Related papers: Pairwise Rearrangement is Fixed-Parameter Tractabl…
We show fixed-parameter tractability of the Directed Multicut problem with three terminal pairs (with a randomized algorithm). This problem, given a directed graph $G$, pairs of vertices (called terminals) $(s_1,t_1)$, $(s_2,t_2)$, and…
We study the well-established problem of finding an optimal routing of unsplittable flows in a graph. While by now there is an extensive body of work targeting the problem on graph classes such as paths and trees, we aim at using the…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
We consider problems in which a simple path of fixed length, in an undirected graph, is to be shifted from a start position to a goal position by moves that add an edge to either end of the path and remove an edge from the other end. We…
Probabilistic circuits (PCs) are a unifying representation for probabilistic models that support tractable inference. Numerous applications of PCs like controllable text generation depend on the ability to efficiently multiply two circuits.…
A set of vertices in a graph is c-colorable if the subgraph induced by the set has a proper c-coloring. In this paper, we study the problem of finding a step-by-step transformation (reconfiguration) between two c-colorable sets in the same…
The parameters of a linear compartment model are usually estimated from experimental input-output data. A problem arises when infinitely many parameter values can yield the same result; such a model is called unidentifiable. In this case,…
The NP-hard general factor problem asks, given a graph and for each vertex a list of integers, whether the graph has a spanning subgraph where each vertex has a degree that belongs to its assigned list. The problem remains NP-hard even if…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies,…
In a reconfiguration problem, we are given two feasible solutions of a combinatorial problem and our goal is to determine whether it is possible to reconfigure one into the other, with the steps dictated by specific reconfiguration rules.…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
Parameterized analysis provides powerful mechanisms for obtaining fine-grained insights into different types of algorithms. In this work, we combine this field with evolutionary algorithms and provide parameterized complexity analysis of…
Inference and learning of graphical models are both well-studied problems in statistics and machine learning that have found many applications in science and engineering. However, exact inference is intractable in general graphical models,…
Given an undirected graph $G$, a collection $\{(s_1,t_1),..., (s_k,t_k)\}$ of pairs of vertices, and an integer $p$, the Edge Multicut problem ask if there is a set $S$ of at most $p$ edges such that the removal of $S$ disconnects every…
We study the parameterized complexity of scheduling unit-time jobs on parallel, identical machines under generalized precedence constraints for minimization of the makespan and the sum of completion times. In our setting, each job is…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We show that for various classes C of sparse graphs, and several measures of distance to such classes (such as edit distance and elimination distance), the problem of determining the distance of a given graph G to C is fixed-parameter…