Search results for "probability"
showing 10 items of 3417 documents
Vector coherent states and intertwining operators
2009
In this paper we discuss a general strategy to construct vector coherent states of the Gazeau-Klauder type and we use them to built up examples of isospectral hamiltonians. For that we use a general strategy recently proposed by the author and which extends well known facts on intertwining operators. We also discuss the possibility of constructing non-isospectral hamiltonians with related eigenstates.
Pathway analysis of high-throughput biological data within a Bayesian network framework
2011
Abstract Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. Results: Proposed method takes into account the connectivity and relatedness between nodes of the p…
Blind Source Separation Based on Joint Diagonalization in R: The Packages JADE and BSSasymp
2017
Blind source separation (BSS) is a well-known signal processing tool which is used to solve practical data analysis problems in various fields of science. In BSS, we assume that the observed data consists of linear mixtures of latent variables. The mixing system and the distributions of the latent variables are unknown. The aim is to find an estimate of an unmixing matrix which then transforms the observed data back to latent sources. In this paper we present the R packages JADE and BSSasymp. The package JADE offers several BSS methods which are based on joint diagonalization. Package BSSasymp contains functions for computing the asymptotic covariance matrices as well as their data-based es…
Fast Estimation of the Median Covariation Matrix with Application to Online Robust Principal Components Analysis
2017
International audience; The geometric median covariation matrix is a robust multivariate indicator of dispersion which can be extended without any difficulty to functional data. We define estimators, based on recursive algorithms, that can be simply updated at each new observation and are able to deal rapidly with large samples of high dimensional data without being obliged to store all the data in memory. Asymptotic convergence properties of the recursive algorithms are studied under weak conditions. The computation of the principal components can also be performed online and this approach can be useful for online outlier detection. A simulation study clearly shows that this robust indicat…
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
2014
Abstract Motivation: Protein–protein interaction (PPI) networks are powerful models to represent the pairwise protein interactions of the organisms. Clustering PPI networks can be useful for isolating groups of interacting proteins that participate in the same biological processes or that perform together specific biological functions. Evolutionary orthologies can be inferred this way, as well as functions and properties of yet uncharacterized proteins. Results: We present an overview of the main state-of-the-art clustering methods that have been applied to PPI networks over the past decade. We distinguish five specific categories of approaches, describe and compare their main features and …
Anthropometry: An R Package for Analysis of Anthropometric Data
2017
The development of powerful new 3D scanning techniques has enabled the generation of large up-to-date anthropometric databases which provide highly valued data to improve the ergonomic design of products adapted to the user population. As a consequence, Ergonomics and Anthropometry are two increasingly quantitative fields, so advanced statistical methodologies and modern software tools are required to get the maximum benefit from anthropometric data. This paper presents a new R package, called Anthropometry, which is available on the Comprehensive R Archive Network. It brings together some statistical methodologies concerning clustering, statistical shape analysis, statistical archetypal an…
Bayesian regularization for flexible baseline hazard functions in Cox survival models.
2019
Fully Bayesian methods for Cox models specify a model for the baseline hazard function. Parametric approaches generally provide monotone estimations. Semi-parametric choices allow for more flexible patterns but they can suffer from overfitting and instability. Regularization methods through prior distributions with correlated structures usually give reasonable answers to these types of situations. We discuss Bayesian regularization for Cox survival models defined via flexible baseline hazards specified by a mixture of piecewise constant functions and by a cubic B-spline function. For those "semi-parametric" proposals, different prior scenarios ranging from prior independence to particular c…
mRNAStab—a web application for mRNA stability analysis
2013
Abstract Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at h…
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
2014
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20 for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
FLP estimation of semi-parametric models for space-time point processes and diagnostic tools
2015
Abstract The conditional intensity function of a space–time branching model is defined by the sum of two main components: the long-run term intensity and short-run term one. Their simultaneous estimation is a complex issue that usually requires the use of hard computational techniques. This paper deals with a new mixed estimation approach for a particular space–time branching model, the Epidemic Type Aftershock Sequence model. This approach uses a simultaneous estimation of the different model components, alternating a parametric step for estimating the induced component by Maximum Likelihood and a non-parametric estimation step, for the background intensity, by FLP (Forward Predictive Like…