Related papers: Upper Bounds to Genome Rearrangement Problem using…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
We use the reconfiguration framework to analyze problems that involve the rearrangement of items among groups. In various applications, a group of items could correspond to the files or jobs assigned to a particular machine, and the goal of…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
The problem of storing permutations in a distributed manner arises in several common scenarios, such as efficient updates of a large, encrypted, or compressed data set. This problem may be addressed in either a combinatorial or a coding…
Given a probability distribution over a set of n words to be transmitted, the Huffman Coding problem is to find a minimal-cost prefix free code for transmitting those words. The basic Huffman coding problem can be solved in O(n log n) time…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
The $(1+(\lambda,\lambda))$ genetic algorithm is a bright example of an evolutionary algorithm which was developed based on the insights from theoretical findings. This algorithm uses crossover, and it was shown to asymptotically outperform…
Superposition, the ability of neural networks to represent more features than neurons, is increasingly seen as key to the efficiency of large models. This paper investigates the theoretical foundations of computing in superposition,…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Rank modulation has been recently proposed as a scheme for storing information in flash memories. While rank modulation has advantages in improving write speed and endurance, the current encoding approach is based on the "push to the top"…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
Gene expression programming is an evolutionary optimization algorithm with the potential to generate interpretable and easily implementable equations for regression problems. Despite knowledge gained from previous optimizations being…
Permutation is the different arrangements that can be made with a given number of things taking some or all of them at a time. The notation P(n,r) is used to denote the number of permutations of n things taken r at a time. Permutation is…
The dose delivered to the planning target volume by proton beams is highly conformal, sparing organs at risk and normal tissues. New treatment planning systems adapted to spot scanning techniques have been recently proposed to…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
In the online labeling problem with parameters n and m we are presented with a sequence of n keys from a totally ordered universe U and must assign each arriving key a label from the label set {1,2,...,m} so that the order of labels…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
In this paper, we examine the computational complexity of enumeration in certain genome rearrangement models. We first show that the Pairwise Rearrangement problem in the Single Cut-and-Join model (Bergeron, Medvedev, & Stoye, J. Comput.…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
Genetic algorithms are high-level heuristic optimization methods which enjoy great popularity thanks to their intuitive description, flexibility, and, of course, effectiveness. The optimization procedure is based on the evolution of…