Related papers: Estimating Genome Reversal Distance by Genetic Alg…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
We address the problem of finding the minimum decomposition of a permutation in terms of transpositions with non-uniform cost. For arbitrary non-negative cost functions, we describe polynomial-time, constant-approximation decomposition…
In this study, we consider a variant of unlabelled sensing where the measurements are sparsely permuted, and additionally, a few correspondences are known. We present an estimator to solve for the unknown vector. We derive a theoretical…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…
In this work, we address the problem of Hessian inversion bias in distributed second-order optimization algorithms. We introduce a novel shrinkage-based estimator for the resolvent of gram matrices which is asymptotically unbiased, and…
Genetic programming is a powerful heuristic search technique that is used for a number of real world applications to solve among others regression, classification, and time-series forecasting problems. A lot of progress towards a theoretic…
Learning to hash pictures a list-wise sorting problem. Its testing metrics, e.g., mean-average precision, count on a sorted candidate list ordered by pair-wise code similarity. However, scarcely does one train a deep hashing model with the…
In recent works, both sparsity-based methods as well as learning-based methods have proven to be successful in solving several challenging linear inverse problems. However, sparsity priors for natural signals and images suffer from poor…
Breakpoint graphs are ubiquitous structures in the field of genome rearrangements. Their cycle decomposition has proved useful in computing and bounding many measures of (dis)similarity between genomes, and studying the distribution of…
The Permutation Pattern Matching problem asks, given two permutations $\sigma$ on $n$ elements and $\pi$, whether $\sigma$ admits a subsequence with the same relative order as $\pi$ (or, in the counting version, how many such subsequences…
Sorting is one of the most basic primitives in many algorithms and data analysis tasks. Comparison-based sorting algorithms, like quick-sort and merge-sort, are known to be optimal when the outcome of each comparison is error-free. However,…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
Distributed quantum computing has been well-known for many years as a system composed of a number of small-capacity quantum circuits. Limitations in the capacity of monolithic quantum computing systems can be overcome by using distributed…
Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…
In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a…
{\bf Motivation:} Permutation-based gene set tests are standard approaches for testing relationshi ps between collections of related genes and an outcome of interest in high throughput expression analyses. Using $M$ random permutations, one…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as…