Parameter estimation for biochemical reaction networks using Wasserstein distances

DOI10.1088/1751-8121/AB5877MaRDI QIDQ5870307zbMATH OpenOpenAlexFDO

Authors Kaan Öcal, Ramon Grima, Guido Sanguinetti

Publication date 9 January 2023

Published in Journal of Physics A: Mathematical and Theoretical (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1907.07986

zbMATH Keywords

Bayesian optimizationchemical master equationparameter estimationWasserstein distance

Mathematics Subject Classification ID

Quantum theory (81-XX) Statistical mechanics, structure of matter (82-XX)

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Cites work

• A derivative matching approach to moment closure for the stochastic logistic model
• Approximation and inference methods for stochastic biochemical kinetics -- a tutorial review
• Bayesian optimization for likelihood-free inference of simulator-based statistical models
• Convergence properties of the expected improvement algorithm with fixed mean and covariance functions
• Gaussian processes for machine learning.
• Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks
• Optimal Transport
• Stochastic processes in physics and chemistry.

Cited in

(10)

• Generalized method of moments for stochastic reaction networks in equilibrium
• Bayesian learning of effective chemical master equations in crowded intracellular conditions
• A data-driven method to learn a jump diffusion process from aggregate biological gene expression data
• Parameter reconstruction for biochemical networks using interval analysis
• Parameter estimation for metabolic networks with two stage Bregman regularization homotopy inversion algorithm
• Statistics of nascent and mature RNA fluctuations in a stochastic model of transcriptional initiation, elongation, pausing, and termination
• Parameter estimation for stochastic models of biochemical reactions.
• Parameter estimation for stochastic hybrid models of biochemical reaction networks
• Identifiability of Chemical Reaction Networks with Intrinsic and Extrinsic Noise from Stationary Distributions
• Bayesian optimization over the probability simplex

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