Related papers: On the Complexity of Minimum Labeling Alignment of…
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…
A proper labeling of a graph is an assignment of integers to some elements of a graph, which may be the vertices, the edges, or both of them, such that we obtain a proper vertex coloring via the labeling subject to some conditions. The…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
We show that computing the minimum rank of a sign pattern matrix is NP hard. Our proof is based on a simple but useful connection between minimum ranks of sign pattern matrices and the stretchability problem for pseudolines arrangements. In…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
Block Sorting is a well studied problem, motivated by its applications in Optical Character Recognition (OCR), and Computational Biology. Block Sorting has been shown to be NP-Hard, and two separate polynomial time 2-approximation…
Linearizing two partial orders to maximize the number of adjacencies and minimize the number of breakpoints is APX-hard. This holds even if one of the two partial orders is already a linear order and the other is an interval order, or if…
We present several new results pertaining to haplotyping. These results concern the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype fragments. We consider the complexity of the…
We show that given a satisfiable instance of the 2-to-1 Label Cover problem, it is NP-hard to find a $(23/24 + \eps)$-satisfying assignment.
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
The problem of Distance Edge Labeling is a variant of Distance Vertex Labeling (also known as $L_{2,1}$ labeling) that has been studied for more than twenty years and has many applications, such as frequency assignment. The Distance Edge…
A labelled, undirected graph is a graph whose edges have assigned labels, from a specific set. Given a labelled, undirected graph, the well-known minimum labelling spanning tree problem is aimed at finding the spanning tree of the graph…
Discrete energy minimization is widely-used in computer vision and machine learning for problems such as MAP inference in graphical models. The problem, in general, is notoriously intractable, and finding the global optimal solution is…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
We discuss the feasibility of the following learning problem: given unmatched samples from two domains and nothing else, learn a mapping between the two, which preserves semantics. Due to the lack of paired samples and without any…
The paper presents complexity results and performance guaranties for a family of approximation algorithms for an optimisation problem arising in software testing and manufacturing. The problem is formulated as a partitioning of a set where…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…
Placing a minimum number of guards on a given watchman route in a polygonal domain is called the {\em minimum vision points problem}. We prove that finding the minimum number of vision points on a shortest watchman route in a simple polygon…