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Parametric Empirical Bayes Inference: Theory and Applications
Abstract
This article reviews the state of multiparameter shrinkage estimators with emphasis on the empirical Bayes viewpoint, particularly in the case of parametric prior distributions. Some successful applications of major importance are considered. Recent results concerning estimates of error and confidence intervals are described and illustrated with data.
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“The highly parallel nature of gene expression experiments lends itself to a particular class of statistical methods, called parametric empirical Bayes, that borrow information between genes in a dynamic way (14,15).”
From limma powers differential expression analyses for RNA-sequencing and microarray studies (2015) · cites this paper as [15]
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Empirical Bayes Methods for Smoothing Data and for Simultaneous Estimation of Many Parameters
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“Hence, rather than fixing their values, we treat them as unknown and estimate them from the data using a quasi-empirical Bayes approach [25], [26].”
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Lockwood, J. R., Castellano, K. E., & Shear, B. R. (2018) · Journal of Educational and Behavioral Statistics · doi:10.3102/1076998618795124 · Cited by 7
“…a specification for Fð ; Þ, there are two common estimation approaches for models such as the FH-HETOP model: an empirical Bayesian approach (Carlin & Louis, 2000; Casella, 1985; Efron & Morris, 1973; Morris, 1983), and a fully Bayesian approach (see, e.g., Gelman, Carlin, Stern, & Rubin, 1995).”
MethodmetaCOVID : A web‐application for living meta‐analyses of COVID ‐19 trials
Evrenoglou, T., Boutron, I., Seitidis, G., Ghosn, L., & Chaimani, A. (2023) · Research Synthesis Methods · doi:10.1002/jrsm.1627 · Cited by 9
“Therefore, within metaCOVID we provide as an option alternative estimators: the DerSimonian – Laird estimator, 15 the Paul – Mandel estimator, 16 the Sidik-Jonkman estimator, 17 the estimator that is based on empirical Bayes inference, 18 and finally the maximum likelihood estimator.”
MethodInferences About the Between‐Study Variance in Meta‐Analysis with Normally Distributed Outcomes
Tian, L. (2008) · Biometrical Journal · doi:10.1002/bimj.200710408 · Cited by 7
Gini’s criticisms to the theory of inference: a missed opportunity
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Shrinkage Estimators Applied to Prediction of French Winter Wheat Yield
Hébel, P., Faivre, R., Goffinet, B., & Wallach, D. (1993) · Biometrics · doi:10.2307/2532623 · Cited by 7
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“The plug-in estimators can be regarded as maximum likelihood estimators in multiple stage approaches and somewhat akin to empirical Bayes methods, thus relying on implicit assumptions of exchangeability of the observations, which may not be always justified in practice and can introduce bias in the estimation of poste…”
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Parametric Empirical Bayes Tolerance Intervals
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Empirical Bayes regionalization methods for spatial stochastic processes
Butcher, J., Medina, M. Á., & Marín, C. M. (1991) · Water Resources Research · doi:10.1029/90wr01879 · Cited by 7
The superiority of empirical Bayes estimator of parameters in linear model
Zhang, W., Wei, L., & Yang, Y. (2005) · Statistics & Probability Letters · doi:10.1016/j.spl.2004.12.001 · Cited by 7
Intent to treat: TheReductio ad absurdumthat became gospel
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Frequentist inference on random effects based on summarizability
Paik, M. C., Lee, Y., & Ha, I. D. (2014) · Statistica Sinica · doi:10.5705/ss.2013.137 · Cited by 7
“In the empirical Bayesian approach, the empirical posterior distribution is used to predict random effects via posterior mean or mode evaluated at an estimated fixed parameter (e.g., Morris (1983); Maritz and Lwin (1989)).”
MethodBraun, H. I., & Zwick, R. (1993) · Journal of Educational Statistics · doi:10.3102/10769986018004285 · Cited by 7
Estimation in an empirical bayes model for longitudinal and cross‐sectionally clustered binary data
Sashegyi, A. I., Brown, K. S., & Farrell, P. J. (2000) · Canadian Journal of Statistics · doi:10.2307/3314762 · Cited by 7
“Parameter estimation in mixed eects models can be accomplished by empirical Bayes methods, wherein a prior distribution for the random eects is specied and the posterior distribution of the parameters and random eects is maximized, conditional on an estimate of the random eects variance; cf. Morris (1983) .”
