Skip to main content

Bayesian Nonparametrics for Missing Data in Longitudinal Clinical Trials

  • Chapter
Nonparametric Bayesian Inference in Biostatistics

Part of the book series: Frontiers in Probability and the Statistical Sciences ((FROPROSTAS))

Abstract

We discuss the problem of performing inference on a causal effect of interest, such as an intention-to-treat effect, in the context of longitudinal clinical trials with informatively missing data. Addressing this problem requires the modeling of infinite-dimensional nuisance parameters; modeling these nuisance parameters poorly can result in substantial bias in the original estimation problem. Additionally, the presence of informative (nonignorable) missingness results in effects of interest being unidentified in the absence of strong, unverifiable, assumptions. We argue that Bayesian nonparametric methods are natural in this setting because they (1) allow for flexible modeling and (2) allow for uncertainty in untestable assumptions to be taken into account through the use of informative priors elicited from subject matter experts. We further argue that a sensitivity analysis to assess the impact of unverifiable assumptions is essential. Flexible Bayesian approaches which incorporate the longitudinal structure of the data are presented in the context of categorical and continuous outcomes, and strategies for sensitivity analysis are discussed in both cases. The methods are illustrated on data from a clinical trial designed to assess the efficacy of treatments for acute Schizophrenia.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Birmingham, J., Rotnitzky, A., and Fitzmaurice, G. M. (2003). Pattern-mixture and selection models for analysing longitudinal data with monotone missing patterns. Journal of the Royal Statistical Society, Series B., 65, 275–297.

    Article  MathSciNet  MATH  Google Scholar 

  • Creemers, A., Hens, N., Aerts, M., Molenberghs, G., Verbeke, G., and Kenward, M. G. (2010). A sensitivity analysis for shared-parameter models for incomplete longitudinal outcomes. Biometrical Journal, 52(1), 111–125.

    MathSciNet  MATH  Google Scholar 

  • Daniels, M., Wang, C., and Marcus, B. (2014). Fully Bayesian inference under ignorable missingness in the presence of auxiliary covariates. Biometrics, 70(1), 62–72.

    Article  MathSciNet  MATH  Google Scholar 

  • Daniels, M. J. (1999). A prior for the variance in hierarchical models. Canadian Journal of Statistics, 27(3), 567–578.

    Article  MathSciNet  MATH  Google Scholar 

  • Daniels, M. J. and Hogan, J. W. (2000). Reparameterizing the pattern mixture model for sensitivity analyses under informative dropout. Biometrics, 56(4), 1241–1248.

    Article  MathSciNet  MATH  Google Scholar 

  • Daniels, M. J. and Hogan, J. W. (2008). Missing data in longitudinal studies: Strategies for Bayesian modeling and sensitivity analysis. CRC Press.

    Google Scholar 

  • Daniels, M. J. and Pourahmadi, M. (2002). Bayesian analysis of covariance matrices and dynamic models for longitudinal data. Biometrika, 89(3), 553–566.

    Article  MathSciNet  MATH  Google Scholar 

  • Daniels, M. J., Chatterjee, A. S., and Wang, C. (2012). Bayesian model selection for incomplete data using the posterior predictive distribution. Biometrics, 68(4), 1055–1063.

    Article  MathSciNet  MATH  Google Scholar 

  • Diggle, P. and Kenward, M. G. (1994). Informative drop-out in longitudinal data analysis. Applied statistics, pages 49–93.

    Google Scholar 

  • Dunson, D. B. (2006). Bayesian dynamic modeling of latent trait distributions. Biostatistics, 7(4), 551–568.

    Article  MATH  Google Scholar 

  • Dunson, D. B. (2007). Bayesian methods for latent trait modelling of longitudinal data. Statistical Methods in Medical Research, 16, 399–415.

    Article  MathSciNet  MATH  Google Scholar 

  • Dunson, D. B. and Herring, A. H. (2006). Semiparametric Bayesian latent trajectory models. Technical report, ISDS Discussion Paper 16, Duke Univ., Durham, NC, USA.

    Google Scholar 

  • Dunson, D. B. and Perreault, S. D. (2001). Factor analytic models of clustered multivariate data with informative censoring. Biometrics, 57(1), 302–308.

    Article  MathSciNet  MATH  Google Scholar 

  • Fieuws, S. and Verbeke, G. (2006). Pairwise fitting of mixed models for the joint modeling of multivariate longitudinal profiles. Biometrics, 62(2), 424–431.

    Article  MathSciNet  Google Scholar 

  • Gael, J. V., Teh, Y. W., and Ghahramani, Z. (2009). The infinite factorial hidden Markov model. In Advances in Neural Information Processing Systems, pages 1697–1704.

    Google Scholar 

  • Gelman, A., Jakulin, A., Pittau, M. G., and Su, Y.-S. (2008). A weakly informative default prior distribution for logistic and other regression models. The Annals of Applied Statistics, pages 1360–1383.

