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Inference in complex biological systems with Gaussian processes and parallel tempering

Gruppo Istituto Poligrafico Europeo SRL
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  • Biology
  • Computer Science
  • Logic
  • Mathematics


Parameter inference in mathematical models of complex biological systems, expressed as coupled ordinary differential equations (ODEs), is a challenging problem. These depend on kinetic parameters, which cannot all be measured and have to be ascertained a different way. However, the computational costs associated with repeatedly solving the ODEs are often staggering, making many techniques impractical. Therefore, aimed at reducing this cost, new concepts using gradient matching have been proposed. This paper combines current adaptive gradient matching approaches, using Gaussian processes, with a parallel tempering scheme, in order to compare 2 different paradigms using the same nonlinear regression method. We use 2 ODE systems to assess our technique, showing an improvement over the recent method in Calderhead et al. (2008).

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