Related papers: Genomic Problems Involving Copy Number Profiles: C…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
The Critical Node Problem (CNP) is to identify a subset of nodes in a graph whose removal maximally degrades pairwise connectivity. The CNP is an important variant of the Critical Node Detection Problem (CNDP) with wide applications. Due to…
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…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…
Single nucleotide polymorphisms (SNPs) often appear in clusters along the length of a chromosome. This is due to variation in local coalescent times caused by,for example, selection or recombination. Here we investigate whether…
The K-way vertex cut problem} consists in, given a graph G, finding a subset of vertices of a given size, whose removal partitions G into the maximum number of connected components. This problem has many applications in several areas. It…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
The computational problem of inferring the full haplotype of a cell starting from read sequencing data is known as haplotype assembly, and consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…
It has been observed in many places that constant-factor approximable problems often admit polynomial or even linear problem kernels for their decision versions, e.g., Vertex Cover, Feedback Vertex Set, and Triangle Packing. While there…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Critical node problems involve identifying a subset of critical nodes from an undirected graph whose removal results in optimizing a pre-defined measure over the residual graph. As useful models for a variety of practical applications,…
Learning to predict solutions to real-valued combinatorial graph problems promises efficient approximations. As demonstrated based on the NP-hard edge clique cover number, recurrent neural networks (RNNs) are particularly suited for this…
Copy detection, which is a task to determine whether an image is a modified copy of any image in a database, is an unsolved problem. Thus, we addressed copy detection by training convolutional neural networks (CNNs) with contrastive…
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…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…