Evaluation of optimisation and Bayesian inference methods for reaction rates in atmospheric chemical mechanisms

Constraining reaction rate coefficients is a central challenge in the development of explicit atmospheric chemical mechanisms, particularly for autoxidation systems where many reaction pathways are only indirectly observed through high-resolution mass spectrometry. In this study, we evaluate rate-coefficient optimisation methods for a toy-case autoxidation mechanism using synthetic data with known ground truth. Two complementary approaches are compared: ODE-constrained neural-network optimisation, which provides efficient point estimates of uncertain rate coefficients, and the Markov Chain Monte Carlo (MCMC) approach, which samples the posterior distribution of rate coefficients and quantifies parameter uncertainty. The methods are tested using direct concentration observations and mass-spectral observations under different noise levels. For unperturbed and low-noise synthetic observations, both methods converged towards the known rate coefficients, with the neural-network optimiser providing faster point estimates. Under high-noise conditions (with the signal-to-noise ratio approximately S / N = 1), however, MCMC was substantially more robust in recovering the rate coefficients. The posterior analysis shows that mass-spectral aggregation broadens credible intervals even at low noise, and that high-noise mass spectra can leave many individual reaction rates weakly identifiable. Posterior predictive validation nevertheless shows how broad parameter uncertainty constrained by MCMC remains consistent with accurate reproduction of the observable mass spectrum. These results demonstrate that point-estimation and Bayesian sampling methods provide complementary information: neural-network optimisation is effective for informative data, whereas MCMC is essential for diagnosing uncertainty, non-uniqueness, and identifiability in noisy or aggregated inverse problems.