Related papers: Pairwise Rearrangement is Fixed-Parameter Tractabl…
In this paper, we present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…
The MULTICUT problem, given a graph G, a set of terminal pairs T={(s_i,t_i) | 1 <= i <= r} and an integer p, asks whether one can find a cutset consisting of at most p non-terminal vertices that separates all the terminal pairs, i.e., after…
We consider the parameterized complexity of the problem of tracking shortest s-t paths in graphs, motivated by applications in security and wireless networks. Given an undirected and unweighted graph with a source s and a destination t,…
An st-shortest path, or st-path for short, in a graph G is a shortest (induced) path from s to t in G. Two st-paths are said to be adjacent if they differ on exactly one vertex. A reconfiguration sequence between two st-paths P and Q is a…
The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
The task of finding an extension to a given partial drawing of a graph while adhering to constraints on the representation has been extensively studied in the literature, with well-known results providing efficient algorithms for…
Optimal Morse matchings reveal essential structures of cell complexes which lead to powerful tools to study discrete geometrical objects, in particular discrete 3-manifolds. However, such matchings are known to be NP-hard to compute on…
We study the approximation of high-dimensional rank one tensors using point evaluations and consider deterministic as well as randomized algorithms. We prove that for certain parameters (smoothness and norm of the $r$th derivative) this…
To enumerate 3-manifold triangulations with a given property, one typically begins with a set of potential face pairing graphs (also known as dual 1-skeletons), and then attempts to flesh each graph out into full triangulations using an…
We investigate exact crossing minimization for graphs that differ from trees by a small number of additional edges, for several variants of the crossing minimization problem. In particular, we provide fixed parameter tractable algorithms…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We consider the following natural graph cut problem called Critical Node Cut (CNC): Given a graph $G$ on $n$ vertices, and two positive integers $k$ and $x$, determine whether $G$ has a set of $k$ vertices whose removal leaves $G$ with at…
The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
We study the linearizability monitoring problem, which asks whether a given concurrent history of a data structure is equivalent to some sequential execution of the same data structure. In general, this problem is $\textsf{NP}$-hard, even…
Given a static vertex-selection problem (e.g. independent set, dominating set) on a graph, we can define a corresponding temporally satisfying reconfiguration problem on a temporal graph which asks for a sequence of solutions to the…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
We introduce a new framework for reconfiguration problems, and apply it to independent sets as the first example. Suppose that we are given an independent set $I_0$ of a graph $G$, and an integer $l \ge 0$ which represents a lower bound on…
Given an edge-weighted graph $G$ on $n$ nodes, the NP-hard Max-Cut problem asks for a node bipartition such that the sum of edge weights joining the different partitions is maximized. We propose a fixed-parameter tractable algorithm…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…