Brute force meets Bruno force in parameter optimisation: introduction of novel constraints for parameter accuracy improvement by symbolic computation.
Recent remarkable advances in computer performance have enabled us to estimate parameter values by the huge power of numerical computation, the so-called 'Brute force', resulting in the high-speed simultaneous estimation of a large number of parameter values. However, these advancements have not been fully utilised to improve the accuracy of parameter estimation. Here the authors review a novel method for parameter estimation using symbolic computation power, 'Bruno force', named after Bruno Buchberger, who found the Gröbner base. In the method, the objective functions combining the symbolic computation techniques are formulated. First, the authors utilise a symbolic computation technique, differential elimination, which symbolically reduces an equivalent system of differential equations to a system in a given model. Second, since its equivalent system is frequently composed of large equations, the system is further simplified by another symbolic computation. The performance of the authors' method for parameter accuracy improvement is illustrated by two representative models in biology, a simple cascade model and a negative feedback model in comparison with the previous numerical methods. Finally, the limits and extensions of the authors' method are discussed, in terms of the possible power of 'Bruno force' for the development of a new horizon in parameter estimation.
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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Nakatsui
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Horimoto
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Lemaire
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Ürgüplü
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Sedoglavic
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Boulier
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008432:Mathematical Computing; D008962:Models, Theoretical; D009716:Numerical Analysis, Computer-Assisted; D011381:Programming Languages; D012016:Reference Values; D012984:Software; D049490:Systems Biology