相关论文: The zero exemplar distance problem
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
We present an exact and complete algorithm to isolate the real solutions of a zero-dimensional bivariate polynomial system. The proposed algorithm constitutes an elimination method which improves upon existing approaches in a number of…
We introduce a new variant of the $k$-deck problem, which in its traditional formulation asks for determining the smallest $k$ that allows one to reconstruct any binary sequence of length $n$ from the multiset of its $k$-length…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
The current paper investigates the bounded distance decoding (BDD) problem for ensembles of lattices whose generator matrices have sub-Gaussian entries. We first prove that, for these ensembles the BDD problem is NP-hard in the worst case.…
The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information…
We study a generalization of the classic Global Min-Cut problem, called Global Label Min-Cut (or sometimes Global Hedge Min-Cut): the edges of the input (multi)graph are labeled (or partitioned into color classes or hedges), and removing…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
Let $\mathcal{Q}$ be a vertex subset problem on graphs. In a reconfiguration variant of $\mathcal{Q}$ we are given a graph $G$ and two feasible solutions $S_s, S_t\subseteq V(G)$ of $\mathcal{Q}$ with $|S_s|=|S_t|=k$. The problem is to…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Determining whether two STRIPS planning instances are isomorphic is the simplest form of comparison between planning instances. It is also a particular case of the problem concerned with finding an isomorphism between a planning instance…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
The Skolem Problem asks to determine whether a given linear recurrence sequence (LRS) $\langle u_n \rangle_{n=0}^\infty$ over the integers has a zero term, that is, whether there exists $n$ such that $u_n = 0$. Decidability of the problem…
We solve the long-standing problem of making n perfect clones from m copies of one of two known pure states with minimum failure probability in the general case where the known states have arbitrary a priori probabilities. The solution…
We focus in this paper on dataset reduction techniques for use in k-nearest neighbor classification. In such a context, feature and prototype selections have always been independently treated by the standard storage reduction algorithms.…
In the number partitioning problem (NPP) one aims to partition a given set of $N$ real numbers into two subsets with approximately equal sum. The NPP is a well-studied optimization problem and is famous for possessing a…
The minimum constraint removal problem seeks to find the minimum number of constraints, i.e., obstacles, that need to be removed to connect a start to a goal location with a collision-free path. This problem is NP-hard and has been studied…