arXiv subjects

Dirk Husmeier

Publications and source records attributed to Dirk Husmeier.

10 recordsLinked to original sources

arXiv2023

Computational framework for the generation of one-dimensional vascular models accounting for uncertainty in networks extracted from medical images

Patient-specific computational modeling is a popular, non-invasive method to answer medical questions. Medical images are used to extract geometric domains necessary to create these models, providing a predictive tool for clinicians. However, in vivo imaging is subject to uncertainty, impacting vessel dimensions essential to the mathematical modeling process. While there are numerous programs available to provide information about vessel length, radii, and position, there is currently no exact way to determine and calibrate these features. This raises the question, if we are building patient-specific models based on uncertain measurements, how accurate are the geometries we extract and how can we best represent a patient's vasculature? In this study, we develop a novel framework to determine vessel dimensions using change points. We explore the impact of uncertainty in the network extraction process on hemodynamics by varying vessel dimensions and segmenting the same images multiple times. Our analyses reveal that image segmentation, network size, and minor changes in radius and length have significant impacts on pressure and flow dynamics in rapidly branching structures and tapering vessels. Accordingly, we conclude that it is critical to understand how uncertainty in network geometry propagates to fluid dynamics, especially in clinical applications.

q-bio.TO↗

arXiv2022

Temporal extrapolation of heart wall segmentation in cardiac magnetic resonance images via pixel tracking

In this study, we have tailored a pixel tracking method for temporal extrapolation of the ventricular segmentation masks in cardiac magnetic resonance images. The pixel tracking process starts from the end-diastolic frame of the heart cycle using the available manually segmented images to predict the end-systolic segmentation mask. The superpixels approach is used to divide the raw images into smaller cells and in each time frame, new labels are assigned to the image cells which leads to tracking the movement of the heart wall elements through different frames. The tracked masks at the end of systole are compared with the already available manually segmented masks and dice scores are found to be between 0.81 to 0.84. Considering the fact that the proposed method does not necessarily require a training dataset, it could be an attractive alternative approach to deep learning segmentation methods in scenarios where training data are limited.

eess.IV↗

arXiv2022

The Fully Convolutional Transformer for Medical Image Segmentation

We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Networks to learn effective image representations, and combines them with the ability of Transformers to effectively capture long-term dependencies in its inputs. The FCT is the first fully convolutional Transformer model in medical imaging literature. It processes its input in two stages, where first, it learns to extract long range semantic dependencies from the input image, and then learns to capture hierarchical global attributes from the features. FCT is compact, accurate and robust. Our results show that it outperforms all existing transformer architectures by large margins across multiple medical image segmentation datasets of varying data modalities without the need for any pre-training. FCT outperforms its immediate competitor on the ACDC dataset by 1.3%, on the Synapse dataset by 4.4%, on the Spleen dataset by 1.2% and on ISIC 2017 dataset by 1.1% on the dice metric, with up to five times fewer parameters. Our code, environments and models will be available via GitHub.

eess.IV↗

arXiv2019

Fast Parameter Inference in a Biomechanical Model of the Left Ventricle using Statistical Emulation

A central problem in biomechanical studies of personalised human left ventricular (LV) modelling is estimating the material properties and biophysical parameters from in-vivo clinical measurements in a time frame suitable for use within a clinic. Understanding these properties can provide insight into heart function or dysfunction and help inform personalised medicine. However, finding a solution to the differential equations which mathematically describe the kinematics and dynamics of the myocardium through numerical integration can be computationally expensive. To circumvent this issue, we use the concept of emulation to infer the myocardial properties of a healthy volunteer in a viable clinical time frame using in-vivo magnetic resonance image (MRI) data. Emulation methods avoid computationally expensive simulations from the LV model by replacing the biomechanical model, which is defined in terms of explicit partial differential equations, with a surrogate model inferred from simulations generated before the arrival of a patient, vastly improving computational efficiency at the clinic. We compare and contrast two emulation strategies: (i) emulation of the computational model outputs and (ii) emulation of the loss between the observed patient data and the computational model outputs. These strategies are tested with two different interpolation methods, as well as two different loss functions...

stat.AP↗

arXiv2019

Influence of image segmentation on one-dimensional fluid dynamics predictions in the mouse pulmonary arteries

