Search results for "Computation"
showing 10 items of 7362 documents
Establishing some order amongst exact approximations of MCMCs
2016
Exact approximations of Markov chain Monte Carlo (MCMC) algorithms are a general emerging class of sampling algorithms. One of the main ideas behind exact approximations consists of replacing intractable quantities required to run standard MCMC algorithms, such as the target probability density in a Metropolis-Hastings algorithm, with estimators. Perhaps surprisingly, such approximations lead to powerful algorithms which are exact in the sense that they are guaranteed to have correct limiting distributions. In this paper we discover a general framework which allows one to compare, or order, performance measures of two implementations of such algorithms. In particular, we establish an order …
The conditional censored graphical lasso estimator
2020
© 2020, Springer Science+Business Media, LLC, part of Springer Nature. In many applied fields, such as genomics, different types of data are collected on the same system, and it is not uncommon that some of these datasets are subject to censoring as a result of the measurement technologies used, such as data generated by polymerase chain reactions and flow cytometer. When the overall objective is that of network inference, at possibly different levels of a system, information coming from different sources and/or different steps of the analysis can be integrated into one model with the use of conditional graphical models. In this paper, we develop a doubly penalized inferential procedure for…
Adaptive reference-free compression of sequence quality scores
2014
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…
Latin hypercube sampling with inequality constraints
2010
International audience; In some studies requiring predictive and CPU-time consuming numerical models, the sampling design of the model input variables has to be chosen with caution. For this purpose, Latin hypercube sampling has a long history and has shown its robustness capabilities. In this paper we propose and discuss a new algorithm to build a Latin hypercube sample (LHS) taking into account inequality constraints between the sampled variables. This technique, called constrained Latin hypercube sampling (cLHS), consists in doing permutations on an initial LHS to honor the desired monotonic constraints. The relevance of this approach is shown on a real example concerning the numerical w…
Reassessing Accuracy Rates of Median Decisions
2007
We show how Bruno de Finetti''s fundamental theorem of prevision has computable applications in statistical problems that involve only partial information. Specifically, we assess accuracy rates for median decision procedures used in the radiological diagnosis of asbestosis. Conditional exchangeability of individual radiologists'' diagnoses is recognized as more appropriate than independence which is commonly presumed. The FTP yields coherent bounds on probabilities of interest when available information is insufficient to determine a complete distribution. Further assertions that are natural to the problem motivate a partial ordering of conditional probabilities, extending the computation …
Can the Adaptive Metropolis Algorithm Collapse Without the Covariance Lower Bound?
2011
The Adaptive Metropolis (AM) algorithm is based on the symmetric random-walk Metropolis algorithm. The proposal distribution has the following time-dependent covariance matrix at step $n+1$ \[ S_n = Cov(X_1,...,X_n) + \epsilon I, \] that is, the sample covariance matrix of the history of the chain plus a (small) constant $\epsilon>0$ multiple of the identity matrix $I$. The lower bound on the eigenvalues of $S_n$ induced by the factor $\epsilon I$ is theoretically convenient, but practically cumbersome, as a good value for the parameter $\epsilon$ may not always be easy to choose. This article considers variants of the AM algorithm that do not explicitly bound the eigenvalues of $S_n$ away …
Importance sampling correction versus standard averages of reversible MCMCs in terms of the asymptotic variance
2017
We establish an ordering criterion for the asymptotic variances of two consistent Markov chain Monte Carlo (MCMC) estimators: an importance sampling (IS) estimator, based on an approximate reversible chain and subsequent IS weighting, and a standard MCMC estimator, based on an exact reversible chain. Essentially, we relax the criterion of the Peskun type covariance ordering by considering two different invariant probabilities, and obtain, in place of a strict ordering of asymptotic variances, a bound of the asymptotic variance of IS by that of the direct MCMC. Simple examples show that IS can have arbitrarily better or worse asymptotic variance than Metropolis-Hastings and delayed-acceptanc…
The Heisenberg picture in the analysis of stock markets and in other sociological contexts
2007
We review some recent results concerning some toy models of stock markets. Our models are suggested by the discrete nature of the number of shares and of the cash which are exchanged in a real market, and by the existence of conserved quantities, like the total number of shares or some linear combination of the cash and the shares. This suggests to use the same tools used in quantum mechanics and, in particular, the Heisenberg picture to describe the time behavior of the portfolio of each trader. We finally propose the use of this same framework in other sociological contexts.
Assessing uncertainty of voter transitions estimated from aggregated data. Application to the 2017 French presidential election
2020
[EN] Inferring electoral individual behaviour from aggregated data is a very active research area, with ramifications in sociology and political science. A new approach based on linear programming is proposed to estimate voter transitions among parties (or candidates) between two elections. Compared to other linear and quadratic programming models previously published, our approach presents two important innovations. Firstly, it explicitly deals with new entries and exits in the election census without assuming unrealistic hypotheses, enabling a reasonable estimation of vote behaviour of young electors voting for the first time. Secondly, by exploiting the information contained in the model…
Fitting generalized linear models with unspecified link function: A P-spline approach
2008
Generalized linear models (GLMs) outline a wide class of regression models where the effect of the explanatory variables on the mean of the response variable is modelled throughout the link function. The choice of the link function is typically overlooked in applications and the canonical link is commonly used. The estimation of GLMs with unspecified link function is discussed, where the linearity assumption between the link and the linear predictor is relaxed and the unspecified relationship is modelled flexibly by means of P-splines. An estimating algorithm is presented, alternating estimation of two working GLMs up to convergence. The method is applied to the analysis of quit behavior of…