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Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

ABSTRACT: Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

SUBMITTER: Schillings C

PROVIDER: S-EPMC4552555 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

Schillings Claudia C Sunnåker Mikael M Stelling Jörg J Schwab Christoph C

PLoS computational biology 20150828 8

Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative ...[more]

PMID: 26317784

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Project description:The key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dynamics. The model dynamics are crucially dependent on the parameter values which are often estimated from observations. Over the past decade, the interest in parameter and state estimation in models of (bio-) chemical reaction networks (BRNs) grew considerably. The related inference problems are also encountered in many other tasks including model calibration, discrimination, identifiability, and checking, and optimum experiment design, sensitivity analysis, and bifurcation analysis. The aim of this review paper is to examine the developments in literature to understand what BRN models are commonly used, and for what inference tasks and inference methods. The initial collection of about 700 documents concerning estimation problems in BRNs excluding books and textbooks in computational biology and chemistry were screened to select over 270 research papers and 20 graduate research theses. The paper selection was facilitated by text mining scripts to automate the search for relevant keywords and terms. The outcomes are presented in tables revealing the levels of interest in different inference tasks and methods for given models in the literature as well as the research trends are uncovered. Our findings indicate that many combinations of models, tasks and methods are still relatively unexplored, and there are many new research opportunities to explore combinations that have not been considered-perhaps for good reasons. The most common models of BRNs in literature involve differential equations, Markov processes, mass action kinetics, and state space representations whereas the most common tasks are the parameter inference and model identification. The most common methods in literature are Bayesian analysis, Monte Carlo sampling strategies, and model fitting to data using evolutionary algorithms. The new research problems which cannot be directly deduced from the text mining data are also discussed.

Dataset Information

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

Publications

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

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