We propose to accelerate Hamiltonian and Lagrangian Monte Carlo algorithms by coupling them with Gaussian processes for emulation of the log unnormalised posterior distribution. We provide proofs of ...detailed balance with respect to the exact posterior distribution for these algorithms, and validate the correctness of the samplers’ implementation by Geweke consistency tests. We implement these algorithms in a delayed acceptance (DA) framework, and investigate whether the DA scheme can offer computational gains over the standard algorithms. A comparative evaluation study is carried out to assess the performance of the methods on a series of models described by differential equations, including a real-world application of a 1D fluid-dynamics model of the pulmonary blood circulation. The aim is to identify the algorithm which gives the best trade-off between accuracy and computational efficiency, to be used in nonlinear DE models, which are computationally onerous due to repeated numerical integrations in a Bayesian analysis. Results showed no advantage of the DA scheme over the standard algorithms with respect to several efficiency measures based on the effective sample size for most methods and DE models considered. These gradient-driven algorithms register a high acceptance rate, thus the number of expensive forward model evaluations is not significantly reduced by the first emulator-based stage of DA. Additionally, the Lagrangian Dynamical Monte Carlo and Riemann Manifold Hamiltonian Monte Carlo tended to register the highest efficiency (in terms of effective sample size normalised by the number of forward model evaluations), followed by the Hamiltonian Monte Carlo, and the No U-turn sampler tended to be the least efficient.
The past few decades have witnessed an explosive synergy between physics and the life sciences. In particular, physical modelling in medicine and physiology is a topical research area. The present ...work focuses on parameter inference and uncertainty quantification in a 1D fluid‐dynamics model for quantitative physiology: the pulmonary blood circulation. The practical challenge is the estimation of the patient‐specific biophysical model parameters, which cannot be measured directly. In principle this can be achieved based on a comparison between measured and predicted data. However, predicting data requires solving a system of partial differential equations (PDEs), which usually have no closed‐form solution, and repeated numerical integrations as part of an adaptive estimation procedure are computationally expensive. In the present article, we demonstrate how fast parameter estimation combined with sound uncertainty quantification can be achieved by a combination of statistical emulation and Markov chain Monte Carlo (MCMC) sampling. We compare a range of state‐of‐the‐art MCMC algorithms and emulation strategies, and assess their performance in terms of their accuracy and computational efficiency. The long‐term goal is to develop a method for reliable disease prognostication in real time, and our work is an important step towards an automatic clinical decision support system.
Uncertainty quantification in a complex physiological model of the pulmonary circulation can be made computationally feasible by combining state‐of‐the‐art numerical Bayesian methods with statistical emulation using Gaussian Processes. A comparative assessment in terms of computational efficiency of several novel Bayesian (MCMC) algorithms identifies the most efficient algorithm among several state‐of‐the‐art alternatives, which could potentially be used for clinical decision making in real time. A multivariate classifier is trained to learn ‐ via an iterative algorithm ‐ to automatically handle unknown constraints in parameter space, caused by the violation of the physical model assumptions.
Computational fluid dynamics (CFD) models are emerging tools for assisting in diagnostic assessment of cardiovascular disease. Recent advances in image segmentation have made subject-specific ...modelling of the cardiovascular system a feasible task, which is particularly important in the case of pulmonary hypertension, requiring a combination of invasive and non-invasive procedures for diagnosis. Uncertainty in image segmentation propagates to CFD model predictions, making the quantification of segmentation-induced uncertainty crucial for subject-specific models. This study quantifies the variability of one-dimensional CFD predictions by propagating the uncertainty of network geometry and connectivity to blood pressure and flow predictions. We analyse multiple segmentations of a single, excised mouse lung using different pre-segmentation parameters. A custom algorithm extracts vessel length, vessel radii and network connectivity for each segmented pulmonary network. Probability density functions are computed for vessel radius and length and then sampled to propagate uncertainties to haemodynamic predictions in a fixed network. In addition, we compute the uncertainty of model predictions to changes in network size and connectivity. Results show that variation in network connectivity is a larger contributor to haemodynamic uncertainty than vessel radius and length.
