrees rooted at nodes found by an XML query. Since XML subtree reconstruction can be expensive, one approach to improve query response time is to use reconstruction views -…

Searching in partially ordered structures has been considered in the context of information retrieval and efficient tree-like indexes, as well as in hierarchy based knowledge representation. In this paper we focus on tree-like partial…