Efficient transfer entropy analysis of non-stationary neural time series

Information theory allows us to investigate information processing in neural systems in terms of information transfer, storage and modification. Especially the measure of information transfer, transfer entropy, has seen a dramatic surge of interest in neuroscience. Estimating transfer entropy from two processes requires the observation of multiple realizations of these processes to estimate associated probability density functions. To obtain these observations, available estimators assume stationarity of processes to allow pooling of observations over time. This assumption however, is a major obstacle to the application of these estimators in neuroscience as observed processes are often non-stationary. As a solution, Gomez-Herrero and colleagues theoretically showed that the stationarity assumption may be avoided by estimating transfer entropy from an ensemble of realizations. Such an ensemble is often readily available in neuroscience experiments in the form of experimental trials. Thus, in this work we combine the ensemble method with a recently proposed transfer entropy estimator to make transfer entropy estimation applicable to non-stationary time series. We present an efficient implementation of the approach that deals with the increased computational demand of the ensemble method's practical application. In particular, we use a massively parallel implementation for a graphics processing unit to handle the computationally most heavy aspects of the ensemble method. We test the performance and robustness of our implementation on data from simulated stochastic processes and demonstrate the method's applicability to magnetoencephalographic data. While we mainly evaluate the proposed method for neuroscientific data, we expect it to be applicable in a variety of fields that are concerned with the analysis of information transfer in complex biological, social, and artificial systems.Comment: 27 pages, 7 figures, submitted to PLOS ON

Wavelet Estimators in Nonparametric Regression: A Comparative Simulation Study

Wavelet analysis has been found to be a powerful tool for the nonparametric estimation of spatially-variable objects. We discuss in detail wavelet methods in nonparametric regression, where the data are modelled as observations of a signal contaminated with additive Gaussian noise, and provide an extensive review of the vast literature of wavelet shrinkage and wavelet thresholding estimators developed to denoise such data. These estimators arise from a wide range of classical and empirical Bayes methods treating either individual or blocks of wavelet coefficients. We compare various estimators in an extensive simulation study on a variety of sample sizes, test functions, signal-to-noise ratios and wavelet filters. Because there is no single criterion that can adequately summarise the behaviour of an estimator, we use various criteria to measure performance in finite sample situations. Insight into the performance of these estimators is obtained from graphical outputs and numerical tables. In order to provide some hints of how these estimators should be used to analyse real data sets, a detailed practical step-by-step illustration of a wavelet denoising analysis on electrical consumption is provided. Matlab codes are provided so that all figures and tables in this paper can be reproduced

Decision support for build-to-order supply chain management through multiobjective optimization

This paper aims to identify the gaps in decision-making support based on multiobjective optimization for build-to-order supply chain management (BTOSCM). To this end, it reviews the literature available on modelling build-to-order supply chains (BTO-SC) with the focus on adopting multiobjective optimization (MOO) techniques as a decision support tool. The literature has been classified based on the nature of the decisions in different part of the supply chain, and the key decision areas across a typical BTO-SC are discussed in detail. Available software packages suitable for supporting decision making in BTO supply chains are also identified and their related solutions are outlined. The gap between the modelling and optimization techniques developed in the literature and the decision support needed in practice are highlighted and future research directions to better exploit the decision support capabilities of MOO are proposed

A Random Force is a Force, of Course, of Coarse: Decomposing Complex Enzyme Kinetics with Surrogate Models

The temporal autocorrelation (AC) function associated with monitoring order parameters characterizing conformational fluctuations of an enzyme is analyzed using a collection of surrogate models. The surrogates considered are phenomenological stochastic differential equation (SDE) models. It is demonstrated how an ensemble of such surrogate models, each surrogate being calibrated from a single trajectory, indirectly contains information about unresolved conformational degrees of freedom. This ensemble can be used to construct complex temporal ACs associated with a "non-Markovian" process. The ensemble of surrogates approach allows researchers to consider models more flexible than a mixture of exponentials to describe relaxation times and at the same time gain physical information about the system. The relevance of this type of analysis to matching single-molecule experiments to computer simulations and how more complex stochastic processes can emerge from a mixture of simpler processes is also discussed. The ideas are illustrated on a toy SDE model and on molecular dynamics simulations of the enzyme dihydrofolate reductase.Comment: 11 pages / 6 figure

Decision support for build-to-order supply chain management through multiobjective optimization

This is the post-print version of the final paper published in International Journal of Production Economics. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2010 Elsevier B.V.This paper aims to identify the gaps in decision-making support based on multiobjective optimization (MOO) for build-to-order supply chain management (BTO-SCM). To this end, it reviews the literature available on modelling build-to-order supply chains (BTO-SC) with the focus on adopting MOO techniques as a decision support tool. The literature has been classified based on the nature of the decisions in different part of the supply chain, and the key decision areas across a typical BTO-SC are discussed in detail. Available software packages suitable for supporting decision making in BTO supply chains are also identified and their related solutions are outlined. The gap between the modelling and optimization techniques developed in the literature and the decision support needed in practice are highlighted. Future research directions to better exploit the decision support capabilities of MOO are proposed. These include: reformulation of the extant optimization models with a MOO perspective, development of decision supports for interfaces not involving manufacturers, development of scenarios around service-based objectives, development of efficient solution tools, considering the interests of each supply chain party as a separate objective to account for fair treatment of their requirements, and applying the existing methodologies on real-life data sets.Brunel Research Initiative and Enterprise Fund (BRIEF

CARBayes: an R package for Bayesian spatial modeling with conditional autoregressive priors

Conditional autoregressive models are commonly used to represent spatial autocorrelation in data relating to a set of non-overlapping areal units, which arise in a wide variety of applications including agriculture, education, epidemiology and image analysis. Such models are typically specified in a hierarchical Bayesian framework, with inference based on Markov chain Monte Carlo (MCMC) simulation. The most widely used software to fit such models is WinBUGS or OpenBUGS, but in this paper we introduce the R package CARBayes. The main advantage of CARBayes compared with the BUGS software is its ease of use, because: (1) the spatial adjacency information is easy to specify as a binary neighbourhood matrix; and (2) given the neighbourhood matrix the models can be implemented by a single function call in R. This paper outlines the general class of Bayesian hierarchical models that can be implemented in the CARBayes software, describes their implementation via MCMC simulation techniques, and illustrates their use with two worked examples in the fields of house price analysis and disease mapping

On the use of Structural Equation Models and PLS Path Modeling to build composite indicators

Nowadays there is a pre-eminent need to measure very complex phenomena like poverty, progress, well-being, etc. As is well known, the main feature of a composite indicator is that it summarizes complex and multidimensional issues. Thanks to its features, Structural Equation Modeling seems to be a useful tool for building systems of composite indicators. Among the several methods that have been developed to estimate Structural Equation Models we focus on the PLS Path Modeling approach (PLS-PM), because of the key role that estimation of the latent variables (i.e. the composite indicators) plays in the estimation process. In this work, first we present Structural Equation Models and PLS-PM. Then we provide a suite of statistical methodologies for handling categorical indicators in PLS-PM. In particular, in order to take categorical indicators into account, we propose to use a modified version of the PLS-PM algorithm recently presented by Russolillo [2009]. This new approach provides a quantification of the categorical indicators in such a way that the weight of each quantified indicator is coherent with the explicative ability of the corresponding categorical indicator. To conclude, an application involving data taken from a paper by Russet [1964] will be presented.PLS Path Modeling,Categorical Indicators,Structural Equation Modeling,Composite Indicators

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1