Related papers: A new distance between DNA sequences
For a bounded metric space X, we define a metric on the set of all finite subsets of X. This generalizes the sequence-subset distance introduced by Wentu Song, Kui Cai and Kees A. Schouhamer Immink to study error correcting codes for DNA…
Most classifiers rely on discriminative boundaries that separate instances of each class from everything else. We argue that discriminative boundaries are counter-intuitive as they define semantics by what-they-are-not; and should be…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
This paper proposes a new method for determining similarity and anomalies between time series, most practically effective in large collections of (likely related) time series, by measuring distances between structural breaks within such a…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…
The progression of X-ray technology introduces diverse image styles that need to be adapted to the preferences of radiologists. To support this task, we introduce a novel deep learning-based metric that quantifies style differences of…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…
In this work, we propose to study the global geometrical properties of generative models. We introduce a new Riemannian metric to assess the similarity between any two data points. Importantly, our metric is agnostic to the parametrization…
With the recent success of generative models in image and text, the evaluation of generative models has gained a lot of attention. Whereas most generative models are compared in terms of scalar values such as Frechet Inception Distance…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
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…
It is an important task to construct quantum maximum-distance-separable (MDS) codes with good parameters. In the present paper, we provide six new classes of q-ary quantum MDS codes by using generalized Reed-Solomon (GRS) codes and…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…