scholarly journals Functional regression approximate Bayesian computation for Gaussian process density estimation

2016 ◽  
Vol 103 ◽  
pp. 229-241 ◽  
Author(s):  
G.S. Rodrigues ◽  
David J. Nott ◽  
S.A. Sisson
2019 ◽  
Author(s):  
Evgeny Tankhilevich ◽  
Jonathan Ish-Horowicz ◽  
Tara Hameed ◽  
Elisabeth Roesch ◽  
Istvan Kleijn ◽  
...  

ABSTRACTApproximate 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.URL: https://github.com/tanhevg/GpABC.jl


Stat ◽  
2013 ◽  
Vol 2 (1) ◽  
pp. 34-48 ◽  
Author(s):  
Yanan Fan ◽  
David J. Nott ◽  
Scott A. Sisson

2020 ◽  
Vol 36 (10) ◽  
pp. 3286-3287 ◽  
Author(s):  
Evgeny Tankhilevich ◽  
Jonathan Ish-Horowicz ◽  
Tara Hameed ◽  
Elisabeth Roesch ◽  
Istvan Kleijn ◽  
...  

Abstract Motivation 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. Results 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 sequential Monte Carlo ABC or (ii) ABC with Gaussian process emulation. The latter significantly reduces the computational cost. Availability and implementation https://github.com/tanhevg/GpABC.jl.


Author(s):  
Cecilia Viscardi ◽  
Michele Boreale ◽  
Fabio Corradi

AbstractWe consider the problem of sample degeneracy in Approximate Bayesian Computation. It arises when proposed values of the parameters, once given as input to the generative model, rarely lead to simulations resembling the observed data and are hence discarded. Such “poor” parameter proposals do not contribute at all to the representation of the parameter’s posterior distribution. This leads to a very large number of required simulations and/or a waste of computational resources, as well as to distortions in the computed posterior distribution. To mitigate this problem, we propose an algorithm, referred to as the Large Deviations Weighted Approximate Bayesian Computation algorithm, where, via Sanov’s Theorem, strictly positive weights are computed for all proposed parameters, thus avoiding the rejection step altogether. In order to derive a computable asymptotic approximation from Sanov’s result, we adopt the information theoretic “method of types” formulation of the method of Large Deviations, thus restricting our attention to models for i.i.d. discrete random variables. Finally, we experimentally evaluate our method through a proof-of-concept implementation.


2021 ◽  
Vol 62 (2) ◽  
Author(s):  
Jason D. Christopher ◽  
Olga A. Doronina ◽  
Dan Petrykowski ◽  
Torrey R. S. Hayden ◽  
Caelan Lapointe ◽  
...  

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