    Google Scholar 

  • Harel, O. and Schafer, J. L. (2009). Partial and latent ignorability in missing-data problems. Biometrika, 96(1), 37–50.

    Article  MathSciNet  MATH  Google Scholar 

  • Heckman, J. J. (1979). Sample selection bias as a specification error. Econometrica: Journal of the Econometric Society, pages 153–161.

    Google Scholar 

  • Henderson, R., Diggle, P., and Dobson, A. (2000). Joint modelling of longitudinal measurements and event time data. Biostatistics, 1(4), 465–480.

    Article  MATH  Google Scholar 

  • Hogan, J. W. and Laird, N. M. (1997). Mixture models for the joint distribution of repeated measures and event times. Statistics in medicine, 16(3), 239–257.

    Article  Google Scholar 

  • Hogan, J. W., Daniels, M. J., and Hu, L. (2014). A bayesian perspective on assessing sensitivity to assumptions about unobserved data. In G. Molenberghs, G. Fitzmaurice, M. G. Kenward, A. Tsiatis, and G. Verbeke, editors, Handbook of Missing Data Methodology. CRC Press.

    Google Scholar 

  • Johnson, V. E. and Albert, J. H. (1999). Ordinal Data Modeling. Statistics for Social Science and Public Policy. New York: Springer-Verlag.

    Google Scholar 

  • Kenward, M., Molenberghs, G., and Thijs, H. (2003). Pattern-mixture models with proper time dependence. Biometrika, 90, 53–71.

    Article  MathSciNet  MATH  Google Scholar 

  • Kim, C., Daniels, M. J., and Roy, J. A. (2015). A framework for Bayesian nonparametric inference for causal effects of mediation. Technical Report.

    Google Scholar 

  • Kleinman, K. P. and Ibrahim, J. G. (1998). A semiparametric Bayesian approach to the random effects model. Biometrics, pages 921–938.

    Google Scholar 

  • Kottas, A., Müller, P., and Quintana, F. (2005). Nonparametric Bayesian modeling for multivariate ordinal data. Journal of Computational and Graphical Statistics, 14(3), 610–625.

    Article  MathSciNet  Google Scholar 

  • Linero, A. R. (2015a). Bayesian nonparametric analysis of longitudinal studies in the presence of informative missingness. Technical Report.

    Google Scholar 

  • Linero, A. R. (2015b). Nonparametric Bayes: Inference Under Nonignorable Missingness and Model Selection. Ph.D. thesis, University of Florida.

    Google Scholar 

  • Linero, A. R. and Daniels, M. J. (2015). A flexible Bayesian approach to monotone missing data in longitudinal studies with nonignorable missingness with application to an acute schizophrenia clinical trial. Journal of the American Statistical Association, in press.

    Google Scholar 

  • Little, R. J. A. (1993). Pattern-mixture models for multivariate incomplete data. Journal of the American Statistical Association, 88(421), 125–134.

    MATH  Google Scholar 

  • Little, R. J. A. (1994). A class of pattern-mixture models for normal incomplete data. Biometrika, 81(3), 471–483.

    Article  MathSciNet  MATH  Google Scholar 

  • Little, R. J. A. and Rubin, D. B. (1986). Statistical analysis with missing data. John Wiley & Sons.

    Google Scholar 

  • Manski, C. F. (2009). Identification for prediction and decision. Harvard University Press.

    Google Scholar 

  • Meng, X. L. (1994). Multiple-imputation inferences with uncongenial sources of input. Statistical Science, pages 538–558.

    Google Scholar 

  • Molenberghs, G., Michiels, B., Kenward, M. G., and Diggle, P. J. (1998). Monotone missing data and pattern-mixture models. Statistica Neerlandica, 52, 153–161.

    Article  MathSciNet  MATH  Google Scholar 

  • Molenberghs, G., Fitzmaurice, G., Kenward, M. G., Tsiatis, A., and Verbeke, G. (2014). Handbook of Missing Data Methodology. CRC Press.

    Google Scholar 

  • National Research Council (2010). The Prevention and Treatment of Missing Data in Clinical Trials. The National Academies Press.

    Google Scholar 

  • Njagi, E. N., Molenberghs, G., Kenward, M. G., Verbeke, G., and Rizopoulos, D. (2014). A characterization of missingness at random in a generalized shared-parameter joint modeling framework for longitudinal and time-to-event data, and sensitivity analysis. Biometrical Journal, 56(6), 1001–1015.

    Article  MathSciNet  Google Scholar 

  • Pati, D., Reich, B. J., and Dunson, D. B. (2011). Bayesian geostatistical modelling with informative sampling locations. Biometrika, 98(1), 35–48.

    Article  MathSciNet  MATH  Google Scholar 

  • Ren, L., Dunson, D. B., and Carin, L. (2008). The dynamic hierarchical Dirichlet process. In Proceedings of the 25th international conference on Machine learning, pages 824–831. ACM.

