ISAP-MATLAB Package for Sensitivity Analysis of High-Dimensional Stochastic Chemical Networks
- Univ. of Massachusetts, Amherst, MA (United States)
Stochastic simulation and modeling play an important role to elucidate the fundamental mechanisms in complex biochemical networks. The parametric sensitivity analysis of reaction networks becomes a powerful mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. However, due to overwhelming computational cost, parametric sensitivity analysis is a extremely challenging problem for stochastic models with a high-dimensional parameter space and for which existing approaches are very slow. Here we present an information-theoretic sensitivity analysis in path-space (ISAP) MATLAB package that simulates stochastic processes with various algorithms and most importantly implements a gradient-free approach to quantify the parameter sensitivities of stochastic chemical reaction network dynamics using the pathwise Fisher information matrix (PFIM; Pantazis, Katsoulakis, and Vlachos 2013). The sparse, block-diagonal structure of the PFIM makes its computational complexity scale linearly with the number of model parameters. As a result of the gradientfree and the sparse nature of the PFIM, it is highly suitable for the sensitivity analysis of stochastic reaction networks with a very large number of model parameters, which are typical in the modeling and simulation of complex biochemical phenomena. Finally, the PFIM provides a fast sensitivity screening method (Arampatzis, Katsoulakis, and Pantazis 2015) which allows it to be combined with any existing sensitivity analysis software.
- Research Organization:
- Univ. of Massachusetts, Amherst, MA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); Defense Advanced Research Projects Agency (DARPA) (United States)
- Grant/Contract Number:
- SC0010723; W911NF1520122
- OSTI ID:
- 1509830
- Journal Information:
- Journal of Statistical Software, Vol. 85, Issue 3; ISSN 1548-7660
- Publisher:
- Foundation for Open Access StatisticsCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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