相关论文: Estimating Genome Reversal Distance by Genetic Alg…
Generalized sorting problem, also known as sorting with forbidden comparisons, was first introduced by Huang et al. together with a randomized algorithm which requires $\tilde O(n^{3/2})$ probes. We study this problem with additional…
We investigate a family of $(\mu+\lambda)$ Genetic Algorithms (GAs) which creates offspring either from mutation or by recombining two randomly chosen parents. By scaling the crossover probability, we can thus interpolate from a fully…
Genetic Algorithms are a popular set of optimization algorithms often used to aid software testing. However, no work has been done to apply systematic software testing techniques to genetic algorithms because of the stochasticity and the…
In genome rearrangements, the mutational event transposition swaps two adjacent blocks of genes in one chromosome. The Transposition Distance Problem (TDP) aims to find the minimum number of transpositions required to transform one…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The genetic algorithm includes some parameters that should be adjusted, so as to get reliable results. Choosing a representation of the problem addressed, an initial population, a method of selection, a crossover operator, mutation…
This paper discusses an outer-approximation guided optimization method for constrained neural network inverse problems with rectified linear units. The constrained neural network inverse problems refer to an optimization problem to find the…
We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation…
We introduce an algorithm to determine when a sorting operation, such as stack-sort or bubble-sort, outputs a given pattern. The algorithm provides a new proof of the description of West-2-stack-sortable permutations, that is permutations…
In this work, we consider a restricted case of the well studied Sorting by Block Interchanges problem. We put an upper bound k on the length of the blocks (substrings) to be interchanged at each step. We call the problem Sorting by k-Block…
One of the most basic computational problems is the task of finding a desired item in an ordered list of N items. While the best classical algorithm for this problem uses log_2 N queries to the list, a quantum computer can solve the problem…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Some genes can change their relative locations in a genome. Thus for different individuals of the same species, the orders of genes might be different. Such jumping genes are called transposons. A practical problem is to determine…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
We present a deterministic comparison-based algorithm that sorts sequences avoiding a fixed permutation $\pi$ in linear time, even if $\pi$ is a priori unkown. Moreover, the dependence of the multiplicative constant on the pattern $\pi$…
Ordered search is the task of finding an item in an ordered list using comparison queries. The best exact classical algorithm for this fundamental problem uses $\lceil \log_{2}{n}\rceil$ queries for a list of length $n$. Quantum computers…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Researchers in genetics and other life sciences commonly use permutation tests to evaluate differences between groups. Permutation tests have desirable properties, including exactness if data are exchangeable, and are applicable even when…
Pancake flipping, a famous open problem in computer science, can be formalised as the problem of sorting a permutation of positive integers using as few prefix reversals as possible. In that context, a prefix reversal of length k reverses…
A genetic algorithm procedure is demonstrated that refines the selection of interpolation points of the discrete empirical interpolation method (DEIM) when used for constructing reduced order models for time dependent and/or parametrized…