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Operating Characteristics of Partial Least Squares in Right-Censored Data Analysis and Its Application in Predicting the Change of HIV-I RNA

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Probability, Statistics and Modelling in Public Health
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Abstract

It is often of interest to effectively use the information on a large number of covariates in predicting response or outcome. Various statistical tools have been developed to overcome the difficulties caused by the high-dimensionality of the covariate space in the setting of a linear regression model. This paper focuses on the situation where the outcomes of interest are subjected to right censoring. We implement the extended partial least squares method along with other commonly used approaches for analyzing the high dimensional covariates to a data set from AIDS clinical trials (ACTG333). Predictions were computed on the covariate effect and the response for a future subject with a set of covariates. Simulation studies were conducted to compare our proposed methods with other prediction procedures for different numbers of covariates, different correlations among the covariates and different failure time distributions. Mean squared prediction error and mean absolute distance were used to measure the accuracy of prediction on the covariate effect and the response, respectively. We also compared the prediction performance of different approaches using numerical studies. The results show that the Buckley-James based partial least squares, stepwise subset model selection and principal components regression have similar predictive power and the partial least squares method has several advantages in terms of interpretability and numerical computation.

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References

  1. Brown, P., Measurement, Regression, and Calibration. Clarendon: Oxford (1993)

    Google Scholar 

  2. J. Buckley and I. James, “Linear regression with censored data,” Biometrika vol. 66, pp. 429–436, 1979.

    Google Scholar 

  3. N. Butler and M. Denham, “The peculiar shrinkage properties of partial least squares regression,” J. Roy. Stat. Soc., Ser. B vol. 62, pp. 585–593, 2000.

    MathSciNet  Google Scholar 

  4. Collier, A., Coombs, R., Schoenfeld, D., Bassett, R., Timpone, J., Baruch, A., Jones, M., Facey, K., Whitacre, C., McAuliffe, V., Friedman, H., Merigan, T., Reichman, R., Hopper, C., Corey L.: Treatment of human immunodeficiency virus infection with saquinavir, zidovudine, and zalcitabine: AIDS Clinical Trial Group. N. Engl. J. Med. 16, 1011–1017 (1996)

    Google Scholar 

  5. J. Condra, W. Schleif, O. Blahy, L. Gabryelski, D. Graham, J. Quintero, A. Rhodes, H. Robbins, E. Roth, M. Shivaprakash, D. Titus, T. Yang, H. Tepplert, K. Squires, P. Deutsch and E. Emini, “In vivo emergence of HIV-I variants resistant to multiple protease inhibitors,” Nature vol. 374, pp. 569–571, 1995.

    Article  Google Scholar 

  6. J. Condra, D. Holder, W. Schleif, and et al., “Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type I protease inhibitor,” J. Virol. vol. 70, 8270–8276, 1996.

    Google Scholar 

  7. D. Cox, “Regression models and life tables,” J. Roy. Stat. Soc., Ser. B vol. 34, pp. 187–220, 1972.

    MATH  Google Scholar 

  8. I. Currie, “A note on Buckley-James estimators for censored data,” Biometrika vol. 83, pp. 912–915, 1996.

    Article  MATH  Google Scholar 

  9. S. de Jong, “SIMPLS: an alternative approach to partial least squares regression,” Chem. Intell. Lab. Syst. vol. 18, pp. 251–263, 1993.

    Google Scholar 

  10. M. Denham, Calibration in infrared spectroscopy, Ph.D. Dissertaion, University of Liverpool, 1991.

    Google Scholar 

  11. N. Draper and H. Smith, Applied Regression Analysis, John Wiley and Sons: New York, 1981.

    Google Scholar 

  12. I. Frank and J. Friedman, “A statistical view of some chemometrics regression tools,” Technometrics vol. 35, pp. 109–134, 1993.

    Google Scholar 

  13. C. Goutis, “Partial least squares algorithm yields shrinkage estimators,” Ann. Stat. vol. 24, pp. 816–824, 1996.

    MATH  MathSciNet  Google Scholar 

  14. R. Gunst, “Regression analysis with multicollinear predictor variables: Definition, detection, and effects,” Commun. Stat. Theo. Meth. vol. 12, pp. 2217–2260, 1983.

    MATH  MathSciNet  Google Scholar 

  15. I. Helland, “On the structure of partial least squares regression,” Commun. Stat. Simu. Comp. vol. 17, pp. 581–607, 1988.

    MATH  MathSciNet  Google Scholar 

  16. G. Heller and J. Simonoff, “Prediction in censored survival data: a comparison of the proportional hazards and linear regression models,” Biometrics vol. 48, pp. 101–115, 1992.

    Google Scholar 

  17. R. Hocking, “The analysis and selection of variables in linear regression,” Biometrics vol. 32, pp. 1–49, 1976.

    MATH  MathSciNet  Google Scholar 

  18. H. Hotelling, “Analysis of a complex of statistical variables into principal components,” J. Educ. Psychol. vol. 24, pp. 417–441, 498–520, 1933.

    MATH  Google Scholar 

  19. J. Hughes, “Mixed effects models with censored data with applications to HIV RNA levels,” Biometrics vol 55, pp. 625–629, 1999.

    Article  MATH  Google Scholar 

  20. J. Huang and D. Harrington, “Iterative partial least squares with right-censored data analysis: A comparision to other dimension reduction technique,” Biometrics, in press, March 2005.

