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390
Selecting the Number of Knots For Penalized Splines
, 2000
"... Penalized splines, or Psplines, are regression splines fit by leastsquares with a roughness penaly. Psplines have much in common with smoothing splines, but the type of penalty used with a Pspline is somewhat more general than for a smoothing spline. Also, the number and location of the knots ..."
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Cited by 101 (10 self)
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Penalized splines, or Psplines, are regression splines fit by leastsquares with a roughness penaly. Psplines have much in common with smoothing splines, but the type of penalty used with a Pspline is somewhat more general than for a smoothing spline. Also, the number and location of the knots of a Pspline is not fixed as with a smoothing spline. Generally, the knots of a Pspline are at fixed quantiles of the independent variable and the only tuning parameter to choose is the number of knots. In this article, the effects of the number of knots on the performance of Psplines are studied. Two algorithms are proposed for the automatic selection of the number of knots. The myoptic algorithm stops when no improvement in the generalized cross validation statistic (GCV) is noticed with the last increase in the number of knots. The full search examines all candidates in a fixed sequence of possible numbers of knots and chooses the candidate that minimizes GCV. The myoptic algo...
Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks
 In Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 03
, 2003
"... We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including proteinprotein interactions, proteinDNA interactions, binding site information, existing literature and so on. Unfortunately, m ..."
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Cited by 80 (6 self)
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We propose a statistical method for estimating a gene network based on Bayesian networks from microarray gene expression data together with biological knowledge including proteinprotein interactions, proteinDNA interactions, binding site information, existing literature and so on. Unfortunately, microarray data do not contain enough information for constructing gene networks accurately in many cases. Our method adds biological knowledge to the estimation method of gene networks under a Bayesian statistical framework, and also controls the tradeoff between microarray information and biological knowledge automatically. We conduct Monte Carlo simulations to show the effectiveness of the proposed method. We analyze Saccharomyces cerevisiae gene expression data as an application. 1.
Geoadditive Models
, 2000
"... this paper is a recent article on modelbased geostatistics by Diggle, Tawn and Moyeed (1998) where pure kriging (i.e. no covariates) is the focus. Our paper inherits some of its aspects: modelbased and with mixed model connections. In particular the comment by Bowman (1998) in the ensuing discussi ..."
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Cited by 79 (4 self)
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this paper is a recent article on modelbased geostatistics by Diggle, Tawn and Moyeed (1998) where pure kriging (i.e. no covariates) is the focus. Our paper inherits some of its aspects: modelbased and with mixed model connections. In particular the comment by Bowman (1998) in the ensuing discussion suggested that additive modelling would be a worthwhile extension. This paper essentially follows this suggestion. However, this paper is not the first to combine the notions of geostatistics and additive modelling. References known to us are Kelsall and Diggle (1998), Durban Reguera (1998) and Durban, Hackett, Currie and Newton (2000). Nevertheless, we believe that our approach has a number of attractive features (see (1)(4) above), not all shared by these references. Section 2 describes the motivating application and data in detail. Section 3 shows how one can express additive models as a mixed model, while Section 4 does the same for kriging and merges the two into the geoadditive model. Issues concerning the amount of smoothing are discussed in Section 5 and inferential aspects are treated in Section 6. Our analysis of the Upper Cape Cod reproductive data is presented in Section 7. Section 8 discusses extension to the generalised context.We close the paper with some disussion in Section 9. 2 Description of the application and data
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data
 Biosystems
, 2003
"... Abstract. We propose a dynamic Bayesian network and nonparametric regression model for constructing a gene network from time series microarray gene expression data. The proposed method can overcome a shortcoming of the Bayesian network model in the sense of the construction of cyclic regulations. Th ..."
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Cited by 78 (12 self)
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Abstract. We propose a dynamic Bayesian network and nonparametric regression model for constructing a gene network from time series microarray gene expression data. The proposed method can overcome a shortcoming of the Bayesian network model in the sense of the construction of cyclic regulations. The proposed method can analyze the microarray data as continuous data and can capture even nonlinear relations among genes. It can be expected that this model will give a deeper insight into the complicated biological systems. We also derive a new criterion for evaluating an estimated network from Bayes approach. We demonstrate the effectiveness of our method by analyzing Saccharomyces cerevisiae gene expression data. 1
Smoothing Splines Estimators in Functional Linear Regression with ErrorsinVariables
, 2006
"... This work deals with a generalization of the Total Least Squares method in the context of the functional linear model. We first propose a smoothing splines estimator of the functional coefficient of the model without noise in the covariates and we obtain an asymptotic result for this estimator. Then ..."
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Cited by 67 (3 self)
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This work deals with a generalization of the Total Least Squares method in the context of the functional linear model. We first propose a smoothing splines estimator of the functional coefficient of the model without noise in the covariates and we obtain an asymptotic result for this estimator. Then, we adapt this estimator to the case where the covariates are noisy and we also derive an upper bound for the convergence speed. Our estimation procedure is evaluated by means of simulations.
Statistical challenges with high dimensionality: feature selection in knowledge discovery
, 2006
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The Rhythmic Structure
, 1960
"... additive regression for spacetime data: A mixed model approach ..."
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Cited by 57 (1 self)
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additive regression for spacetime data: A mixed model approach
Spatiallyadaptive penalties for spline fitting
 Australian and New Zealand Journal of Statistics
, 2000
"... We study spline fitting with a roughness penalty that adapts to spatial heterogeneity in the regression function. Our estimates are pth degree piecewise polynomials with p − 1 continuous derivatives. A large and fixed number of knots is used and smoothing is achieved by putting a quadratic penalty ..."
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Cited by 52 (7 self)
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We study spline fitting with a roughness penalty that adapts to spatial heterogeneity in the regression function. Our estimates are pth degree piecewise polynomials with p − 1 continuous derivatives. A large and fixed number of knots is used and smoothing is achieved by putting a quadratic penalty on the jumps of the pth derivative at the knots. To be spatially adaptive, the logarithm of the penalty is itself a linear spline but with relatively few knots and with values at the knots chosen to minimize GCV. This locallyadaptive spline estimator is compared with other spline estimators in the literature such as cubic smoothing splines and knotselection techniques for leastsquares regression. Our estimator can be interpreted as an empirical Bayes estimate for a prior allowing spatial heterogeneity. In cases of spatially heterogeneous regression functions,
Bayesian analysis for penalized spline regression using WinBUGS
 J. Statist. Soft
, 2005
"... Penalized splines can be viewed as BLUPs in a mixed model framework, which allows the use of mixed model software for smoothing. Thus, software originally developed for Bayesian analysis of mixed models can be used for penalized spline regression. Bayesian inference for nonparametric models enjoys t ..."
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Cited by 52 (6 self)
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Penalized splines can be viewed as BLUPs in a mixed model framework, which allows the use of mixed model software for smoothing. Thus, software originally developed for Bayesian analysis of mixed models can be used for penalized spline regression. Bayesian inference for nonparametric models enjoys the flexibility of nonparametric models and the exact inference provided by the Bayesian inferential machinery. This paper provides a simple, yet comprehensive, set of programs for the implementation of nonparametric Bayesian analysis in WinBUGS. Good mixing properties of the MCMC chains are obtained by using lowrank thinplate splines, while simulation times per iteration are reduced employing WinBUGS specific computational tricks.