相关论文: Iterative Rounding for the Closest String Problem

Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…

In this work, we present a new iterative exact solution algorithm for the weighted fair sequences problem, which is a recently introduced NP-hard sequencing problem with applications in diverse areas such as TV advertisement scheduling,…

The problem of sparse approximation and the closely related compressed sensing have received tremendous attention in the past decade. Primarily studied from the viewpoint of applied harmonic analysis and signal processing, there have been…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

We study a combinatorial problem arising from microarrays synthesis. The synthesis is done by a light-directed chemical process. The objective is to minimize unintended illumination that may contaminate the quality of experiments.…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…

Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…

Strip packing is a classical packing problem, where the goal is to pack a set of rectangular objects into a strip of a given width, while minimizing the total height of the packing. The problem has multiple applications, e.g. in scheduling…

Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…

Protein/Peptide microarrays are rapidly gaining momentum in the diagnosis of cancer. High-density and highthroughput peptide arrays are being extensively used to detect tumor biomarkers, examine kinase activity, identify antibodies having…

The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence…

Bound propagation is an important Artificial Intelligence technique used in Constraint Programming tools to deal with numerical constraints. It is typically embedded within a search procedure ("branch and prune") and used at every node of…

Stemming or suffix stripping, an important part of the modern Information Retrieval systems, is to find the root word (stem) out of a given cluster of words. Existing algorithms targeting this problem have been developed in a haphazard…

Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…

This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…

In this paper we consider two problems concerning string factorisation. Specifically given a string $w$ and an integer $k$ find a factorisation of $w$ where each factor has length bounded by $k$ and has the minimum (the FmD problem) or the…

In the Shortest Common Superstring problem (SCS), one needs to find the shortest superstring for a set of strings. While SCS is NP-hard and MAX-SNP-hard, the Greedy Algorithm "choose two strings with the largest overlap; merge them; repeat"…

In this paper it is shown that given a sufficient number of (noisy) random binary linear equations, the Learning from Parity with Noise (LPN) problem can be solved in essentially cube root time in the number of unknowns. The techniques used…

In this paper, we propose an efficient algorithm for the network slicing problem which attempts to map multiple customized virtual network requests (also called services) to a common shared network infrastructure and allocate network…

In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximizes information about a 'relevance' variable, Y,…