Related papers: On the Complexity of Several Haplotyping Problems
We show that the problem of finding a Resolution refutation that is at most polynomially longer than a shortest one is NP-hard. In the parlance of proof complexity, Resolution is not automatizable unless P = NP. Indeed, we show it is…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
3-SAT problem is of great importance to many technical and scientific applications. This paper presents a new hybrid evolutionary algorithm for solving this satisfiability problem. 3-SAT problem has the huge search space and hence it is…
The Hypergraph Partitioning (HGP) problem is a well-studied problem that finds applications in a variety of domains. The literature on the HGP problem has heavily focused on developing fast heuristic approaches. In several application…
In the literature, the optimization problem to identify a set of composite hypotheses H, which will yield the $k$ largest $P(H|S_e)$ where a composite hypothesis is an instantiation of all the nodes in the network except the evidence nodes…
A new optimization design is proposed for matrix completion by weighting the measurements and deriving the corresponding error bound. Accordingly, the Haplotype reconstruction using nuclear norm minimization with Weighted Constraint…
Given a redundant dictionary $\Phi$, represented by an $M \times N$ matrix ($\Phi \in \mathbb{R}^{M \times N}$) and a target signal $y \in \mathbb{R}^M$, the \emph{sparse approximation problem} asks to find an approximate representation of…
The problem of computing all maximal induced subgraphs of a graph G that have a graph property P, also called the maximal P-subgraphs problem, is considered. This problem is studied for hereditary, connected-hereditary and rooted-hereditary…
The main purpose of this paper is to study the NP-complete subset-sum problem, not in the usual context of time-complexity-based classification of the algorithms (exponential/polynomial), but through a new kind of algorithmic classification…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
Recently, Hajirasouliha and Raphael (WABI 2014) proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer…
Unlike the matrix case, computing low-rank approximations of tensors is NP-hard and numerically ill-posed in general. Even the best rank-1 approximation of a tensor is NP-hard. In this paper, we use convex optimization to develop…
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…
The multi-homogeneous Bezout number is a bound for the number of solutions of a system of multi-homogeneous polynomial equations, in a suitable product of projective spaces. Given an arbitrary, not necessarily multi-homogeneous system, one…
Motivated by the problem of enumerating all tree decompositions of a graph, we consider in this article the problem of listing all the minimal chordal completions of a graph. In \cite{carmeli2020} (\textsc{Pods 2017}) Carmeli \emph{et al.}…
Computing haplotypes from sequencing data, i.e. haplotype assembly, is an important component of molecular and population genetics problems, including interpreting the effects of genetic variation on complex traits and reconstructing…
Minimum cost homomorphism problems can be viewed as a generalization of list homomorphism problems. They also extend two well-known graph colouring problems: the minimum colour sum problem and the optimum cost chromatic partition problem.…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
In this paper we propose a new approach for developing a proof that P=NP. We propose to use a polynomial-time reduction of a NP-complete problem to Linear Programming. Earlier such attempts used polynomial-time transformation which is a…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…