    Google Scholar 

  21. J. Huang and D. Harrington, “Dimension reduction in the linear model for right-censored data: predicting the change of HIV-I RNA levels using clinical and protease gene mutation data,” Lifetime Data Analysis, in press, December 2004.

    Google Scholar 

  22. H. Jacobsen, M. Hanggi, M. Ott, I. Duncan, S. Owen, M. Andreoni, S. Vella, and J. Mous, “In vivo resistance to a human immunodeficiency virus type I protease inhibitor: mutations, kinetics, and frequencies,” J. Inf. Dis. vol. 173, pp. 1379–1387, 1996.

    Google Scholar 

  23. H. Jacqmin-Gadda and R. Thiébaut, “Analysis of left censored longitudinal data with application to viral load in HIV infection,” Biostatistics vol. 1, pp. 355–368, 2000.

    Article  Google Scholar 

  24. Z. Jin, D. Lin, L. Wei, and Z. Ying, “Rank-based inference for the accelerated failure time model,” Biometrika vol. 90, pp. 341–353, 2003.

    Article  MathSciNet  Google Scholar 

  25. I. Jolliffe, Principal Component Analysis, Springer-Verlag: New York, 1986.

    Google Scholar 

  26. N. Laird and J. Ware, “Random effects models for longitudinal data,” Biometrics vol. 38, pp. 963–974, 1982.

    Google Scholar 

  27. I. Marschner, R. Betensky, V. Degruttola, S. Hammer, and D. Kuritzkes, “Clinical trials using HIV-1 RNA-based primary endpoints: statistical analysis and potential biases,”Ť J. Acq. Imm. Def. Syndr. Hum. Retr. vol. 20, pp. 220Ů227, 1999.

    Google Scholar 

  28. A. Miller, Subset Selection in Regression, Chapman and Hall: London, 1990.

    Google Scholar 

  29. R. Miller and J. Halpern, “Regression with censored data,” Biometrika vol. 69, pp. 521–531, 1982.

    MathSciNet  Google Scholar 

  30. D. Nguyen and D. Rocke, “Partial least squares proportional hazard regression for application to DNA microarray survival data,” Bioinformatics vol. 18, pp. 1625–1632, 2002.

    Google Scholar 

  31. M. Para, D. Glidden, R. Coombs, A. Collier, J. Condra, C. Craig, R. Bassett, S. Leavitt, V. McAuliffe, and C. Roucher, “Baseline human immunodeficiency virus type I phenotype, genotype, and RNA response after switching from long-term hard-capsule saquinavir to indinavir or softgel-capsule in AIDS clinical trials group protocol 333,” J. Inf. Dis. vol. 182, pp. 733–743, 2000.

    Google Scholar 

  32. P. Park, L. Tian and I. Kohane, “Linking gene expression data with patient survival times using partial least squares,” Bioinformatics vol. 18, pp. S120–S127, 2002.

    Google Scholar 

  33. M. Stone and R. Brooks, “Continuum regression: cross-validation sequentially constructed prediction embracing ordinary least squares, partial least squares and principal components regression,” J. Roy. Stat. Soc., Ser. B vol. 52, pp. 237–269, 1990.

    MathSciNet  Google Scholar 

  34. R. Tibshirani, “Regression shrinkage and selection via the lasso,” J. Roy. Stat. Soc., Ser. B vol. 58, pp. 267–288, 1996.

    MATH  MathSciNet  Google Scholar 

  35. A. Tsiatis, “Estimation regression parameters using linear rank tests for censored data model with censored data,” Ann. Stat. vol. 18, pp. 354–372, 1990.

    MATH  MathSciNet  Google Scholar 

  36. M. Vaillancourt, R. Irlbeck, T. Smith, R. Coombs, and R. Swanstrom, “The HIV type I protease inhibitor saquinavir can select for multiple mutations that confer increasing resistance,” AIDS Res. Hum. Retr. vol. 15, pp. 355–363, 1999.

    Google Scholar 

  37. P. Wentzell and L. Montoto, “Comparison of principal components regression and partial least squares through generic simulations of complex mixtures,” Chem. Intell. Lab. Syst. vol. 65, pp. 257–279, 2003.

    Google Scholar 

  38. H. Wold, “Nonlinear estimation by iterative least squares procedures,” Research papers in Statistics: Festschrift for J. Neyman John Wiley and Sons: New York, pp. 411–444, 1966.

    Google Scholar 

  39. H. Wold, “Soft modeling by latent variables: The non-linear iterative partial least squares (NIPALS) approach,” Perspectives in Probability and Statistics, In Honor of M. S. Bartlett Academic: New York, pp. 117–144, 1976.

    Google Scholar 

  40. S. Wold, H. Wold, W. Dunn, and A. Ruhe, “The collinearity problem in linear regression: The partial least squares (PLS) approach to generalized inverse,” SIAM J. Sci. Stat. Comput. vol. 5, pp. 735–743, 1984.

    Article  Google Scholar 

  41. Z. Ying, L. Wei, and D. Lin, “Prediction of survival probability based on a linear regression model,” Biometrika vol. 79, pp. 205–209, 1992.

    MathSciNet  Google Scholar 

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Huang, J., Harrington, D. (2006). Operating Characteristics of Partial Least Squares in Right-Censored Data Analysis and Its Application in Predicting the Change of HIV-I RNA. In: Nikulin, M., Commenges, D., Huber, C. (eds) Probability, Statistics and Modelling in Public Health. Springer, Boston, MA. https://doi.org/10.1007/0-387-26023-4_14

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