Code generator for distributed parameter biological model simulation with PDE numerical schemes

Florencio Rusty Punzalan, Yoshiharu Yamashita, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, Akira Amano

研究成果: 著書/レポートタイプへの貢献会議での発言

1 引用 (Scopus)

抄録

The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code.

元の言語英語
ホスト出版物のタイトル2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
ページ1494-1497
ページ数4
DOI
出版物ステータス出版済み - 10 31 2013
イベント2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 - Osaka, 日本
継続期間: 7 3 20137 7 2013

出版物シリーズ

名前Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
ISSN(印刷物)1557-170X

その他

その他2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013
日本
Osaka
期間7/3/137/7/13

Fingerprint

Biological Models
Partial differential equations
Pharmacokinetics
Boundary conditions
Tissue

All Science Journal Classification (ASJC) codes

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics

これを引用

Punzalan, F. R., Yamashita, Y., Kawabata, M., Shimayoshi, T., Kuwabara, H., Kunieda, Y., & Amano, A. (2013). Code generator for distributed parameter biological model simulation with PDE numerical schemes. : 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013 (pp. 1494-1497). [6609795] (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/EMBC.2013.6609795

Code generator for distributed parameter biological model simulation with PDE numerical schemes. / Punzalan, Florencio Rusty; Yamashita, Yoshiharu; Kawabata, Masanari; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi; Amano, Akira.

2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. 2013. p. 1494-1497 6609795 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

研究成果: 著書/レポートタイプへの貢献会議での発言

Punzalan, FR, Yamashita, Y, Kawabata, M, Shimayoshi, T, Kuwabara, H, Kunieda, Y & Amano, A 2013, Code generator for distributed parameter biological model simulation with PDE numerical schemes. : 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013., 6609795, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, pp. 1494-1497, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013, Osaka, 日本, 7/3/13. https://doi.org/10.1109/EMBC.2013.6609795
Punzalan FR, Yamashita Y, Kawabata M, Shimayoshi T, Kuwabara H, Kunieda Y その他. Code generator for distributed parameter biological model simulation with PDE numerical schemes. : 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. 2013. p. 1494-1497. 6609795. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS). https://doi.org/10.1109/EMBC.2013.6609795
Punzalan, Florencio Rusty ; Yamashita, Yoshiharu ; Kawabata, Masanari ; Shimayoshi, Takao ; Kuwabara, Hiroaki ; Kunieda, Yoshitoshi ; Amano, Akira. / Code generator for distributed parameter biological model simulation with PDE numerical schemes. 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. 2013. pp. 1494-1497 (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).
@inproceedings{459a1a1930104e5299b4e1ba7612388f,
title = "Code generator for distributed parameter biological model simulation with PDE numerical schemes",
abstract = "The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code.",
author = "Punzalan, {Florencio Rusty} and Yoshiharu Yamashita and Masanari Kawabata and Takao Shimayoshi and Hiroaki Kuwabara and Yoshitoshi Kunieda and Akira Amano",
year = "2013",
month = "10",
day = "31",
doi = "10.1109/EMBC.2013.6609795",
language = "English",
isbn = "9781457702167",
series = "Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS",
pages = "1494--1497",
booktitle = "2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013",

}

TY - GEN

T1 - Code generator for distributed parameter biological model simulation with PDE numerical schemes

AU - Punzalan, Florencio Rusty

AU - Yamashita, Yoshiharu

AU - Kawabata, Masanari

AU - Shimayoshi, Takao

AU - Kuwabara, Hiroaki

AU - Kunieda, Yoshitoshi

AU - Amano, Akira

PY - 2013/10/31

Y1 - 2013/10/31

N2 - The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code.

AB - The physiological simulation at the tissue and organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and in cases like pharmacokinetics, distributed parameters add to the complexity of the PDE solution. These factors make most PDE solutions and their corresponding program codes tailored for specific problems. We propose a general approach for handling PDEs in computational models using a replacement scheme for discretization. This method allows for the handling of the different PDE types. The replacement scheme involves substituting all the partial differential terms with the numerical solution equations. Once the model equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to determine the simulation loop structure and generate the program code.

UR - http://www.scopus.com/inward/record.url?scp=84886503101&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84886503101&partnerID=8YFLogxK

U2 - 10.1109/EMBC.2013.6609795

DO - 10.1109/EMBC.2013.6609795

M3 - Conference contribution

SN - 9781457702167

T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

SP - 1494

EP - 1497

BT - 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013

ER -