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An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics

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  • Gruber Susan

    (University of California, Berkeley)

  • van der Laan Mark J.

    (University of California, Berkeley)

Abstract

A concrete example of the collaborative double-robust targeted likelihood estimator (C-TMLE) introduced in a companion article in this issue is presented, and applied to the estimation of causal effects and variable importance parameters in genomic data. The focus is on non-parametric estimation in a point treatment data structure. Simulations illustrate the performance of C-TMLE relative to current competitors such as the augmented inverse probability of treatment weighted estimator that relies on an external non-collaborative estimator of the treatment mechanism, and inefficient estimation procedures including propensity score matching and standard inverse probability of treatment weighting. C-TMLE is also applied to the estimation of the covariate-adjusted marginal effect of individual HIV mutations on resistance to the anti-retroviral drug lopinavir. The influence curve of the C-TMLE is used to establish asymptotically valid statistical inference. The list of mutations found to have a statistically significant association with resistance is in excellent agreement with mutation scores provided by the Stanford HIVdb mutation scores database.

Suggested Citation

  • Gruber Susan & van der Laan Mark J., 2010. "An Application of Collaborative Targeted Maximum Likelihood Estimation in Causal Inference and Genomics," The International Journal of Biostatistics, De Gruyter, vol. 6(1), pages 1-31, May.
    • Handle: RePEc:bpj:ijbist:v:6:y:2010:i:1:n:18
    DOI: 10.2202/1557-4679.1182
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    References listed on IDEAS

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    1. van der Laan Mark J. & Polley Eric C & Hubbard Alan E., 2007. "Super Learner," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 6(1), pages 1-23, September.
    2. van der Laan Mark J. & Rubin Daniel, 2006. "Targeted Maximum Likelihood Learning," The International Journal of Biostatistics, De Gruyter, vol. 2(1), pages 1-40, December.
    3. Gruber Susan & van der Laan Mark J., 2010. "A Targeted Maximum Likelihood Estimator of a Causal Effect on a Bounded Continuous Outcome," The International Journal of Biostatistics, De Gruyter, vol. 6(1), pages 1-18, August.
    4. Rosenblum Michael & van der Laan Mark J., 2010. "Targeted Maximum Likelihood Estimation of the Parameter of a Marginal Structural Model," The International Journal of Biostatistics, De Gruyter, vol. 6(2), pages 1-30, April.
    5. van der Laan Mark J. & Gruber Susan, 2010. "Collaborative Double Robust Targeted Maximum Likelihood Estimation," The International Journal of Biostatistics, De Gruyter, vol. 6(1), pages 1-71, May.
    6. Alberto Abadie & Guido W. Imbens, 2006. "Large Sample Properties of Matching Estimators for Average Treatment Effects," Econometrica, Econometric Society, vol. 74(1), pages 235-267, January.
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    Cited by:

    1. Noémi Kreif & Richard Grieve & Iván Díaz & David Harrison, 2015. "Evaluation of the Effect of a Continuous Treatment: A Machine Learning Approach with an Application to Treatment for Traumatic Brain Injury," Health Economics, John Wiley & Sons, Ltd., vol. 24(9), pages 1213-1228, September.
    2. Matthew Cefalu & Francesca Dominici & Nils Arvold & Giovanni Parmigiani, 2017. "Model averaged double robust estimation," Biometrics, The International Biometric Society, vol. 73(2), pages 410-421, June.
    3. Kreif, N. & Grieve, R. & Díaz, I. & Harrison, D., 2014. "Health econometric evaluation of the effects of a continuous treatment: a machine learning approach," Health, Econometrics and Data Group (HEDG) Working Papers 14/19, HEDG, c/o Department of Economics, University of York.
    4. Tuglus Catherine & van der Laan Mark J., 2011. "Repeated Measures Semiparametric Regression Using Targeted Maximum Likelihood Methodology with Application to Transcription Factor Activity Discovery," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-31, January.
    5. Cantoni, Eva & de Luna, Xavier, 2020. "Semiparametric inference with missing data: Robustness to outliers and model misspecification," Econometrics and Statistics, Elsevier, vol. 16(C), pages 108-120.

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