Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks

We present a procedure for effective estimation of entropy and mutual information from small-sample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically as well as computationally. Despite its simplicity, we show that it outperforms eight other entropy estimation procedures across a diverse range of sampling scenarios and data-generating models, even in cases of severe undersampling. We illustrate the approach by analyzing E. coli gene expression data and computing an entropy-based gene-association network from gene expression data. A computer program is available that implements the proposed shrinkage estimator.Comment: 18 pages, 3 figures, 1 tabl

Shrinkage Estimators in Online Experiments

We develop and analyze empirical Bayes Stein-type estimators for use in the estimation of causal effects in large-scale online experiments. While online experiments are generally thought to be distinguished by their large sample size, we focus on the multiplicity of treatment groups. The typical analysis practice is to use simple differences-in-means (perhaps with covariate adjustment) as if all treatment arms were independent. In this work we develop consistent, small bias, shrinkage estimators for this setting. In addition to achieving lower mean squared error these estimators retain important frequentist properties such as coverage under most reasonable scenarios. Modern sequential methods of experimentation and optimization such as multi-armed bandit optimization (where treatment allocations adapt over time to prior responses) benefit from the use of our shrinkage estimators. Exploration under empirical Bayes focuses more efficiently on near-optimal arms, improving the resulting decisions made under uncertainty. We demonstrate these properties by examining seventeen large-scale experiments conducted on Facebook from April to June 2017

Shrinkage Confidence Procedures

The possibility of improving on the usual multivariate normal confidence was first discussed in Stein (1962). Using the ideas of shrinkage, through Bayesian and empirical Bayesian arguments, domination results, both analytic and numerical, have been obtained. Here we trace some of the developments in confidence set estimation.Comment: Published in at http://dx.doi.org/10.1214/10-STS319 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

In-season prediction of batting averages: A field test of empirical Bayes and Bayes methodologies

Batting average is one of the principle performance measures for an individual baseball player. It is natural to statistically model this as a binomial-variable proportion, with a given (observed) number of qualifying attempts (called ``at-bats''), an observed number of successes (``hits'') distributed according to the binomial distribution, and with a true (but unknown) value of $p_i$ that represents the player's latent ability. This is a common data structure in many statistical applications; and so the methodological study here has implications for such a range of applications. We look at batting records for each Major League player over the course of a single season (2005). The primary focus is on using only the batting records from an earlier part of the season (e.g., the first 3 months) in order to estimate the batter's latent ability, $p_i$, and consequently, also to predict their batting-average performance for the remainder of the season. Since we are using a season that has already concluded, we can then validate our estimation performance by comparing the estimated values to the actual values for the remainder of the season. The prediction methods to be investigated are motivated from empirical Bayes and hierarchical Bayes interpretations. A newly proposed nonparametric empirical Bayes procedure performs particularly well in the basic analysis of the full data set, though less well with analyses involving more homogeneous subsets of the data. In those more homogeneous situations better performance is obtained from appropriate versions of more familiar methods. In all situations the poorest performing choice is the na\"{{\i}}ve predictor which directly uses the current average to predict the future average.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS138 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Small Area Shrinkage Estimation

The need for small area estimates is increasingly felt in both the public and private sectors in order to formulate their strategic plans. It is now widely recognized that direct small area survey estimates are highly unreliable owing to large standard errors and coefficients of variation. The reason behind this is that a survey is usually designed to achieve a specified level of accuracy at a higher level of geography than that of small areas. Lack of additional resources makes it almost imperative to use the same data to produce small area estimates. For example, if a survey is designed to estimate per capita income for a state, the same survey data need to be used to produce similar estimates for counties, subcounties and census divisions within that state. Thus, by necessity, small area estimation needs explicit, or at least implicit, use of models to link these areas. Improved small area estimates are found by "borrowing strength" from similar neighboring areas.Comment: Published in at http://dx.doi.org/10.1214/11-STS374 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Blind Minimax Estimation

We consider the linear regression problem of estimating an unknown, deterministic parameter vector based on measurements corrupted by colored Gaussian noise. We present and analyze blind minimax estimators (BMEs), which consist of a bounded parameter set minimax estimator, whose parameter set is itself estimated from measurements. Thus, one does not require any prior assumption or knowledge, and the proposed estimator can be applied to any linear regression problem. We demonstrate analytically that the BMEs strictly dominate the least-squares estimator, i.e., they achieve lower mean-squared error for any value of the parameter vector. Both Stein's estimator and its positive-part correction can be derived within the blind minimax framework. Furthermore, our approach can be readily extended to a wider class of estimation problems than Stein's estimator, which is defined only for white noise and non-transformed measurements. We show through simulations that the BMEs generally outperform previous extensions of Stein's technique.Comment: 12 pages, 7 figure