MethodEstimation in the generalized linear empirical bayes model using the extended quasi-likelihood
Lu, W.-S., & Morris, C. (1994) · Communication in Statistics- Theory and Methods · doi:10.1080/03610929408831279 · Cited by 9
Analysis of a random sample of 2-year carcinogen bioassays from the NCI data base*1
Louis, T. A. (1989) · Fundamental and Applied Toxicology · doi:10.1016/0272-0590(89)90039-0 · Cited by 7
Strengthened estimates of individual pain trends in children following bone marrow transplantation
Donaldson, G. W., & Moinpour, C. M. (1992) · Pain · doi:10.1016/0304-3959(92)90050-l · Cited by 7
“The strengthened estimate we develop below has been shown to have just this property (James and Stein 1961; Efron and Morris 1973; Morris 1983).”
BackgroundMethodInfluentialAssessing Psychiatric Morbidity from Community Registers: Methods for Bayesian Adjustment
Congdon, P. D., Smith, A., & Dean, C. (1998) · Urban Studies · doi:10.1080/0042098983908 · Cited by 7
Learning About and From Variation in Program Impacts Using Multisite TrialsPreprint
Raudenbush, S. W., & Bloom, H. S. (2015) · SSRN Electronic Journal · doi:10.2139/ssrn.2609419 · Cited by 7
“There is considerable reason to believe that these empirical Bayes “shrinkage estimators” will, on average, better predict true site-specific impacts under crossvalidation (see Morris, 1983, for a review).”
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Potamites, L., Booker, K., Chaplin, D., & Isenberg, E. (2009) · RePEc: Research Papers in Economics · Cited by 7
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Gaver, D. P. (1985) · Defense Technical Information Center (DTIC) · Cited by 7
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Bertoni, E., Elacqua, G., Vargas, C. M., & Santos, H. (2023) · Educational Evaluation and Policy Analysis · doi:10.3102/01623737221149417 · Cited by 6
“Then, to estimate the EB value-added measure, we use a routine produced by Mathematica Policy Research, based on Morris (1983) and described in Herrmann et al. (2016).”
MethodSuperiority of empirical Bayes estimator of the mean vector in multivariate normal distribution
Yuan, M., Wan, C., & Wei, L. (2016) · Science China Mathematics · doi:10.1007/s11425-015-5098-x · Cited by 6
Adall, S. W., & Xu, J. (2021) · Pharmaceutical Statistics · doi:10.1002/pst.2126 · Cited by 6
“Based on the proposed empirical Bayes shrinkage estimator, the left hand side of (18) is approximated by”
MethodHermann, Z., Péntek, M., Gulàcsi, L., Németh, I. A. K., & Zrubka, Z. (2022) · The European Journal of Health Economics · doi:10.1007/s10198-021-01424-8 · Cited by 6
“To reduce the mean square error of prediction, the empirical Bayes or shrinkage approach optimally balances the measurement error of direct estimates of CAj from the JE response set of each respondent and model error of parametric estimates of CAj from the combined JE response of all respondents [28, 29].”
MethodAdjusting for treatment selection in phase II/III clinical trials with time to event data
Khan, J. N., Kimani, P., Glimm, E., & Stallard, N. (2022) · Statistics in Medicine · doi:10.1002/sim.9606 · Cited by 6
Tatas, Z., Koutsiouroumpa, O., Seehra, J., Mavridis, D., & Pandis, N. (2023) · European Journal of Orthodontics · doi:10.1093/ejo/cjad031 · Cited by 6
Professional Motivations in the Public Sector: Evidence from Police Officers
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Improved Estimation for Multiple Means with Heterogeneous Variances
Green, E. J., Strawderman, W. E., Amateis, R. L., & Reams, G. A. (2005) · Forest Science · doi:10.1093/forestscience/51.1.1 · Cited by 6
Posterior Propriety for Hierarchical Models with Log-Likelihoods That Have Norm Bounds
Michalak, S., & Morris, C. N. (2015) · Bayesian Analysis · doi:10.1214/15-ba962 · Cited by 6
“…models for Normal data and computing Bayesian 95% credible intervals for this prior thus far has produced confidence intervals that usually exceed and at worst nearly meet their nominal 95% rates, e.g., Morris (1983b), Everson and Morris (2000), Morris and Tang (2011), and Morris and Lysy (2012).”
BackgroundResultWang, X., Duverger, P., & Bansal, H. S. (2013) · International Journal of Pure and Apllied Mathematics · doi:10.12732/ijpam.v88i3.1 · Cited by 6
“On the theoretical side, hierarchical models allow a more objective approach to inference by estimating the parameters of prior distributions from data, rather than requiring them to be specified using subjective information (see James and Stein, 1960, Efron and Morris, 1975, and Morris, 1983).”
