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Reducing Dimensionality in Molecular Systems: A Bayesian Non-parametric Approach

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Abstract

In this paper we present a methodology that can be used to design experiments of complex systems characterized by a huge number of variables. The strategy combines the evolutionary principles with the information provided by statistical models tailored to the problem under consideration. Here, we are concerned with the process of design molecules, which is a quite challenging problem due to the presence of a high number of variables with a binary structure. Recent works on clustering of binary data and variable selection in the high-dimensional setting allow to develop an approach capable of recovering useful information derived from the incorporation of a grouping structure into the model.

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References

  1. Fan, J., Lv, J.: A selective overview of variable selection in high dimensional feature space. Stat. Sin. 20, 101–148 (2010)

    MathSciNet  MATH  Google Scholar 

  2. Ma, Y., Zhu, L.: A review on dimension reduction. Int. Stat. Rev. 81(1), 134–150 (2013)

    Article  MathSciNet  Google Scholar 

  3. Baragona, R., Battaglia, F., Poli, I.: Evolutionary Statistical Procedures: An Evolutionary Computation Approach to Statistical Procedures Designs and Applications. Springer, Heidelberg (2013)

    MATH  Google Scholar 

  4. Borrotti, M., De March, D., Slanzi, D., Poli, I.: Designing lead optimization of MMP-12 inhibitors. Comput. Math. Methods Med. 2014, 1–8 (2014)

    Article  Google Scholar 

  5. Pickett, S.D., Green, D.V.S., Hunt, D.L., Pardoe, D.A., Hughes, I.: Automated lead optimization of MMP-12 inhibitors using a genetic algorithm. ACS Med. Chem. Lett. 2(1), 28–33 (2011)

    Article  Google Scholar 

  6. Slanzi, D., De Lucrezia, D., Poli, I.: Querying Bayesian networks to design experiments with application to 1AGY serine esterase protein engineering. Chemometr. Intell. Lab. 149, 28–38 (2015)

    Article  Google Scholar 

  7. Santra, T.: A Bayesian non-parametric method for clustering high-dimensional binary data (2016). https://arxiv.org/pdf/1603.02494

  8. Breheny, P., Huang, J.: Penalized methods for bi-level variable selection. Stat. Interface 2(3), 369–380 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  9. Lameijer, E.-W., Bäck, T., Kok, J.N., Ijzerman, A.D.P.: Evolutionary algorithms in drug design. Nat. Comput. 4(3), 177–243 (2005)

    Article  MathSciNet  Google Scholar 

  10. Huang, J., Breheny, P., Ma, S.: A selective review of group selection in high-dimensional models. Stat. Sci. 27(4), 481–499 (2012)

    Article  MathSciNet  MATH  Google Scholar 

  11. Liu, J., Wang, F., Gao, X., Zhang, H., Wan, X., Yang, C.: A penalized regression approach for integrative analysis in genome-wide association studies. J. Biom. Biostat. 6(228), 1–7 (2015)

    Google Scholar 

  12. Ogutu, J.O., Piepho, H.P.: Regularized group regression methods for genomic prediction: Bridge, MCP, SCAD, group bridge, group lasso, sparse group lasso, group MCP and group SCAD. BMC Proc. 8(Suppl. 5), S7 (2014)

    Article  Google Scholar 

  13. Tibshirani, R.: Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Series B Stat. Methodol. 58(1), 267–288 (1996)

    MathSciNet  MATH  Google Scholar 

  14. Zhang, C.-H.: Nearly unbiased variable selection under minimax concave penalty. Ann. Stat. 38(2), 894–942 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  15. Bühlmann, P., Rütimann, P., van de Geer, S., Zhang, C.H.: Correlated variables in regression: clustering and sparse estimation. J. Stat. Plan. Infer. 143(11), 1835–1858 (2013)

    Article  MathSciNet  MATH  Google Scholar 

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Acknowledgements

The authors would like to acknowledge Professor Philip J. Brown and the GlaxoSmithKline Medicines Research Centre (UK) for the very fruitful collaboration in developing this research.

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Correspondence to Valentina Mameli .

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Mameli, V., Lunardon, N., Khoroshiltseva, M., Slanzi, D., Poli, I. (2017). Reducing Dimensionality in Molecular Systems: A Bayesian Non-parametric Approach. In: Rossi, F., Piotto, S., Concilio, S. (eds) Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry. WIVACE 2016. Communications in Computer and Information Science, vol 708. Springer, Cham. https://doi.org/10.1007/978-3-319-57711-1_10

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  • DOI: https://doi.org/10.1007/978-3-319-57711-1_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-57710-4

  • Online ISBN: 978-3-319-57711-1

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