Skip to main content

A Graphical Processing Unit Accelerated NORmal to Anything Algorithm for High Dimensional Multivariate Simulation

  • Conference paper
  • First Online:
16th International Conference on Information Technology-New Generations (ITNG 2019)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 800))

  • 1608 Accesses

Abstract

Many complex real world systems can be represented as correlated high dimensional vectors (up to 20,501 in this paper). While univariate analysis is simpler, it does not account for correlations between variables. This omission often misleads researchers by producing results based on unrealistic assumptions. As the generation of large correlated data sets is time consuming and resource heavy, we propose a graphical processing unit (GPU) accelerated version of the established NORmal To Anything (NORTA) algorithm. NORTA involves many independent and parallelizeable operations—sparking our interest to deploy a Compute Unified Device Architecture (CUDA) implementation for use on Nvidia GPUs. NORTA begins by simulating independent standard normal vectors and transforms them into correlated vectors with arbitrary marginal distributions (heterogenous random variables). In our benchmark studies using a Tesla Nvidia card, the speedup obtained over a sequential NORTA coded in R (R-NORTA) peaks at 19.6× for 2000 simulated random vectors with dimension 5000. Moreover, the speedup obtained for GPU-NORTA over a commonly used R package for multivariate simulation (the copula package) was 2093× for 2000 simulated random vectors with dimension 20,501. Our study serves as a preliminary proof of concept with opportunities for further optimization, implementation, and additional features.

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 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

  1. Pucher, B.M., Zeleznik, O.A., Thallinger, G.G.: Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data. Brief. Bioinform. 1–11 (2018). [Online]. Available: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby027/4982568

  2. Gatti, D.M., Barry, W.T., Nobel, A.B., Rusyn, I., Wright, F.A.: Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics 11(1), 574 (2010). [Online]. Available: https://doi.org/10.1186/1471-2164-11-574

  3. Wilkins, M.F., Morris, C., Boddy, L.: A comparison of radial basis function and backpropagation neural networks for identification of marine phytoplankton from multivariate flow cytometry data. Bioinformatics 10(3), 285–294 (1994). [Online]. Available: http://dx.doi.org/10.1093/bioinformatics/10.3.285

  4. Russkova, T.V.: Monte Carlo simulation of the solar radiation transfer in a cloudy atmosphere with the use of graphic processor and NVIDIA CUDA technology. Atmos. Oceanic Opt. 31(2), 119–130 (2018). [Online]. Available: https://link-springer-com.unr.idm.oclc.org/content/pdf/10.1134/S1024856018020100.pdf

  5. Häyrinen, K., Saranto, K., Nykänen, P.: Definition, structure, content, use and impacts of electronic health records: a review of the research literature. Int. J. Med. Inform. 77(5), 291–304 (2008). [Online]. Available: https://www.sciencedirect.com/science/article/pii/S1386505607001682

  6. Niaki, S.T.A., Abbasi, B.: Generating correlation matrices for normal random vectors in NORTA algorithm using artificial neural networks. J. Uncertain Syst. 2(3), 192–201 (2008). [Online]. Available: http://www.worldacademicunion.com/journal/jus/jusVol02No3paper04.pdf

  7. Cario, M.C., Nelson, B.L.: Modeling and generating random vectors with arbitrary marginal distributions and correlation matrix. Northwestern University, Technical Report (1997). [Online]. Available: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.48.281

    Google Scholar 

  8. Casella, G., Berger, R.L.: Statistical Inference. Duxbury, Pacific Grove (2002)

    Google Scholar 

  9. Strang, G.: Introduction to Linear Algebra. Cambridge Press, Wellesley (1993)

    MATH  Google Scholar 

  10. Rizzo, M.L.: Statistical Computing with R. Chapman and Hall/CRC (2007). [Online]. Available: https://www.taylorfrancis.com/books/9781420010718

  11. Genest, C., Mackay, J.: The joy of copulas: bivariate distributions with uniform marginals. Am. Stat. 40(4), 280–283 (1986). [Online]. Available: https://www.tandfonline.com/doi/abs/10.1080/00031305.1986.10475414

  12. Sklar, M.: Fonctions de répartition à n dimensions et leurs marges. Publ. Inst. Statist. Univ. Paris 8, 229–231 (1959)

    MathSciNet  MATH  Google Scholar 

  13. Sanders, J., Kandrot, E.: CUDA by example: an introduction to general-purpose GPU programming, 1st edn. Addison-Wesley Professional, Upper Saddle River (2010)

    Google Scholar 

  14. Nobile, M.S., Cazzaniga, P., Besozzi, D., Pescini, D., Mauri, G.: cuTauLeaping: a GPU-powered Tau-leaping stochastic simulator for massive parallel analyses of biological systems. PLoS One 9(3), e91963 (2014). [Online]. Available: http://dx.plos.org/10.1371/journal.pone.0091963

  15. Harris, M.: Unified memory in CUDA 6 (2013). [Online]. Available: https://devblogs.nvidia.com/unified-memory-in-cuda-6/

  16. Harris, M.: CUDA 8 features revealed: pascal, unified memory and more (2016). [Online]. Available: https://devblogs.nvidia.com/cuda-8-features-revealed/

  17. Yan, J.: Enjoy the joy of copulas: with a package copula. J. Stat. Softw. 21(4), 1–21 (2007). [Online]. Available: http://www.jstatsoft.org/v21/i04/

  18. cuSOLVER::CUDA Toolkit Documentation (2018). [Online]. Available: https://docs.nvidia.com/cuda/cusolver/index.html

  19. cuRAND::CUDA Toolkit Documentation (2018). [Online]. Available: https://docs.nvidia.com/cuda/curand/notices-header.html#notices-header

  20. cuBLAS::CUDA Toolkit Documentation (2018). [Online]. Available: https://docs.nvidia.com/cuda/cublas/index.html

  21. O’Hara, K.: StatsLib (2018). [Online]. Available: https://github.com/kthohr/stats

Download references

Acknowledgements

This material is based upon work supported by the National Science Foundation under grant number IIA1301726. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Frederick C. Harris Jr. .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Li, X., Schissler, A.G., Wu, R., Barford, L., Harris, F.C. (2019). A Graphical Processing Unit Accelerated NORmal to Anything Algorithm for High Dimensional Multivariate Simulation. In: Latifi, S. (eds) 16th International Conference on Information Technology-New Generations (ITNG 2019). Advances in Intelligent Systems and Computing, vol 800. Springer, Cham. https://doi.org/10.1007/978-3-030-14070-0_46

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-14070-0_46

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-14069-4

  • Online ISBN: 978-3-030-14070-0

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics