On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

被引:21
作者
Andreychenko, Aleksandr [1 ]
Crouzen, Pepijn [1 ]
Mikeev, Linar [1 ]
Wolf, Verena [1 ]
机构
[1] Saarland Univ, Saarbrucken, Germany
来源
ELECTRONIC PROCEEDINGS IN THEORETICAL COMPUTER SCIENCE | 2011年 / 57期
关键词
D O I
10.4204/EPTCS.57.1
中图分类号
TP301 [理论、方法];
学科分类号
081202 ;
摘要
This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an under-approximation of the original, infinite system. We present experimental results to show the applicability of our technique.
引用
收藏
页码:1 / 15
页数:15
相关论文
共 16 条
[1]  
Arkin A, 1998, GENETICS, V149, P1633
[2]   On the Numerical Analysis of Inhomogeneous Continuous-Time Markov Chains [J].
Arns, M. ;
Buchholz, P. ;
Panchenko, A. .
INFORMS JOURNAL ON COMPUTING, 2010, 22 (03) :416-432
[3]  
Ciardo G., 1995, DISCRETE TIME MARKOV
[4]   Fast Adaptive Uniformization of the Chemical Master Equation [J].
Didier, Frederic ;
Henzinger, Thomas A. ;
Mateescu, Maria ;
Wolf, Verena .
2009 INTERNATIONAL WORKSHOP ON HIGH PERFORMANCE COMPUTATIONAL SYSTEMS BIOLOGY, PROCEEDINGS, 2009, :118-+
[5]   Computing the moments of high dimensional solutions of the master equation [J].
Engblom, Stefan .
APPLIED MATHEMATICS AND COMPUTATION, 2006, 180 (02) :498-515
[6]   GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) :403-434
[7]   EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF PHYSICAL CHEMISTRY, 1977, 81 (25) :2340-2361
[8]  
Grassmann W. K., 1990, HDB OPERATIONS RES M, V2, P199, DOI [10.1016/S0927-0507(05)80169-0, DOI 10.1016/S0927-0507(05)80169-0]
[9]   Markoff Chains as an Aid in the Study of Markoff Processes [J].
Jensen, Arne .
SKANDINAVISK AKTUARIETIDSKRIFT, 1953, 36 (1-2) :87-91
[10]   MARKOV POPULATION PROCESSES [J].
KINGMAN, JFC .
JOURNAL OF APPLIED PROBABILITY, 1969, 6 (01) :1-&