Related papers: Spectral concepts in genome informational analysis
Light passing through scattering media will be strongly scattered and diffused into complex speckle pattern, which contains almost all the spatial information and spectral information of the objects. Although various methods have been…
The scale and complexity of modern data sets and the limitations associated with testing large numbers of hypotheses underline the need for feature selection methods. Spectral techniques rank features according to their degree of…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous…
In this paper we discuss the relevance of, and possible scientific gains which can be acquired from studying circumstellar molecular spectra toward evolved stars. Where can we expect circumstellar molecular spectra, why would we want to…
Spectral classification is the division of stars into classes based on their spectral characteristics. Different classification systems have existed since the 19th century but the term is used nowadays mostly to refer to the Morgan-Keenan…
The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…
The paper studies functions defined on continuous branching lines connected into a system. A notion of spectrum degeneracy for these functions is introduced. This degeneracy is based on the properties of the Fourier transforms for processes…
In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to…
Our goal is to provide simple and practical algorithms in higher-order Fourier analysis which are based on spectral decompositions of operators. We propose a general framework for such algorithms and provide a detailed analysis of the…
Quantum channels describe the most general dynamics of open quantum systems. A quantum channel, as a linear map on vectorized quantum states, can be represented by a single matrix, whose spectrum is called the channel spectrum. Here we…
The cross-spectrum method consists in measuring a signal $c(t)$ simultaneously with two independent instruments. Each of these instruments contributes to the global noise by its intrinsec (white) noise, whereas the signal $c(t)$ that we…
This paper addresses the three following questions. (i) How the structures of group and of chain of groups enter nuclear, atomic and molecular spectroscopy? (ii) How these structures can be exploited, in a quantum- mechanical framework, in…
We introduce propagation kernels, a general graph-kernel framework for efficiently measuring the similarity of structured data. Propagation kernels are based on monitoring how information spreads through a set of given graphs. They leverage…
Multi-object or integral field spectrographs are recognized techniques for achieving simultaneous spectroscopic observations of different or extended sky objects with a high multiplex factor. In this communication is described a…
Spectral imaging is an umbrella term for energy-resolved x-ray imaging in medicine. The technique makes use of the energy dependence of x-ray attenuation to either increase the contrast-to-noise ratio, or to provide quantitative image data…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
We introduce a formalism to produce several families of spectral sequences involving the derived functors of the limit and colimit functors over a finite partially ordered set. The first type of spectral sequences involves the left derived…
Frequency-domain analysis has emerged as a powerful paradigm for time series analysis, offering unique advantages over traditional time-domain approaches while introducing new theoretical and practical challenges. This survey provides a…