    Google Scholar 

  • Robins, J. (1989). The control of confounding by intermediate variables. Statistics in medicine, 8(6), 679–701.

    Article  MathSciNet  MATH  Google Scholar 

  • Robins, J. M. (1986). A new approach to causal inference in mortality studies with sustained exposure periods – application to control of the healthy worker survivor effect. Math Modeling, 7, 1393–1512.

    Article  MathSciNet  MATH  Google Scholar 

  • Robins, J. M. (1997). Non-response models for the analysis of non-monotone non-ignorable missing data. Statistics in Medicine, 16(1), 21–37.

    Article  Google Scholar 

  • Robins, J. M. and Ritov, Y. (1997). Toward a curse of dimensionality appropriate(CODA) asymptotic theory for semi-parametric models. Statistics in medicine, 16(3), 285–319.

    Article  Google Scholar 

  • Robins, J. M., Rotnitzky, A., and Scharfstein, D. O. (2000). Sensitivity analysis for selection bias and unmeasured confounding in missing data and causal inference models. In Statistical models in epidemiology, the environment, and clinical trials, pages 1–94. Springer.

    Google Scholar 

  • Roy, J. (2003). Modeling longitudinal data with nonignorable dropouts using a latent dropout class model. Biometrics, 59(4), 829–836.

    Article  MathSciNet  MATH  Google Scholar 

  • Rubin, D. (1976). Inference and missing data. Biometrika, 63, 581–592.

    Article  MathSciNet  MATH  Google Scholar 

  • Rubin, D. B. (1987). Multiple Imputation for Nonresponse in Surveys. Wiley.

    Google Scholar 

  • Scharfstein, D., McDermott, A., Olson, W., and Wiegand, F. (2014). Global sensitivity analysis for repeated measures studies with informative dropout: A fully parametric approach. Statistics in Biopharmaceutical Research, 6(4), 338–348.

    Article  Google Scholar 

  • Scharfstein, D. O., Rotnitzky, A., and Robins, J. M. (1999). Adjusting for nonignorable dropout using semiparametric nonresponse models. Journal of the American Statistical Association, 94, 1096–1146.

    Article  MathSciNet  MATH  Google Scholar 

  • Scharfstein, D. O., Daniels, M. J., and Robins, J. M. (2003). Incorporating prior beliefs about selection bias into the analysis of randomized trials with missing outcomes. Biostatistics, 4(4), 495–512.

    Article  MATH  Google Scholar 

  • Si, Y. and Reiter, J. P. (2013). Nonparametric Bayesian multiple imputation for incomplete categorical variables in large-scale assessment surveys. Journal of Educational and Behavioral Statistics, 38(5), 499–521.

    Article  Google Scholar 

  • Teh, Y. W., Jordan, M. I., Beal, M. J., and Blei, D. M. (2006). Hierarchical Dirichlet processes. Journal of the American Statistical Association, 101(476).

    Google Scholar 

  • Thijs, H., Molenberghs, G., Michiels, B., Verbeke, G., and Curran, D. (2002). Strategies to fit pattern-mixture models. Biostatistics, 3(2), 245–265.

    Article  MATH  Google Scholar 

  • Vansteelandt, S., Goetghebeur, E., Kenward, M., and Molenberghs, G. (2006). Ignorance and uncertainty regions as inferential tools in a sensitivity analysis. Statistica Sinica, 16, 953–979.

    MathSciNet  MATH  Google Scholar 

  • Vansteelandt, S., Rotnitzky, A., and Robins, J. (2007). Estimation of regression models for the mean of repeated outcomes under nonignorable nonmonotone nonresponse. Biometrika, 94(4), 841–860.

    Article  MathSciNet  Google Scholar 

  • Wang, C., Danies, M. J., Scharfstein, D. O., and Land, S. (2010). A Bayesian shrinkage model for incomplete longitudinal binary data with application to the breast cancer prevention trial. Journal of the American Statistical Association, 105, 1333–1346.

    Article  MathSciNet  Google Scholar 

  • Williamson, S., Orbanz, P., and Ghahramani, Z. (2010). Dependent Indian buffet processes. In International conference on artificial intelligence and statistics, pages 924–931.

    Google Scholar 

  • Wu, M. C. and Carroll, R. J. (1988). Estimation and comparison of changes in the presence of informative right censoring by modeling the censoring process. Biometrics, pages 175–188.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michael J. Daniels .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Daniels, M.J., Linero, A.R. (2015). Bayesian Nonparametrics for Missing Data in Longitudinal Clinical Trials. In: Mitra, R., Müller, P. (eds) Nonparametric Bayesian Inference in Biostatistics. Frontiers in Probability and the Statistical Sciences. Springer, Cham. https://doi.org/10.1007/978-3-319-19518-6_21

Download citation

Publish with us

Policies and ethics