相关论文: Worst-case optimal approximation algorithms for ma…
We consider the problem of maximizing the revenue raised from tolls set on the arcs of a transportation network, under the constraint that users are assigned to toll-compatible shortest paths. We first prove that this problem is strongly…
Given a graph $G = (V, E)$, we wish to compute a spanning tree whose maximum vertex degree, i.e. tree degree, is as small as possible. Computing the exact optimal solution is known to be NP-hard, since it generalizes the Hamiltonian path…
Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…
We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…
A complete set of filters $F_n$ for the optimal-depth $n$-input sorting network problem is such that if there exists an $n$-input sorting network of depth $d$ then there exists one of the form $C \oplus C'$ for some $C \in F_n$. Previous…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
In this paper, we study a number of well-known combinatorial optimization problems that fit in the following paradigm: the input is a collection of (potentially inconsistent) local relationships between the elements of a ground set (e.g.,…
The support of a flow $x$ in a network is the subdigraph induced by the arcs $uv$ for which $x(uv)>0$. We discuss a number of results on flows in networks where we put certain restrictions on structure of the support of the flow. Many of…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Optimal decision tree (\odt) is a fundamental problem arising in applications such as active learning, entity identification, and medical diagnosis. An instance of \odt is given by $m$ hypotheses, out of which an unknown ``true'' hypothesis…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
A trie $\mathcal{T}$ is a rooted tree such that each edge is labeled by a single character from the alphabet, and the labels of out-going edges from the same node are mutually distinct. Given a trie $\mathcal{T}$ with $n$ edges, we show how…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Given two phylogenetic trees with the $\{1, \ldots, n\}$ leaf-set the maximum agreement subtree problem asks what is the maximum size of the subset $A \subseteq \{1, \ldots, n\}$ such that the two trees are equivalent when restricted to…
The seminal work of Chow and Liu (1968) shows that approximation of a finite probabilistic system by Markov trees can achieve the minimum information loss with the topology of a maximum spanning tree. Our current paper generalizes the…