Related papers: Heuristics based on Adjacency Graph Packing for DC…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
The container relocation problem is a challenging combinatorial optimisation problem tasked with finding a sequence of container relocations required to retrieve all containers by a given order. Due to the complexity of this problem,…
Local complement is a graph operation formalized by Bouchet which replaces the neighborhood of a chosen vertex with its edge-complement. This operation induces an equivalence relation on graphs; determining the size of the resulting…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Adversarial object rearrangement in the real world (e.g., previously unseen or oversized items in kitchens and stores) could benefit from understanding task scenes, which inherently entail heterogeneous components such as current objects,…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
We introduce an optimal transport based approach for comparing undirected graphs with non-negative edge weights and general vertex labels, and we study connections between the resulting linear program and the graph isomorphism problem. Our…
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to…
We consider the problem of dominating set-based virtual backbone used for routing in asymmetric wireless ad-hoc networks. These networks have non-uniform transmission ranges and are modeled using the well-established disk graphs. The…
We consider heuristic algorithm for solving graph isomorphism problem. The algorithm based on a successive splitting of the eigenvalues of the matrices which are modifications (to positive defined) of graphs' adjacency matrices.…
We consider a Hamiltonian decomposition problem of partitioning a regular graph into edge-disjoint Hamiltonian cycles. It is known that verifying vertex non-adjacency in the 1-skeleton of the symmetric and asymmetric traveling salesperson…
The Distance Geometry Problem (DGP) seeks to find positions for a set of points in geometric space when some distances between pairs of these points are known. The so-called discretization assumptions allow to discretize the search space of…
Graph alignment aims at finding the vertex correspondence between two correlated graphs, a task that frequently occurs in graph mining applications such as social network analysis. Attributed graph alignment is a variant of graph alignment,…
Prediction of protein-ligand complexes for flexible proteins remains still a challenging problem in computational structural biology and drug design. Here we present two novel deep neural network approaches with significant improvement in…
In this thesis I propose an algorithm to heuristically calculate different distance measures on uncertain graphs (i.e. graphs where edges only exist with a certain probability) and apply this to the heuristic calculation of harmonic…
This article reports an algorithm for multi-agent distributed optimization problems with a common decision variable, local linear equality and inequality constraints and set constraints with convergence rate guarantees.…
Correspondence is a ubiquitous problem in computer vision and graph matching has been a natural way to formalize correspondence as an optimization problem. Recently, graph matching solvers have included higher-order terms representing…
Suppose a target is hidden in one of the vertices of an edge-weighted graph according to a known probability distribution. The expanding search problem asks for a search sequence of the vertices so as to minimize the expected time for…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
We survey theoretical, algorithmic, and computational results at the intersection of distance geometry problems and mathematical programming, both with and without adjacencies as part of the input. While mathematical programming methods can…