相关论文: Data structures to represent a set of k-long DNA s…

'Big' high-dimensional data are commonly analyzed in low-dimensions, after performing a dimensionality-reduction step that inherently distorts the data structure. For the same purpose, clustering methods are also often used. These methods…

The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…

A new statistical technique for constructing linear latent structure (LLS) models from available data, supported by well established theoretical results and an efficient algorithm, is presented. The method reduces the problem of estimating…

Succinct data structures give space-efficient representations of large amounts of data without sacrificing performance. They rely one cleverly designed data representations and algorithms. We present here the formalization in Coq/SSReflect…

This paper describes the approach taken to the XML Mining track at INEX 2008 by a group at the Queensland University of Technology. We introduce the K-tree clustering algorithm in an Information Retrieval context by adapting it for document…

We propose and study a multi-scale approach to vector quantization. We develop an algorithm, dubbed reconstruction trees, inspired by decision trees. Here the objective is parsimonious reconstruction of unsupervised data, rather than…

DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…

Among the novel metrics used to study the relative importance of nodes in complex networks, k-core decomposition has found a number of applications in areas as diverse as sociology, proteinomics, graph visualization, and distributed system…

Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…

This short paper gives an introduction to a research project to analyze how digital documents are structured and described. Using a phenomenological approach, this research will reveal common patterns that are used in data, independent from…

Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of…

We address the problem of counting the number of strings in a collection where a given pattern appears, which has applications in information retrieval and data mining. Existing solutions are in a theoretical stage. We implement these…

Named Entity Recognition seeks to extract substrings within a text that name real-world objects and to determine their type (for example, whether they refer to persons or organizations). In this survey, we first present an overview of…

In this paper, we propose a method to represent a fingerprint image by an ordered, fixed-length bit-string providing improved accuracy performance, faster matching time and compressibility. First, we devise a novel minutia-based local…

Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…

The k-truss is a type of cohesive subgraphs proposed recently for the study of networks. While the problem of computing most cohesive subgraphs is NP-hard, there exists a polynomial time algorithm for computing k-truss. Compared with k-core…

Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores…

We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions,…

In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…

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…