Related papers: A Three-Stage Algorithm for the Closest String Pro…
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
A step-search sequential quadratic programming method is proposed for solving nonlinear equality constrained stochastic optimization problems. It is assumed that constraint function values and derivatives are available, but only stochastic…
The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given…
Decoding for many NLP tasks requires an effective heuristic algorithm for approximating exact search since the problem of searching the full output space is often intractable, or impractical in many settings. The default algorithm for this…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,...,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
Beam search is a go-to strategy for decoding neural sequence models. The algorithm can naturally be viewed as a subset optimization problem, albeit one where the corresponding set function does not reflect interactions between candidates.…
Cutting and packing problems are present in many, at first glance unconnected, areas, therefore it's beneficial to have a good understanding of their underlying structure, to select proper techniques for finding solutions. Cutting and…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
We study the problem of efficiently clustering protein sequences in a limited information setting. We assume that we do not know the distances between the sequences in advance, and must query them during the execution of the algorithm. Our…
Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of…
Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…
We formulate and analyze a generic sequential resource access problem arising in a variety of engineering fields, where a user disposes a number of heterogeneous computing, communication, or storage resources, each characterized by the…
Word segmentation is the task of inserting or deleting word boundary characters in order to separate character sequences that correspond to words in some language. In this article we propose an approach based on a beam search algorithm and…
he segment minimization problem consists of finding the smallest set of integer matrices that sum to a given intensity matrix, such that each summand has only one non-zero value, and the non-zeroes in each row are consecutive. This has…