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A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…
Let $G=(V,E)$ be a simple graph with $|V|=n$ nodes and $|E|=m$ links, a subset $K \subseteq V$ of \emph{terminals}, a vector $p=(p_1,\ldots,p_m) \in [0,1]^m$ and a positive integer $d$, called \emph{diameter}. We assume nodes are perfect…
This paper presents the following results on sets that are complete for NP. 1. If there is a problem in NP that requires exponential time at almost all lengths, then every many-one NP-complete set is complete under length-increasing…
Column Generation (CG) is a popular method dedicated to enhancing computational efficiency in large scale Combinatorial Optimization (CO) problems. It reduces the number of decision variables in a problem by solving a pricing problem. For…
In order to formulate mathematical conjectures likely to be true, a number of base cases must be determined. However, many combinatorial problems are NP-hard and the computational complexity makes this research approach difficult using a…
The minimum-cost arborescence problem is a well-studied problem in the area of graph theory, with known polynomial-time algorithms for solving it. Previous literature introduced new variations on the original problem with different…
Imitation learning considerably simplifies policy synthesis compared to alternative approaches by exploiting access to expert demonstrations. For such imitation policies, errors away from the training samples are particularly critical. Even…
In a column-restricted covering integer program (CCIP), all the non-zero entries of any column of the constraint matrix are equal. Such programs capture capacitated versions of covering problems. In this paper, we study the approximability…
What makes a computational problem easy (e.g., in P, that is, solvable in polynomial time) or hard (e.g., NP-hard)? This fundamental question now has a satisfactory answer for a quite broad class of computational problems, so called…
The graph crossing number problem, cr(G)<=k, asks for a drawing of a graph G in the plane with at most k edge crossings. Although this problem is in general notoriously difficult, it is fixed- parameter tractable for the parameter k…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The Shortest Common Supersequence problem (SCS for short) consists in finding a shortest common supersequence of a finite set of words on a fixed alphabet Sigma. It is well-known that its decision version denoted [SR8] in [Garey and…
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 problem of efficiently computing and visualizing the structural resemblance between a pair of protein backbones in 3D has led Bereg et al. to pose the Chain Pair Simplification problem (CPS). In this problem, given two polygonal chains…
Background: Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that need to be taken into account.…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
The minimum distance is one of the most important combinatorial characterizations of a code. The maximum likelihood decoding problem is one of the most important algorithmic problems of a code. While these problems are known to be hard for…
We introduce and study two natural generalizations of the Connected VertexCover (VC) problem: the $p$-Edge-Connected and $p$-Vertex-Connected VC problem (where $p \geq 2$ is a fixed integer). Like Connected VC, both new VC problems are FPT,…