Statistical inference for homologous gene pairs between two circular genomes: a new circular–circular regression model

In this paper, we investigate the problem of determining the relationship, represented by similarity of the homologous gene configuration, between paired circular genomes using a regression analysis. We propose a new regression model for studying two circular genomes, where the Möbius transformation naturally arises and is taken as the link function, and propose the least circular distance estimation method, as an appropriate method for analyzing circular variables. The main utility of the new regression model is in identification of a new angular location of one of a homologous gene pair between two circular genomes, for various types of possible gene mutations, given that of the other gene. Furthermore, we demonstrate the utility of our new regression model for grouping of various genomes based on closeness of their relationship. Using angular locations of homologous genes from the five pairs of circular genomes (Horimoto et al. in Bioinformatics 14:789–802, 1998), the new model is compared with the existing models.     

Non-parametric regression on compositional covariates using Bayesian P-splines

Methods to perform regression on compositional covariates have recently been proposed using isometric log-ratios (ilr) representation of compositional parts. This approach consists of first applying standard regression on ilr coordinates and second, transforming the estimated ilr coefficients into their contrast log-ratio counterparts. This gives easy-to-interpret parameters indicating the relative effect of each compositional part. In this work we present an extension of this framework, where compositional covariate effects are allowed to be smooth in the ilr domain. This is achieved by fitting a smooth function over the multidimensional ilr space, using Bayesian P-splines. Smoothness is achieved by assuming random walk priors on spline coefficients in a hierarchical Bayesian framework. The proposed methodology is applied to spatial data from an ecological survey on a gypsum outcrop located in the Emilia Romagna Region, Italy.     

A flexible generalization of the skew normal distribution based on a weighted normal distribution

The skew normal distribution of Azzalini (Scand J Stat 12:171–178, 1985) has been found suitable for unimodal density but with some skewness present. Through this article, we introduce a flexible extension of the Azzalini (Scand J Stat 12:171–178, 1985) skew normal distribution based on a symmetric component normal distribution (Gui et al. in J Stat Theory Appl 12(1):55–66, 2013). The proposed model can efficiently capture the bimodality, skewness and kurtosis criteria and heavy-tail property. The paper presents various basic properties of this family of distributions and provides two stochastic representations which are useful for obtaining theoretical properties and to simulate from the distribution. Further, maximum likelihood estimation of the parameters is studied numerically by simulation and the distribution is investigated by carrying out comparative fitting of three real datasets.     

Calibration estimation in dual-frame surveys

Survey statisticians make use of auxiliary information to improve estimates. One important example is calibration estimation, which constructs new weights that match benchmark constraints on auxiliary variables while remaining “close” to the design weights. Multiple-frame surveys are increasingly used by statistical agencies and private organizations to reduce sampling costs and/or avoid frame undercoverage errors. Several ways of combining estimates derived from such frames have been proposed elsewhere; in this paper, we extend the calibration paradigm, previously used for single-frame surveys, to calculate the total value of a variable of interest in a dual-frame survey. Calibration is a general tool that allows to include auxiliary information from two frames. It also incorporates, as a special case, certain dual-frame estimators that have been proposed previously. The theoretical properties of our class of estimators are derived and discussed, and simulation studies conducted to compare the efficiency of the procedure, using different sets of auxiliary variables. Finally, the proposed methodology is applied to real data obtained from the Barometer of Culture of Andalusia survey.     

Maximal autocorrelation functions in functional data analysis

This paper proposes a new factor rotation for the context of functional principal components analysis. This rotation seeks to re-express a functional subspace in terms of directions of decreasing smoothness as represented by a generalized smoothing metric. The rotation can be implemented simply and we show on two examples that this rotation can improve the interpretability of the leading components.     

Finie mixures of canonical fundamenal skew $$$$-disribuions

This paper introduces a finite mixture of canonical fundamental skew \(t\) (CFUST) distributions for a model-based approach to clustering where the clusters are asymmetric and possibly long-tailed (in: Lee and McLachlan, arXiv:1401.8182 [statME], 2014b). The family of CFUST distributions includes the restricted multivariate skew \(t\) and unrestricted multivariate skew \(t\) distributions as special cases. In recent years, a few versions of the multivariate skew \(t\) (MST) mixture model have been put forward, together with various EM-type algorithms for parameter estimation. These formulations adopted either a restricted or unrestricted characterization for their MST densities. In this paper, we examine a natural generalization of these developments, employing the CFUST distribution as the parametric family for the component distributions, and point out that the restricted and unrestricted characterizations can be unified under this general formulation. We show that an exact implementation of the EM algorithm can be achieved for the CFUST distribution and mixtures of this distribution, and present some new analytical results for a conditional expectation involved in the E-step.     

New recursive estimators of the time-average variance constant

Estimation of the time-average variance constant (TAVC) of a stationary process plays a fundamental role in statistical inference for the mean of a stochastic process. Wu (2009) proposed an efficient algorithm to recursively compute the TAVC with \(O(1)\) memory and computational complexity. In this paper, we propose two new recursive TAVC estimators that can compute TAVC estimate with \(O(1)\) computational complexity. One of them is uniformly better than Wu’s estimator in terms of asymptotic mean squared error (MSE) at a cost of slightly higher memory complexity. The other preserves the \(O(1)\) memory complexity and is better then Wu’s estimator in most situations. Moreover, the first estimator is nearly optimal in the sense that its asymptotic MSE is \(2^{10/3}3^{-2} \fallingdotseq 1.12\) times that of the optimal off-line TAVC estimator.     

Approximate Bayesian computation with composite score functions

Both approximate Bayesian computation (ABC) and composite likelihood methods are useful for Bayesian and frequentist inference, respectively, when the likelihood function is intractable. We propose to use composite likelihood score functions as summary statistics in ABC in order to obtain accurate approximations to the posterior distribution. This is motivated by the use of the score function of the full likelihood, and extended to general unbiased estimating functions in complex models. Moreover, we show that if the composite score is suitably standardised, the resulting ABC procedure is invariant to reparameterisations and automatically adjusts the curvature of the composite likelihood, and of the corresponding posterior distribution. The method is illustrated through examples with simulated data, and an application to modelling of spatial extreme rainfall data is discussed.     

Computing the log concave NPMLE for interval censored data

In analyzing interval censored data, a non-parametric estimator is often desired due to difficulties in assessing model fits. Because of this, the non-parametric maximum likelihood estimator (NPMLE) is often the default estimator. However, the estimates for values of interest of the survival function, such as the quantiles, have very large standard errors due to the jagged form of the estimator. By forcing the estimator to be constrained to the class of log concave functions, the estimator is ensured to have a smooth survival estimate which has much better operating characteristics than the unconstrained NPMLE, without needing to specify a parametric family or smoothing parameter. In this paper, we first prove that the likelihood can be maximized under a finite set of parameters under mild conditions, although the log likelihood function is not strictly concave. We then present an efficient algorithm for computing a local maximum of the likelihood function. Using our fast new algorithm, we present evidence from simulated current status data suggesting that the rate of convergence of the log-concave estimator is faster (between \(n^{2/5}\) and \(n^{1/2}\)) than the unconstrained NPMLE (between \(n^{1/3}\) and \(n^{1/2}\)).