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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…

An enumeration kernel as defined by Creignou et al. [Theory Comput. Syst. 2017] for a parameterized enumeration problem consists of an algorithm that transforms each instance into one whose size is bounded by the parameter plus a…

Assuming a cloning oracle, satisfiability, which is an NP complete problem, is shown to belong to $BPP^C$ and $BQP^C$ (depending on the ability of the oracle C to clone either a binary random variable or a qubit). The same result is…

We study the Equitable Connected Partition (ECP for short) problem, where we are given a graph G=(V,E) together with an integer p, and our goal is to find a partition of V into p parts such that each part induces a connected sub-graph of G…

For certain image generation tasks, vector graphics such as Scalable Vector Graphics (SVGs) offer clear benefits such as increased flexibility, size efficiency, and editing ease, but remain less explored than raster-based approaches. A core…

Analyzing the computational complexity of evolutionary algorithms for binary search spaces has significantly increased their theoretical understanding. With this paper, we start the computational complexity analysis of genetic programming.…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In…

The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…

Weak-memory models are standard formal specifications of concurrency across hardware, programming languages, and distributed systems. A fundamental computational problem is consistency testing: is the observed execution of a concurrent…

In this paper we consider the problem of finding a vector that can be written as a nonnegative integer linear combination of given 0-1 vectors, the generators, such that the l_1-distance between this vector and a given target vector is…

Qualitative numerical planning is classical planning extended with non-negative real variables that can be increased or decreased "qualitatively", i.e., by positive indeterminate amounts. While deterministic planning with numerical…

A matching is said to be disconnected if the saturated vertices induce a disconnected subgraph and induced if the saturated vertices induce a 1-regular graph. The disconnected and induced matching numbers are defined as the maximum…

Convolutional neural networks (CNNs) are the cutting edge model for supervised machine learning in computer vision. In recent years CNNs have outperformed traditional approaches in many computer vision tasks such as object detection, image…

The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…

Co-clustering, that is, partitioning a numerical matrix into homogeneous submatrices, has many applications ranging from bioinformatics to election analysis. Many interesting variants of co-clustering are NP-hard. We focus on the basic…

Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…

The crossing number of a graph is the minimum number of edge crossings that a graph can have when drawn in the plane. Determining this number, known as the Crossing Number problem, is a celebrated problem in combinatorial optimization. It…

We consider the Minimum Convex Partition problem: Given a set P of n points in the plane, draw a plane graph G on P, with positive minimum degree, such that G partitions the convex hull of P into a minimum number of convex faces. We show…

It is well known that sparse approximation problem is \textsf{NP}-hard under general dictionaries. Several algorithms have been devised and analyzed in the past decade under various assumptions on the \emph{coherence} $\mu$ of the…