Implementation of Sequential Importance Sampling in GPGPU

The estimation of many unknown parameters is carried out using a simplified Sequential Importance Sampling (SIS) algorithm which is implemented in a graphic processing unit (GPU). The aim of the present work is to show technical points to bring out the performance of GPU. Using the implemented code, two numerical experiments are demonstrated. In the first demonstration, it is shown that a parameter estimation involving 109 Monte Carlo samples is completed within eight hours. In the second demonstration, accuracy-guaranteed evaluation of the likelihood is carried out.

[1]  N. Gordon,et al.  Novel approach to nonlinear/non-Gaussian Bayesian state estimation , 1993 .

[2]  Masao Nagasaki,et al.  Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. , 2006, Genome informatics. International Conference on Genome Informatics.

[3]  Hiroshi Matsuno,et al.  A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals , 2006, APBC.

[4]  Shuhei Kimura,et al.  Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm , 2005, Bioinform..

[5]  G. Kitagawa Monte Carlo Filter and Smoother for Non-Gaussian Nonlinear State Space Models , 1996 .

[6]  Masao Nagasaki,et al.  Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing , 2009, Pacific Symposium on Biocomputing.

[7]  Hideaki Kawano,et al.  Tracking of Multiple Moving Objects in Dynamic Image of Omni-Directional Camera Using PHD Filter , 2008, J. Adv. Comput. Intell. Intell. Informatics.

[8]  Petar M. Djuric,et al.  Resampling Algorithms for Particle Filters: A Computational Complexity Perspective , 2004, EURASIP J. Adv. Signal Process..

[9]  Sumio Sugano,et al.  A transcription factor response element for gene expression during circadian night , 2002, Nature.

[10]  Masaru Tomita,et al.  Dynamic modeling of genetic networks using genetic algorithm and S-system , 2003, Bioinform..

[11]  Jun S. Liu,et al.  Monte Carlo strategies in scientific computing , 2001 .

[12]  Masao Nagasaki,et al.  Bayesian learning of biological pathways on genomic data assimilation , 2008, Bioinform..

[13]  G. Kitagawa Smoothness priors analysis of time series , 1996 .

[14]  Petar M. Djuric,et al.  Resampling algorithms and architectures for distributed particle filters , 2005, IEEE Transactions on Signal Processing.