相关论文: Geometric Aspects of Biological Sequence Compariso…
In this work we define a novel edit distance for trees considered with some abstract weights on the edges. The metric is driven by the idea of considering trees as topological summaries in the context of persistence and topological data…
Finite mixture models that allow for a broad range of potentially non-elliptical cluster distributions is an emerging methodological field. Such methods allow for the shape of the clusters to match the natural heterogeneity of the data,…
Assume we are given a set of items from a general metric space, but we neither have access to the representation of the data nor to the distances between data points. Instead, suppose that we can actively choose a triplet of items (A,B,C)…
Measuring similarity between complex objects is a fundamental task in many scientific fields. When objects are represented as graphs, graph similarity/distance measures offer a powerful framework for quantifying structural resemblance.…
This study aims to publish a novel similarity metric to increase the speed of comparison operations. Also the new metric is suitable for distance-based operations among strings. Most of the simple calculation methods, such as string length…
Active feedback between geometry and physics is woven throughout the study of Nature at its fundamental level, and is of key importance in string theory. Methods of complex algebraic geometry in particular have brought about an unrivaled…
In this work we extend Goldberg result \cite{Goldberg} for generalized string links over closed, connected and orientable surfaces of genus $g \geq 1$, i.e., different from the sphere (up to link-homotopy).
Physics relies on mathematical spaces carefully matched to the phenomena under study. Phase space in classical mechanics, Hilbert space in quantum theory, configuration spaces in field theory all provide representations in which physical…
We introduce a categorical language in which it is possible to talk about DNA sequencing, alignment methods, CRISPR, homologous recombination, haplotypes, and genetic linkage. This language takes the form of a class of limit-sketches whose…
In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions.…
Comparative visualization of scalar fields is often facilitated using similarity measures such as edit distances. In this paper, we describe a novel approach for similarity analysis of scalar fields that combines two recently introduced…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
The depinning of an elastic line interacting with a quenched disorder is studied for long range interactions, applicable to crack propagation or wetting. An ultrametric distance is introduced instead of the Euclidean distance, allowing for…
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…
We establish that every second countable completely regularly preordered space (E,T,\leq) is quasi-pseudo-metrizable, in the sense that there is a quasi-pseudo-metric p on E for which the pseudo-metric p\veep^-1 induces T and the graph of…
We explore some aspects of the relationship between biological evolution processes and the mathematical theory of records. For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories…
We survey the emerging area of compression-based, parameter-free, similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a…
This paper is a modified chapter of the author's Ph.D. thesis. We introduce the notions of sequentially approximated types and sequentially approximated Keisler measures. As the names imply, these are types which can be approximated by a…
Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the…
We show that a homeomorphism of Euclidean space is quasiconformal if and only if at each point there exists a sequence of uncentered open sets with bounded eccentricity shrinking to that point whose images also have bounded eccentricity.…