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bioRxiv · 10.1101/769299

GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation

Tankhilevich, E.·Ish-Horowicz, J.·Hameed, T.·Roesch, E.·Stumpf, M.·He, F.
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Abstract

Approximate Bayesian computation (ABC) is an important framework within which to infer the structure and parameters of a systems biology model. It is especially suitable for biological systems with stochastic and nonlinear dynamics, for which the likelihood functions are intractable. However, the associated computational cost often limits ABC to models that are relatively quick to simulate in practice. We here present a Julia package, GpABC, that implements parameter inference and model selection for deterministic or stochastic models using i) standard rejection ABC or ABC-SMC, or ii) ABC with Gaussian process emulation. The latter significantly reduces the computational cost.\n\nURL: https://github.com/tanhevg/GpABC.jl

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Tankhilevich, E., Ish-Horowicz, J., Hameed, T., Roesch, E., Stumpf, M., He, F.. 2019-09-18. GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation. https://doi.org/10.1101/769299

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