Computational fluid dynamics (CFD) models are emerging as tools for assisting in diagnostic assessment of cardiovascular disease. Recent advances in image segmentation has made subject-specific modelling of the cardiovascular system a feasible task, which is particularly important in the case of pulmonary hypertension (PH), which requires a combination of invasive and non-invasive procedures for diagnosis. Uncertainty in image segmentation can easily propagate to CFD model predictions, making uncertainty quantification crucial for subject-specific models. This study quantifies the variability of one-dimensional (1D) CFD predictions by propagating the uncertainty of network geometry and connectivity to blood pressure and flow predictions. We analyse multiple segmentations of an image of an excised mouse lung using different pre-segmentation parameters. A custom algorithm extracts vessel length, vessel radii, and network connectivity for each segmented pulmonary network. We quantify uncertainty in geometric features by constructing probability densities for vessel radius and length, and then sample from these distributions and propagate uncertainties of haemodynamic predictions using a 1D CFD model. Results show that variation in network connectivity is a larger contributor to haemodynamic uncertainty than vessel radius and length.

q-bio.QM↗

arXiv2018

On a New Improvement-Based Acquisition Function for Bayesian Optimization

Bayesian optimization (BO) is a popular algorithm for solving challenging optimization tasks. It is designed for problems where the objective function is expensive to evaluate, perhaps not available in exact form, without gradient information and possibly returning noisy values. Different versions of the algorithm vary in the choice of the acquisition function, which recommends the point to query the objective at next. Initially, researchers focused on improvement-based acquisitions, while recently the attention has shifted to more computationally expensive information-theoretical measures. In this paper we present two major contributions to the literature. First, we propose a new improvement-based acquisition function that recommends query points where the improvement is expected to be high with high confidence. The proposed algorithm is evaluated on a large set of benchmark functions from the global optimization literature, where it turns out to perform at least as well as current state-of-the-art acquisition functions, and often better. This suggests that it is a powerful default choice for BO. The novel policy is then compared to widely used global optimization solvers in order to confirm that BO methods reduce the computational costs of the optimization by keeping the number of function evaluations small. The second main contribution represents an application to precision medicine, where the interest lies in the estimation of parameters of a partial differential equations model of the human pulmonary blood circulation system. Once inferred, these parameters can help clinicians in diagnosing a patient with pulmonary hypertension without going through the standard invasive procedure of right heart catheterization, which can lead to side effects and complications (e.g. severe pain, internal bleeding, thrombosis).

stat.ML↗

arXiv2018

Hemodynamic assessment of pulmonary hypertension in mice: a model based analysis of the disease mechanism

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 hypertensive 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 time scales 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.

physics.flu-dyn↗

arXiv2018

MCMC methods for inference in a mathematical model of pulmonary circulation

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 (DRAM) algorithm, coupled with constraint nonlinear 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 DRAM 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.

stat.AP↗

arXiv2017

Improving the identification of antigenic sites in the H1N1 Influenza virus through accounting for the experimental structure in a sparse hierarchical Bayesian model

Understanding how genetic changes allow emerging virus strains to escape the protection afforded by vaccination is vital for the maintenance of effective vaccines. In the current work, we use structural and phylogenetic differences between pairs of virus strains to identify important antigenic sites on the surface of the influenza A(H1N1) virus through the prediction of haemagglutination inhibition (HI) assay, pairwise measures of the antigenic similarity of virus strains. We propose a sparse hierarchical Bayesian model that can deal with the pairwise structure and inherent experimental variability in the H1N1 data through the introduction of latent variables. The latent variables represent the underlying HI assay measurement of any given pair of virus strains and help account for the fact that for any HI assay measurement between the same pair of virus strains, the difference in the viral sequence remains the same. Through accurately representing the structure of the H1N1 data, the model is able to select virus sites which are antigenic, while its latent structure achieves the computational efficiency required to deal with large virus sequence data, as typically available for the influenza virus. In addition to the latent variable model, we also propose a new method, block integrated Widely Applicable Information Criterion (biWAIC), for selecting between competing models. We show how this allows us to effectively select the random effects when used with the proposed model and apply both methods to an A(H1N1) dataset.

stat.AP↗

arXiv2017

Targeting Bayes factors with direct-path non-equilibrium thermodynamic integration

Thermodynamic integration (TI) for computing marginal likelihoods is based on an inverse annealing path from the prior to the posterior distribution. In many cases, the resulting estimator suffers from high variability, which particularly stems from the prior regime. When comparing complex models with differences in a comparatively small number of parameters, intrinsic errors from sampling fluctuations may outweigh the differences in the log marginal likelihood estimates. In the present article, we propose a thermodynamic integration scheme that directly targets the log Bayes factor. The method is based on a modified annealing path between the posterior distributions of the two models compared, which systematically avoids the high variance prior regime. We combine this scheme with the concept of non-equilibrium TI to minimise discretisation errors from numerical integration. Results obtained on Bayesian regression models applied to standard benchmark data, and a complex hierarchical model applied to biopathway inference, demonstrate a significant reduction in estimator variance over state-of-the-art TI methods.

stat.ME↗