Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing

Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, Tomoyuki Higuchi

研究成果: Conference contribution

26 被引用数 (Scopus)


The aim of this paper is to demonstrate the potential power of large-scale particle filtering for the parameter estimations of in silico biological pathways where time course measurements of biochemical reactions are observable. The method of particle filtering has been a popular technique in the field of statistical science, which approximates posterior distributions of model parameters of dynamic system by using sequentially-generated Monte Carlo samples. In order to apply the particle filtering to system identifications of biological pathways, it is often needed to explore the posterior distributions which are defined over an exceedingly high-dimensional parameter space. It is then essential to use a fairly large amount of Monte Carlo samples to obtain an approximation with a high-degree of accuracy. In this paper, we address some implementation issues on large-scale particle filtering, and then, indicate the importance of large-scale computing for parameter learning of in silico biological pathways. We have tested the ability of the particle filtering with 108 Monte Carlo samples on the transcription circuit of circadian clock that contains 45 unknown kinetic parameters. The proposed approach could reveal clearly the shape of the posterior distributions over the 45 dimensional parameter space.

ホスト出版物のタイトルPacific Symposium on Biocomputing 2009, PSB 2009
出版ステータスPublished - 2009 12 1
イベント14th Pacific Symposium on Biocomputing, PSB 2009 - Kohala Coast, HI, United States
継続期間: 2009 1 52009 1 9


Other14th Pacific Symposium on Biocomputing, PSB 2009
CountryUnited States
CityKohala Coast, HI

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

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