Statistics has moved beyond the frequentist-Bayesian controversies of the past. Where does this leave our ability to interpret results? I suggest that a philosophy compatible with statistical practice, labeled here statistical pragmatism, serves as a foundation for inference. Statistical pragmatism is inclusive and emphasizes the assumptions that connect statistical models with observed data. I argue that introductory courses often mischaracterize the process of statistical inference and I propose an alternative “big picture” depiction.

Using a time series model to mimic an observed time series has a long history. However, with regard to this objective, conventional estimation methods for discrete-time dynamical models are frequently found to be wanting. In fact, they are characteristically misguided in at least two respects: (i) assuming that there is a true model; (ii) evaluating the efficacy of the estimation as if the postulated model is true. There are numerous examples of models, when fitted by conventional methods, that fail to capture some of the most basic global features of the data, such as cycles with good matching periods, singularities of spectral density functions (especially at the origin) and others. We argue that the shortcomings need not always be due to the model formulation but the inadequacy of the conventional fitting methods. After all, all models are wrong, but some are useful if they are fitted properly. The practical issue becomes one of how to best fit the model to data.

Thus, in the absence of a true model, we prefer an alternative approach to conventional model fitting that typically involves one-step-ahead prediction errors. Our primary aim is to match the joint probability distribution of the observable time series, including long-term features of the dynamics that underpin the data, such as cycles, long memory and others, rather than short-term prediction. For want of a better name, we call this specific aim feature matching.

The challenges of model misspecification, measurement errors and the scarcity of data are forever present in real time series modeling. In this paper, by synthesizing earlier attempts into an extended-likelihood, we develop a systematic approach to empirical time series analysis to address these challenges and to aim at achieving better feature matching. Rigorous proofs are included but relegated to the Appendix. Numerical results, based on both simulations and real data, suggest that the proposed catch-all approach has several advantages over the conventional methods, especially when the time series is short or with strong cyclical fluctuations. We conclude with listing directions that require further development.

Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer a comprehensive survey of the population of genes (transcripts) in any sample of interest. This paper introduces a statistical model for estimating isoform abundance from RNA-Seq data and is flexible enough to accommodate both single end and paired end RNA-Seq data and sampling bias along the length of the transcript. Based on the derivation of minimal sufficient statistics for the model, a computationally feasible implementation of the maximum likelihood estimator of the model is provided. Further, it is shown that using paired end RNA-Seq provides more accurate isoform abundance estimates than single end sequencing at fixed sequencing depth. Simulation studies are also given.

A nonnegative martingale with initial value equal to one measures evidence against a probabilistic hypothesis. The inverse of its value at some stopping time can be interpreted as a Bayes factor. If we exaggerate the evidence by considering the largest value attained so far by such a martingale, the exaggeration will be limited, and there are systematic ways to eliminate it. The inverse of the exaggerated value at some stopping time can be interpreted as a p-value. We give a simple characterization of all increasing functions that eliminate the exaggeration.

We attempt to trace the history and development of Markov chain Monte Carlo (MCMC) from its early inception in the late 1940s through its use today. We see how the earlier stages of Monte Carlo (MC, not MCMC) research have led to the algorithms currently in use. More importantly, we see how the development of this methodology has not only changed our solutions to problems, but has changed the way we think about problems.

Identifying the risk factors for mental illnesses is of significant public health importance. Diagnosis, stigma associated with mental illnesses, comorbidity, and complex etiologies, among others, make it very challenging to study mental disorders. Genetic studies of mental illnesses date back at least a century ago, beginning with descriptive studies based on Mendelian laws of inheritance. A variety of study designs including twin studies, family studies, linkage analysis, and more recently, genomewide association studies have been employed to study the genetics of mental illnesses, or complex diseases in general. In this paper, I will present the challenges and methods from a statistical perspective and focus on genetic association studies.

This paper presents a unified treatment of Gaussian process models that extends to data from the exponential dispersion family and to survival data. Our specific interest is in the analysis of data sets with predictors that have an a priori unknown form of possibly nonlinear associations to the response. The modeling approach we describe incorporates Gaussian processes in a generalized linear model framework to obtain a class of nonparametric regression models where the covariance matrix depends on the predictors. We consider, in particular, continuous, categorical and count responses. We also look into models that account for survival outcomes. We explore alternative covariance formulations for the Gaussian process prior and demonstrate the flexibility of the construction. Next, we focus on the important problem of selecting variables from the set of possible predictors and describe a general framework that employs mixture priors. We compare alternative MCMC strategies for posterior inference and achieve a computationally efficient and practical approach. We demonstrate performances on simulated and benchmark data sets.