MethodBeta-binomial ANOVA for multivariate randomized response data.
Fox, J. (2008) · British Journal of Mathematical & Statistical Psychology · doi:10.1348/000711007x226040 · Cited by 5
Asymptotic optimality of hierarchical Bayes estimators and predictors
Datta, G. S., & Glosh, M. (1991) · Journal of Statistical Planning and Inference · doi:10.1016/0378-3758(91)90001-u · Cited by 6
Ghosh, M., & Maiti, T. (2008) · Scandinavian Journal of Statistics · doi:10.1111/j.1467-9469.2008.00597.x · Cited by 6
“The objective of this paper is to provide some simple EB confidence intervals for means of the natural exponential family-quadratic variance function (NEF-QVF) distributions as introduced by Morris (1982, 1983a).”
MethodAn empirical Bayes procedure for the selection of Gaussian graphical models
Donnet, S., & Marin, J. (2011) · Statistics and Computing · doi:10.1007/s11222-011-9285-5 · Cited by 6
“The theory and applications of empirical Bayes methods are given by Morris (1983).”
MethodBayesian structure learning for functional neuroimaging
Park, M., Koyejo, S., Ghosh, J., Poldrack, R. A., & Pillow, J. W. (2013) · Cited by 6
Complex System Approaches to Genetic Analysis
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Blasques, F., & Duplinskiy, A. (2018) · Journal of Econometrics · doi:10.1016/j.jeconom.2018.03.004 · Cited by 6
Settling the Inflation Targeting Debate: Lights from a Meta-Regression Analysis
Balima, H. W., Kilama, E. G., & Tapsoba, R. (2017) · IMF Working Paper · doi:10.5089/9781484320754.001 · Cited by 6
Kucukelbir, A., & Blei, D. M. (2015) · Uncertainty in Artificial Intelligence · Cited by 6
Instant customer base analysis in the financial services sector
Kim, T., Kim, D., & Ahn, Y. (2022) · Expert Systems with Applications · doi:10.1016/j.eswa.2022.117326 · Cited by 9
Candel, M. J. J. M. (2004) · Statistica Neerlandica · doi:10.1046/j.0039-0402.2003.00256.x · Cited by 6
“Since we are interested in the performance of the estimators for a sample of level-2 units, in the sequel we will consider the MSE for the loss averaged across all level-2 units in the sample (cf. MORRIS, 1983).”
BackgroundResultInfluentialEstimating individual benefits of medical or behavioral treatments in severely ill patients
DÍAZ, F. J. (2017) · Statistical Methods in Medical Research · doi:10.1177/0962280217739033 · Cited by 6
Estimation for the Rasch Model When Both Ability and Difficulty Parameters Are Random
Rigdon, S. E., & Tsutakawa, R. K. (1987) · Journal of Educational Statistics · doi:10.2307/1164629 · Cited by 6
BAYESIAN ESTIMATION METHODS FOR CONTINGENCY TABLES
Goutis, C. (1993) · Statistical Methods & Applications · doi:10.1007/bf02589074 · Cited by 11
Interval estimation for Cohen's kappa as a measure of agreement
Blackman, N. J., & Koval, J. J. (2000) · Statistics in Medicine · doi:10.1002/(sici)1097-0258(20000315)19:5 · Cited by 222
Corrected empirical Bayes confidence intervals in nested error regression models
Kubokawa, T. (2009) · Journal of the Korean Statistical Society · doi:10.1016/j.jkss.2009.08.001 · Cited by 6
“Following Morris (1983), Prasad and Rao (1990) proposed another type of the empirical Bayes confidence interval IEB∗i (ψ̂, σ̂ 2) : µ̂EBi (ψ̂)± zα/2 √ msei(σ̂2, ψ̂).”
InfluentialIMPROVED ESTIMATION OF ECOLOGICAL EFFECTS USING AN EMPIRICAL BAYES METHOD1
Reckhow, K. H. (1996) · JAWRA Journal of the American Water Resources Association · doi:10.1111/j.1752-1688.1996.tb04063.x · Cited by 6
Combining environmental information via hierarchical modeling: an example using mutagenic potencies
Simmons, S. J., Piegorsch, W., Nitcheva, D. K., & Zeiger, E. (2003) · Environmetrics · doi:10.1002/env.573 · Cited by 4
“One can also apply methods of empirical Bayes estimation to such hierarchical linear models (Morris, 1983; Castro and Gaviria, 2000), resulting in constructions similar to those we derive above.”
