Related papers: An efficient sampling algorithm for difficult tree…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
This paper deals with the recoverable robust spanning tree problem under interval uncertainty representations. A polynomial time, combinatorial algorithm for the recoverable spanning tree problem is first constructed. This problem…
In this work we consider the Metric Steiner Forest problem in the sublinear time model. Given a set $V$ of $n$ points in a metric space where distances are provided by means of query access to an $n\times n$ distance matrix, along with a…
Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…
In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
In low-dimensional topology, many important decision algorithms are based on normal surface enumeration, which is a form of vertex enumeration over a high-dimensional and highly degenerate polytope. Because this enumeration is subject to…
``Algorithms with predictions'', or ``learning-augmented algorithms'', has proved to be an extremely useful paradigm for combining machine learning with traditional algorithms. One of the textbook settings for this is searching a sorted…
The personnel rostering problem is the problem of finding an optimal way to assign employees to shifts, subject to a set of hard constraints which all valid solutions must follow, and a set of soft constraints which define the relative…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We consider the classical tree edit distance between ordered labeled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
Given a graph $G$ and two spanning trees $T$ and $T'$ in $G$, Spanning Tree Reconfiguration asks whether there is a step-by-step transformation from $T$ to $T'$ such that all intermediates are also spanning trees of $G$, by exchanging an…
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…
Herein we explore a dual tree algorithm for matrix multiplication of $A\in \mathbb{R}^{M\times D}$ and $B\in\mathbb{R}^{D\times N}$, very narrowly effective if the normalized rows of $A$ and columns of $B$, treated as vectors in…
Tree-width and path-width are widely successful concepts. Many NP-hard problems have efficient solutions when restricted to graphs of bounded tree-width. Many efficient algorithms are based on a tree decomposition. Sometimes the more…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Decision tree algorithms have been among the most popular algorithms for interpretable (transparent) machine learning since the early 1980's. The problem that has plagued decision tree algorithms since their inception is their lack of…