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Parallelized Parameter Estimation of Biological Pathway Models

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Book cover Hybrid Systems Biology (HSB 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9271))

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Abstract

We develop a GPU based technique to analyze bio-pathway models consisting of systems of ordinary differential equations (ODEs). A key component in our technique is an online procedure for verifying whether a numerically generated trajectory of a model satisfies a property expressed in bounded linear temporal logic. Using this procedure, we construct a statistical model checking algorithm which exploits the massive parallelism offered by GPUs while respecting the severe constraints imposed by their memory hierarchy and the hardware execution model. To demonstrate the computational power of our method, we use it to solve the parameter estimation problem for bio-pathway models. With three realistic benchmarks, we show that the proposed technique is computationally efficient and scales well with the number of GPU units deployed. Since both the verification framework and the computational platform are generic, our scheme can be used to solve a variety of analysis problems for models consisting of large systems of ODEs.

This research was supported by the Singapore MOE grant MOE2013-T2-2-033.

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Notes

  1. 1.

    Source code available at https://www.comp.nus.edu.sg/~rpsysbio/smcgpu/.

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Authors and Affiliations

  1. School of Computing, National University of Singapore, Singapore, Singapore

    R. Ramanathan, Yan Zhang, Jun Zhou & Weng-Fai Wong

  2. Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA

    Benjamin M. Gyori & P. S. Thiagarajan

Authors
  1. R. Ramanathan
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  2. Yan Zhang
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  3. Jun Zhou
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  4. Benjamin M. Gyori
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  5. Weng-Fai Wong
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  6. P. S. Thiagarajan
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Correspondence to R. Ramanathan .

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Editors and Affiliations

  1. University of Oxford, Oxford, United Kingdom

    Alessandro Abate

  2. Faculty of Informatics, Masaryk University, Brno, Czech Republic

    David Šafránek

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Ramanathan, R., Zhang, Y., Zhou, J., Gyori, B.M., Wong, WF., Thiagarajan, P.S. (2015). Parallelized Parameter Estimation of Biological Pathway Models. In: Abate, A., Šafránek, D. (eds) Hybrid Systems Biology. HSB 2015. Lecture Notes in Computer Science(), vol 9271. Springer, Cham. https://doi.org/10.1007/978-3-319-26916-0_3

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  • DOI: https://doi.org/10.1007/978-3-319-26916-0_3

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