Mukherjee, B., & Chatterjee, N. (2006) · Collection of Biostatistics Research Archive · Cited by 6
ADJUSTED BAYES ESTIMATORS WITH APPLICATIONS TO SMALL AREA ESTIMATION
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Guided model checking with a bayesian meta-heuristic
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Wech, B. A. (2001) · Louisiana State University · doi:10.31390/gradschool_disstheses.371 · Cited by 6
“The HLM modeling is analogous to linear regression, although the Bayes algorithm is used to estimate the Level-1 components, and is suggested to provide superior precision and reliability (Bryk & Raudenbush, 1992; Morris, 1983).”
The Returns to College(s): Relative Value-Added and Match Effects in Higher EducationPreprint
Mountjoy, J., & Hickman, B. R. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3926957 · Cited by 9
Terrier, C., Pathak, P. A., & Ren, K. (2021) · National Bureau of Economic Research · doi:10.3386/w29600 · Cited by 6
“We employ the software developed by Chandra et al. (2016), who follow the procedure of Morris (1983) to compute σ̂2 and ultimately to compute the shrunk estimates of value-added.”
Conviction, Incarceration, and Recidivism: Understanding the Revolving DoorPreprint
Humphries, J. E., Ouss, A., Stavreva, K., Stevenson, M., & van Dijk, W. (2023) · SSRN Electronic Journal · doi:10.2139/ssrn.4507597 · Cited by 6
Tourism and housing prices: a meta-analysis
Tan, S., Wood, J., Yeap, X. W., Li, C., Zhang, C., Yu, W., Chen, Q., & Wu, J. (2025) · Journal of Sustainable Tourism · doi:10.1080/09669582.2025.2586540 · Cited by 5
“To quantify the between-study heterogeneity—commonly known as τ 2 —we employ estimation techniques such as the Restricted Maximum Likelihood (REML) (Harville, 1977) and the Empirical Bayes (EB) (Morris, 1983) approaches.”
Continuous Adaptation with Online Meta-Learning for Non-Stationary Target Regression Tasks
Yamagata, T., Santos‐Rodríguez, R., & Flach, P. A. (2022) · Signals · doi:10.3390/signals3010006 · Cited by 5
Wang, X. (2015) · International Journal of Advanced Statistics and Probability · doi:10.14419/ijasp.v3i2.4573 · Cited by 5
“On the theoretical side, hierarchical models allow a more ”objective” approach rather than requiring them to be specified using subjective information [13, 14, 15].”
BackgroundEstimation of a multivariate mean under model selection uncertainty
Nguefack‐Tsague, G. (2014) · Pakistan Journal of Statistics and Operation Research · doi:10.18187/pjsor.v10i1.449 · Cited by 5
“References include Efron and Morris (1975), Fay and Herriot (1979), Rubin (1981), Morris (1983), Jones (1991), Brown (2008), and Brown et al. (2011).”
BackgroundEmpirical Bayes estimator of parameter, reliability and hazard rate for Kumaraswamy distribution
Kumar, M., Singh, S. K., Singh, U., & Pathak, A. (2019) · Life Cycle Reliability and Safety Engineering · doi:10.1007/s41872-019-00085-0 · Cited by 5
“According to Morris (1983), an empirical Bayesian inference, which is, as expected, a hybrid of frequentist and Bayesian inference.”
MethodData and Information Requirements for the Department of Veterans Affairs Resource Allocation Systems
Lehner, L. A., Burgess, J. F., HULTS, D., & Stefos, T. (1996) · Medical Care · doi:10.1097/00005650-199603001-00003 · Cited by 5
Hierarchical Bayesian analysis of the carryover effect in two-period crossover designs
David, S. R., & Seaman, J. W. (2002) · Mathematical and Computer Modelling · doi:10.1016/s0895-7177(02)00109-7 · Cited by 5
Liao, J., McMurry, T. L., & Berg, A. S. (2013) · Biostatistics · doi:10.1093/biostatistics/kxt026 · Cited by 5
“Empirical Bayes analysis uses a working prior πp in place of π with the parameters in πp estimated from data z1, . . . , zn usually via maximum likelihood (Morris, 1983).”
