相关论文: A path-deformation framework for determining weigh…

Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…

Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…

Imagine that unlabelled tokens are placed on the edges of a graph, such that no two tokens are placed on incident edges. A token can jump to another edge if the edges having tokens remain independent. We study the problem of determining the…

Understanding the metric structure of permutation families is fundamental to combinatorics and has applications in social choice theory, bioinformatics, and coding theory. We study permutation families defined by restriction…

We discuss a class of binary cyclic codes and their dual codes. The minimum distance is determined using algebraic geometry, and an application of Weil's theorem. We relate the weights appearing in the dual codes to the number of rational…

We develop an invariant deformation theory, in a form accessible to practice, for affine schemes $W$ equipped with an action of a reductive algebraic group $G$. Given the defining equations of a $G$-invariant subscheme $X \subset W$, we…

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 renormalization group is a tool that allows one to obtain a reduced description of systems with many degrees of freedom while preserving the relevant features. In the case of quantum systems, in particular, one-dimensional systems…

Biases in observational data of treatments pose a major challenge to estimating expected treatment outcomes in different populations. An important technique that accounts for these biases is reweighting samples to minimize the discrepancy…

Motivated by the challenge of using DNA-seq data to identify viruses in human blood samples, we propose a novel classification algorithm called "Radial Distance Weighted Discrimination" (or Radial DWD). This classifier is designed for…

We propose a novel weakly supervised discriminative algorithm for learning context specific registration metrics as a linear combination of conventional similarity measures. Conventional metrics have been extensively used over the past two…

We use information geometry, in which the local distance between models measures their distinguishability from data, to quantify the flow of information under the renormalization group. We show that information about relevant parameters is…

An edit distance is a measure of the minimum cost sequence of edit operations to transform one structure into another. Edit distance is most commonly encountered within the context of strings, where Wagner and Fischer's string edit distance…

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…

We present new upper and lower bounds on the minimum distance of certain generalized bicycle (GB) codes beyond the reach of techniques for classical codes capable of even capturing the true minimum distance for some cases. These bounds are…

Permutations on a set, endowed with function composition, build a group called a symmetric group. In addition to their algebraic structure, symmetric groups have two metrics that are of particular interest to us here: the Cayley distance…

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…

For a hereditary graph class $\mathcal{H}$, the $\mathcal{H}$-elimination distance of a graph $G$ is the minimum number of rounds needed to reduce $G$ to a member of $\mathcal{H}$ by removing one vertex from each connected component in each…

Consider a finite directed graph without cycles in which the arrows are weighted. We present an algorithm for the computation of a new distance, called path-length-weighted distance, which has proven useful for graph analysis in the context…

The Gilbert-Johnson-Keerthi (GJK) algorithm is an iterative improvement technique for finding the minimum distance between two convex objects. It can easily be extended to work with concave objects and return the pair of closest points. [4]…