Identifiability analysis for stochastic differential equation models in systems biology

AP Browning, DJ Warne, K Burrage… - Journal of the …, 2020 - royalsocietypublishing.org
Mathematical models are routinely calibrated to experimental data, with goals ranging from
building predictive models to quantifying parameters that cannot be measured. Whether or …

Parameter estimation and uncertainty quantification using information geometry

JA Sharp, AP Browning, K Burrage… - Journal of the Royal …, 2022 - royalsocietypublishing.org
In this work, we:(i) review likelihood-based inference for parameter estimation and the
construction of confidence regions; and (ii) explore the use of techniques from information …

Multifidelity multilevel Monte Carlo to accelerate approximate Bayesian parameter inference for partially observed stochastic processes

DJ Warne, TP Prescott, RE Baker… - Journal of Computational …, 2022 - Elsevier
Abstract Models of stochastic processes are widely used in almost all fields of science.
Theory validation, parameter estimation, and prediction all require model calibration and …

Generalised likelihood profiles for models with intractable likelihoods

DJ Warne, OJ Maclaren, EJ Carr, MJ Simpson… - Statistics and …, 2024 - Springer
Likelihood profiling is an efficient and powerful frequentist approach for parameter
estimation, uncertainty quantification and practical identifiablity analysis. Unfortunately …

Bayesian model calibration for diblock copolymer thin film self-assembly using power spectrum of microscopy data and machine learning surrogate

L Cao, K Wu, JT Oden, P Chen, O Ghattas - Computer Methods in Applied …, 2023 - Elsevier
Identifying parameters of computational models from experimental data, or model
calibration, is fundamental for assessing and improving the predictability and reliability of …

Rapid Bayesian inference for expensive stochastic models

DJ Warne, RE Baker, MJ Simpson - Journal of Computational and …, 2022 - Taylor & Francis
Almost all fields of science rely upon statistical inference to estimate unknown parameters in
theoretical and computational models. While the performance of modern computer hardware …

An automatic adaptive method to combine summary statistics in approximate Bayesian computation

JU Harrison, RE Baker - PloS one, 2020 - journals.plos.org
To infer the parameters of mechanistic models with intractable likelihoods, techniques such
as approximate Bayesian computation (ABC) are increasingly being adopted. One of the …

Likelihood-free nested sampling for parameter inference of biochemical reaction networks

J Mikelson, M Khammash - PLoS computational biology, 2020 - journals.plos.org
The development of mechanistic models of biological systems is a central part of Systems
Biology. One major challenge in developing these models is the accurate inference of model …

Mathematical modelling and uncertainty quantification for analysis of biphasic coral reef recovery patterns

DJ Warne, K Crossman, GEM Heron, JA Sharp… - arXiv preprint arXiv …, 2024 - arxiv.org
Coral reefs are increasingly subjected to major disturbances threatening the health of
marine ecosystems. Substantial research underway to develop intervention strategies that …

Fitting individual-based models of spatial population dynamics to long-term monitoring data

AK Malchow, G Fandos, UG Kormann, MU Grüebler… - bioRxiv, 2022 - biorxiv.org
Generating spatial predictions of species distribution is a central task for research and
policy. Currently, correlative species distribution models (cSDMs) are among the most …