TY - JOUR
T1 - Parameter estimation of biological pathways using data assimilation and model checking
AU - Li, Chen
AU - Kuroyanagi, Keisuke
AU - Nagasaki, Masao
AU - Miyano, Satoru
PY - 2011/12/1
Y1 - 2011/12/1
N2 - This paper presents a novel method to estimate kinetic parameter of biological pathways by using observed time-series data and other knowledge that cannot be formulated in the form of time-series data. Our method utilizes data assimilation (DA) framework and model checking (MC) technique, with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). Proposed method is applied to an HFPNe model underlying circadian rhythm in mouse. We first translate 23 rules of biological knowledge with temporal logic for the model checking, which are not described in the time-series data. Next, we employ particle filter often applied to DA for our estimation procedure. Each particle checks whether its simulation result satisfies the rules or not, and the result of the checking is used for its resampling step. Our simulation results show that proposed method is faster and more accurate than previous method.
AB - This paper presents a novel method to estimate kinetic parameter of biological pathways by using observed time-series data and other knowledge that cannot be formulated in the form of time-series data. Our method utilizes data assimilation (DA) framework and model checking (MC) technique, with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). Proposed method is applied to an HFPNe model underlying circadian rhythm in mouse. We first translate 23 rules of biological knowledge with temporal logic for the model checking, which are not described in the time-series data. Next, we employ particle filter often applied to DA for our estimation procedure. Each particle checks whether its simulation result satisfies the rules or not, and the result of the checking is used for its resampling step. Our simulation results show that proposed method is faster and more accurate than previous method.
KW - Data assimilation
KW - Hybrid functional petri net with extension
KW - Model checking
KW - Parameter estimation
KW - Particle filter
KW - Temporal logic
UR - http://www.scopus.com/inward/record.url?scp=84890354986&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84890354986&partnerID=8YFLogxK
M3 - Conference article
AN - SCOPUS:84890354986
VL - 724
SP - 53
EP - 70
JO - CEUR Workshop Proceedings
JF - CEUR Workshop Proceedings
SN - 1613-0073
T2 - 2nd International Workshop on Biological Processes and Petri Nets, BioPPN 2011
Y2 - 20 June 2010 through 20 June 2010
ER -