MethodWalsh, E., & Lipscomb, S. (2013) · Mathematica Policy Research Reports · Cited by 5
Social Spillovers in the Classroom: Identification, Estimation and Policy Analysis
Pereda‐Fernández, S. (2017) · Economica · doi:10.1111/ecca.12228 · Cited by 4
“Such estimates su er an estimation bias because of the incidental parameter problem, and some authors (Kane and Staiger (2008), Chetty et al. (2011) have used Morris (1983) method to correct for this bias.”
Omar, A., & Augustin, T. (2019) · International Journal of Approximate Reasoning · doi:10.1016/j.ijar.2019.09.006 · Cited by 5
Guldi, J., & Williams, B. (2018) · Current Research in Digital History · doi:10.31835/crdh.2018.01 · Cited by 5
Reis, R. D. D., Colosimo, E., & Gilardoni, G. L. (2019) · Brazilian Journal of Probability and Statistics · doi:10.1214/18-bjps393 · Cited by 4
“We follow Guida, Calabria and Pulcini (1989), Oliveira, Colosimo and Gilardoni (2012) and Ryan, Hamada and Reese (2011) and parametrize the PLPs in terms of βi and ηi = Λi(τi) = (τi/θi) βi , mainly in view of the simplifications that result from (1.4) and the consequent orthogonality.”
BackgroundInfluentialBarnett, P. G., Jacobs, J., Jarvik, J. G., Chou, R., Boothroyd, D. B., Lo, J., & Nevedal, A. (2020) · JAMA Network Open · doi:10.1001/jamanetworkopen.2020.10343 · Cited by 5
On the choice of methodology for evaluating dose-rate effects on radiation-related cancer risks
Walsh, L., Shore, R. E., Azizova, T. V., & Rühm, W. (2021) · Radiation and Environmental Biophysics · doi:10.1007/s00411-021-00920-y · Cited by 5
Swanson, D. A. (2008) · Springer eBooks · doi:10.1007/978-1-4020-8329-7_10 · Cited by 5
“Finally, Swanson et al. (1994) note that an important theoretical development in the biased estimator/MSE approach is that it has been linked to Empirical Bayesian (EB) interpretations (Fay and Herriot 1979, Morris 1983a, 1983b, Prasad and Rao 1990, Reinsel 1985).”
BackgroundGriffin, M. A. (1997) · Australian Psychologist · doi:10.1080/00050069708257380 · Cited by 5
An empirical Bayesian forecast in the threshold stochastic volatility models
Fan, T., & Wang, Y. (2011) · Journal of Statistical Computation and Simulation · doi:10.1080/00949655.2011.620251 · Cited by 5
Public and Expert Opinions on Free Trade Agreements in South America
Beck, K., Gawrońska-Nowak, B., & Valdivieso, P. (2019) · Entrepreneurial Business and Economics Review · doi:10.15678/eber.2019.070201 · Cited by 5
“(Sidik & Jonkman, 2005a; 2005b) – ‘SJ’, the maximum-likelihood – ‘ML’ – and restricted maximum-likelihood estimator (Viechtbauer, 2005; Raudenbush, 2009) – ‘REML’, and the empirical Bayes estimator (Morris, 1983; Berkey et al., 1995) – ‘EB’.”
Metadata
- Authors
- Morris, C. N.
- Affiliations
- The University of Texas at Austin (US)
- Corresponding author
- Morris, Carl N.
- Venue
- Journal of the American Statistical Association
- Publisher
- Informa UK Limited
- Published
- 1983-03
- Volume
- 78
- Issue
- 381
- Pages
- 47-55
- ISSN
- 0162-1459 (ISSN-L)
- 1537-274X
- OpenAlex
- W1983607152
- Cited by
- 1,448
- References
- 36
- Citations by year
- 2026: 32 · 2025: 30 · 2024: 52 · 2023: 42 · 2022: 40 · 2021: 51 · 2020: 62 · 2019: 44 · 2018: 49 · 2017: 43 · 2016: 54 · 2015: 63 · 2014: 66 · 2013: 49 · 2012: 48
- FWCI
- 24.44
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of the American Statistical Association (publishedVersion)
- Topics
- Physical Sciences › Mathematics › Statistics and Probability › Statistical Methods and Bayesian Inference
- Physical Sciences › Mathematics › Statistics and Probability › Statistical Methods and Inference
- Physical Sciences › Mathematics › Statistics and Probability › Statistical Distribution Estimation and Applications
- Keywords
- parametric empirical Bayes, confidence intervals, shrinkage estimation
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