Search results for "Programming"

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…

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 …

A multi-local optimization algorithm

1998

The development of efficient algorithms that provide all the local minima of a function is crucial to solve certain subproblems in many optimization methods. A “multi-local” optimization procedure using inexact line searches is presented, and numerical experiments are also reported. An application of the method to a semi-infinite programming procedure is included.

Spatio-temporal modelling of COVID-19 incident cases using Richards’ curve: An application to the Italian regions

2021

Abstract We introduce an extended generalised logistic growth model for discrete outcomes, in which spatial and temporal dependence are dealt with the specification of a network structure within an Auto-Regressive approach. A major challenge concerns the specification of the network structure, crucial to consistently estimate the canonical parameters of the generalised logistic curve, e.g. peak time and height. We compared a network based on geographic proximity and one built on historical data of transport exchanges between regions. Parameters are estimated under the Bayesian framework, using Stan probabilistic programming language. The proposed approach is motivated by the analysis of bot…

Functional Data Analysis with R and Matlab by RAMSAY, J. O., HOOKER, G., and GRAVES, S.

2010

Cotas inferiores para el QAP-Arbol

1985

The Tree-QAP is a special case of the Quadratic Assignment Problem where the flows not equal zero form a tree. No condition is required for the distance matrix. In this paper we present an integer programming formulation for the Tree-QAP. We use this formulation to construct four Lagrangean relaxations that produce several lower bounds for this problem. To solve one of the relaxed problems we present a Dynamic Programming algorithm which is a generalization of the algorithm of this type that gives a lower bound for the Travelling Salesman Problem. A comparison is given between the lower bounds obtained by each ralaxation for examples with size from 12 to 25.

Mixed Non-Parametric and Parametric Estimation Techniques in R Package etasFLP for Earthquakes’ Description

2017

etasFLP is an R package which fits an epidemic type aftershock sequence (ETAS) model to an earthquake catalog; non-parametric background seismicity can be estimated through a forward predictive likelihood approach, while parametric components of triggered seismicity are estimated through maximum likelihood; estimation steps are alternated until convergence is obtained and for each event the probability of being a background event is estimated. The package includes options which allow its wide use. Methods for plot, summary and profile are defined for the main output class object. The paper provides examples of the package's use with description of the underlying R and Fortran routines.

Combining the intensity and sequencing of the poverty experience:a class of longitudinal poverty indices

2011

Summary Traditional measures of the persistence of poverty do not devote enough attention to the sequence of spells of poverty. We propose a new class of indices which measures the severity of chronic poverty, taking into account the way in which spells of poverty and non-poverty follow one another along individual life courses. All the years spent in poverty concur with the measurement of the persistency of poverty, albeit with a decreasing contribution provided that the distance between two consecutive spells of poverty becomes longer. Moreover, the distance from the poverty line and the poverty persistence probabilities are explicitly taken into account. A macrolevel index, which allows …

Bayesian joint ordinal and survival modeling for breast cancer risk assessment

2016

We propose a joint model to analyze the structure and intensity of the association between longitudinal measurements of an ordinal marker and time to a relevant event. The longitudinal process is defined in terms of a proportional-odds cumulative logit model. Time-to-event is modeled through a left-truncated proportionalhazards model, which incorporates information of the longitudinal marker as well as baseline covariates. Both longitudinal and survival processes are connected by means of a common vector of random effects. General inferences are discussed under the Bayesian approach and include the posterior distribution of the probabilities associated to each longitudinal category and the …

Introducing libeemd: a program package for performing the ensemble empirical mode decomposition

2016

The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the deco…