相关论文: The zero exemplar distance problem

In our problem, we are given access to a number of sequences of nonnegative i.i.d. random variables, whose realizations are observed sequentially. All sequences are of the same finite length. The goal is to pick one element from each…

Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…

We study the computational complexity of the optimal transport problem that evaluates the Wasserstein distance between the distributions of two K-dimensional discrete random vectors. The best known algorithms for this problem run in…

The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…

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…

In this paper we propose a nonparametric graphical test based on optimal matching, for assessing the equality of multiple unknown multivariate probability distributions. Our procedure pools the data from the different classes to create a…

DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…

The input of the Test Cover problem consists of a set $V$ of vertices, and a collection ${\cal E}=\{E_1,..., E_m\}$ of distinct subsets of $V$, called tests. A test $E_q$ separates a pair $v_i,v_j$ of vertices if $|\{v_i,v_j\}\cap E_q|=1.$…

This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…

The Skolem Problem asks to determine whether a given integer linear recurrence sequence has a zero term. This problem arises across a wide range of topics in computer science, including loop termination, formal languages, automata theory,…

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…

Let $K$ be a field and $P=K[x_1,\dots,x_n]$. The technique of elimination by substitution is based on discovering a coherently $Z=(z_1,\dots,z_s)$-separating tuple of polynomials $(f_1,\dots,f_s)$ in an ideal $I$, i.e., on finding…

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…

DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

In this paper we investigate the colorful components framework, motivated by applications emerging from comparative genomics. The general goal is to remove a collection of edges from an undirected vertex-colored graph $G$ such that in the…

In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…

This paper surveys results on complexity of the optimal recombination problem (ORP), which consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We…

This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…