Search results for "Interaction"
showing 10 items of 5710 documents
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 …
The affine equivariant sign covariance matrix: asymptotic behavior and efficiencies
2003
We consider the affine equivariant sign covariance matrix (SCM) introduced by Visuri et al. (J. Statist. Plann. Inference 91 (2000) 557). The population SCM is shown to be proportional to the inverse of the regular covariance matrix. The eigenvectors and standardized eigenvalues of the covariance, matrix can thus be derived from the SCM. We also construct an estimate of the covariance and correlation matrix based on the SCM. The influence functions and limiting distributions of the SCM and its eigenvectors and eigenvalues are found. Limiting efficiencies are given in multivariate normal and t-distribution cases. The estimates are highly efficient in the multivariate normal case and perform …
Bivariate Distributed Lag Models for the analysis of temperature-by-pollutant interaction effect on mortality.
2007
This paper introduces Bivariate Distributed Lags Models (BDLMs) to investigate synergic effect of temperature and airborne particles on mortality. These models seem particulary attractive since they allow to model interactions between such environmental variables accounting for possible delayed effects. A B-spline framework is used to approximate the coefficient surface of the temperature-by-pollutant interaction and possible alternatives are also discussed. A case study of mortality time-series data in Palermo, Italy, is presented to illustrate the model. Copyright © 2007 John Wiley & Sons, Ltd.
Using R via PHP for Teaching Purposes: R-php
2006
This paper deals with the R-php statistical software, that is an environment for statistical analysis, freely accessible and attainable through the World Wide Web, based on R. Indeed, this software uses, as "engine" for statistical analyses, R via PHP and its design has been inspired by a paper of de Leeuw (1997). R-php is based on two modules: a base module and a point-and-click module. R-php base allows the simple editing of R code in a form. R-php point-and-click allows some statistical analyses by means of a graphical user interface (GUI): then, to use this module it is not necessary for the user to know the R environment, but all the allowed analyses can be performed by using the compu…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
Fully Bayesian Approach to Image Restoration with an Application in Biogeography
1994
SUMMARY A common method of studying biogeographical ranges is an atlas survey, in which the research area is divided into a square grid and the data consist of the squares where observations occur. Often the observations form only an incomplete map of the true range, and a method is required to decide whether the blank squares indicate true absence or merely a lack of study there. This is essentially an image restoration problem, but it has properties that make the common empirical Bayesian procedures inadequate. Most notably, the observed image is heavily degraded, causing difficulties in the estimation of spatial interaction, and the assessment of reliability of the restoration is emphasi…
Basic networks: Definition and applications
2009
7 pages, 4 figures, 1 table.-- PMID: 19490867 [PubMed]
Graphical User Interfaces for R
2012
Since R was first launched, it has managed to gain the support of an ever-increasing percentage of academic and professional statisticians. However, the spread of its use among novice and occasional users of statistics have not progressed at the same pace, which can be attributed partially to the lack of a graphical user interface (GUI). Nevertheless, this situation has changed in the last years and there is currently several projects that have added GUIs to R. This article discusses briefly the history of GUIs for data analysis and then introduces the papers submitted to an special issue of the Journal of Statistical Software on GUIs for R.
Newton algorithm for Hamiltonian characterization in quantum control
2014
We propose a Newton algorithm to characterize the Hamiltonian of a quantum system interacting with a given laser field. The algorithm is based on the assumption that the evolution operator of the system is perfectly known at a fixed time. The computational scheme uses the Crank-Nicholson approximation to explicitly determine the derivatives of the propagator with respect to the Hamiltonians of the system. In order to globalize this algorithm, we use a continuation method that improves its convergence properties. This technique is applied to a two-level quantum system and to a molecular one with a double-well potential. The numerical tests show that accurate estimates of the unknown paramete…
Gaia DR2 reveals a star formation burst in the disc 2-3 Gyr ago
2019
We use Gaia DR2 magnitudes, colours and parallaxes for stars with G<12 to explore a 15-dimensional space that includes simultaneously the initial mass function (IMF) and a non-parametric star formation history (SFH) for the Galactic disc. This inference is performed by combining the Besancon Galaxy Model fast approximate simulations (BGM FASt) and an approximate Bayesian computation algorithm. We find in Gaia DR2 data an imprint of a star formation burst 2-3 Gyr ago, in the Galactic thin disc domain, and a present star formation rate (SFR) of about 1 Msun. Our results show a decreasing trend of the SFR from 9-10 Gyr to 6-7 Gyr ago. This is consistent with the cosmological star formation …