This study uses Bayesian inference to quantify the uncertainty of model parameters and haemodynamic predictions in a one-dimensional pulmonary circulation model based on an integration of mouse ...haemodynamic and micro-computed tomography imaging data. We emphasize an often neglected, though important source of uncertainty: in the mathematical model form due to the discrepancy between the model and the reality, and in the measurements due to the wrong noise model (jointly called 'model mismatch'). We demonstrate that minimizing the mean squared error between the measured and the predicted data (the conventional method) in the presence of model mismatch leads to biased and overly confident parameter estimates and haemodynamic predictions. We show that our proposed method allowing for model mismatch, which we represent with Gaussian processes, corrects the bias. Additionally, we compare a linear and a nonlinear wall model, as well as models with different vessel stiffness relations. We use formal model selection analysis based on the Watanabe Akaike information criterion to select the model that best predicts the pulmonary haemodynamics. Results show that the nonlinear pressure-area relationship with stiffness dependent on the unstressed radius predicts best the data measured in a control mouse.
This study uses a one-dimensional fluid dynamics arterial network model to infer changes in hemodynamic quantities associated with pulmonary hypertension in mice. Data for this study include blood ...flow and pressure measurements from the main pulmonary artery for 7 control mice with normal pulmonary function and 5 mice with hypoxia-induced pulmonary hypertension. Arterial dimensions for a 21-vessel network are extracted from micro-CT images of lungs from a representative control and hypertensive mouse. Each vessel is represented by its length and radius. Fluid dynamic computations are done assuming that the flow is Newtonian, viscous, laminar, and has no swirl. The system of equations is closed by a constitutive equation relating pressure and area, using a linear model derived from stress–strain deformation in the circumferential direction assuming that the arterial walls are thin, and also an empirical nonlinear model. For each dataset, an inflow waveform is extracted from the data, and nominal parameters specifying the outflow boundary conditions are computed from mean values and characteristic timescales extracted from the data. The model is calibrated for each mouse by estimating parameters that minimize the least squares error between measured and computed waveforms. Optimized parameters are compared across the control and the hypertensive groups to characterize vascular remodeling with disease. Results show that pulmonary hypertension is associated with stiffer and less compliant proximal and distal vasculature with augmented wave reflections, and that elastic nonlinearities are insignificant in the hypertensive animal.
Cushing's disease is considered a rare condition characterized by the hypersecretion of the adrenocorticotropic hormone (ACTH) due to a pituitary adenoma that ultimately causes endogenous ...hypercortisolism by stimulating the adrenal glands. The clinical signs suggesting Cushing's disease, such as obesity, moon face, hirsutism, and facial plethora are already present on presentation. Endogenous hypercortisolism is associated with an increased risk of cardiovascular and metabolic manifestations, as well as respiratory disorders, psychiatric complications, osteoporosis and infections, leading to high rates of morbidity and mortality. It is vital to diagnose Cushing's disease as early as possible and to implement a treatment plan to lead to a successful prognosis and a low number of complications. The goal of this article was to review the clinical, diagnostic and treatment aspects of Cushing's disease using the most recent available guidelines.
This study performs parameter inference in a partial differential equations system of pulmonary circulation. We use a fluid dynamics network model that takes selected parameter values and mimics the ...behaviour of the pulmonary haemodynamics under normal physiological and pathological conditions. This is of medical interest as it enables tracking the progression of pulmonary hypertension. We show how we make the fluids model tractable by reducing the parameter dimension from a 55D to a 5D problem. The Delayed Rejection Adaptive Metropolis algorithm, coupled with constraint non‐linear optimization, is successfully used to learn the parameter values and quantify the uncertainty in the parameter estimates. To accommodate for different magnitudes of the parameter values, we introduce an improved parameter scaling technique in the Delayed Rejection Adaptive Metropolis algorithm. Formal convergence diagnostics are employed to check for convergence of the Markov chains. Additionally, we perform model selection using different information criteria, including Watanabe Akaike Information Criteria.
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