Pre-processing for approximate Bayesian computation in image analysis

Most of the existing algorithms for approximate Bayesian computation (ABC) assume that it is feasible to simulate pseudo-data from the model at each iteration. However, the computational cost of these simulations can be prohibitive for high dimensional data. An important example is the Potts model, which is commonly used in image analysis. Images encountered in real world applications can have millions of pixels, therefore scalability is a major concern. We apply ABC with a synthetic likelihood to the hidden Potts model with additive Gaussian noise. Using a pre-processing step, we fit a binding function to model the relationship between the model parameters and the synthetic likelihood parameters. Our numerical experiments demonstrate that the precomputed binding function dramatically improves the scalability of ABC, reducing the average runtime required for model fitting from 71 hours to only 7 minutes. We also illustrate the method by estimating the smoothing parameter for remotely sensed satellite imagery. Without precomputation, Bayesian inference is impractical for datasets of that scale.Comment: 5th IMS-ISBA joint meeting (MCMSki IV

Bayesian quantification for coherent anti-Stokes Raman scattering spectroscopy

We propose a Bayesian statistical model for analyzing coherent anti-Stokes Raman scattering (CARS) spectra. Our quantitative analysis includes statistical estimation of constituent line-shape parameters, underlying Raman signal, error-corrected CARS spectrum, and the measured CARS spectrum. As such, this work enables extensive uncertainty quantification in the context of CARS spectroscopy. Furthermore, we present an unsupervised method for improving spectral resolution of Raman-like spectra requiring little to no \textit{a priori} information. Finally, the recently-proposed wavelet prism method for correcting the experimental artefacts in CARS is enhanced by using interpolation techniques for wavelets. The method is validated using CARS spectra of adenosine mono-, di-, and triphosphate in water, as well as, equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose

Bayesian modelling and quantification of Raman spectroscopy

Raman spectroscopy can be used to identify molecules such as DNA by the characteristic scattering of light from a laser. It is sensitive at very low concentrations and can accurately quantify the amount of a given molecule in a sample. The presence of a large, nonuniform background presents a major challenge to analysis of these spectra. To overcome this challenge, we introduce a sequential Monte Carlo (SMC) algorithm to separate each observed spectrum into a series of peaks plus a smoothly-varying baseline, corrupted by additive white noise. The peaks are modelled as Lorentzian, Gaussian, or pseudo-Voigt functions, while the baseline is estimated using a penalised cubic spline. This latent continuous representation accounts for differences in resolution between measurements. The posterior distribution can be incrementally updated as more data becomes available, resulting in a scalable algorithm that is robust to local maxima. By incorporating this representation in a Bayesian hierarchical regression model, we can quantify the relationship between molecular concentration and peak intensity, thereby providing an improved estimate of the limit of detection, which is of major importance to analytical chemistry

Theoretical open-loop model of respiratory mechanics in the extremely preterm infant

Non-invasive ventilation is increasingly used for respiratory support in preterm infants, and is associated with a lower risk of chronic lung disease. However, this mode is often not successful in the extremely preterm infant in part due to their markedly increased chest wall compliance that does not provide enough structure against which the forces of inhalation can generate sufficient pressure. To address the continued challenge of studying treatments in this fragile population, we developed a nonlinear lumped-parameter model of respiratory system mechanics of the extremely preterm infant that incorporates nonlinear lung and chest wall compliances and lung volume parameters tuned to this population. In particular we developed a novel empirical representation of progressive volume loss based on compensatory alveolar pressure increase resulting from collapsed alveoli. The model demonstrates increased rate of volume loss related to high chest wall compliance, and simulates laryngeal braking for elevation of end-expiratory lung volume and constant positive airway pressure (CPAP). The model predicts that low chest wall compliance (chest stiffening) in addition to laryngeal braking and CPAP enhance breathing and delay lung volume loss. These results motivate future data collection strategies and investigation into treatments for chest wall stiffening.Comment: 22 pages, 5 figure

Optimising the impact of a multi-intervention outreach programme on progression to Higher Education:recommendations for future practice and research

Despite substantial financial commitment to widening participation activities internationally, robust evidence demonstrating ‘what works’ in facilitating disadvantaged learners to access Higher Education (HE) is remarkably sparse. Much effort has been directed at measuring immediate post-intervention changes in the aspirations, attitudes and behaviours thought to drive access to HE, rather than actual access itself. Here, we present an innovative quasi-experimental study of a multi-intervention outreach programme (UniConnect) consisting of 1,386 learners from the Aimhigher West Midlands database whose HE application results were known, while controlling for multiple variables, including estimates of deprivation. The results showed that any engagement with UniConnect, no matter how limited, was associated with an improved chance of achieving a place in HE, but the type of engagement, the extent of engagement and the combination of types of engagement all mattered. The more learners engaged with UniConnect, the greater were their chances of HE acceptance, but the benefit of each additional engagement beyond five or six engagements was small. To our knowledge, these findings are the first to indicate the number, type and combinations of interventions that are most effective in supporting progression to HE. These results therefore have important implications for future practice, enabling funding for such work to be used for optimal impact. Furthermore, we found large differences in success between schools, even when controlling for several other variables; a finding which has important implications for future evaluation research

Evaluation of access and participation plans: Understanding what works

We present an analysis of two current policy options to improve evaluation of access and participation work: independent external evaluation vs. in-house evaluation. Evaluation of access and participation work needs to be well-conducted, objective and widely disseminated, regardless of the outcome. Independent external evaluation is likely to provide objectivity and the right skills, but providing effective and timely feedback may be prohibitively expensive. Without support, in-house practitioner teams risk lack of objectivity and skills. Neither external nor in-house evaluation is likely to solve issues of publication bias; usage of open science principles could help. Working with academics and other experts internal to the institution could provide the skills to work well under the open science framework. Working as a sector to avoid duplication of effort is likely to get us further, faster

Evaluation of access and participation plans: Understanding what works

We present an analysis of two current policy options to improve evaluation of access and participation work: independent external evaluation vs. in-house evaluation. Evaluation of access and participation work needs to be well-conducted, objective and widely disseminated, regardless of the outcome. Independent external evaluation is likely to provide objectivity and the right skills, but providing effective and timely feedback may be prohibitively expensive. Without support, in-house practitioner teams risk lack of objectivity and skills. Neither external nor in-house evaluation is likely to solve issues of publication bias; usage of open science principles could help. Working with academics and other experts internal to the institution could provide the skills to work well under the open science framework. Working as a sector to avoid duplication of effort is likely to get us further, faster

Bilateral capital physeal dysplasia in a ferret (Mustela putorius furo) treated with femoral head ostectomy

A six-month-old male entire ferret presented for investigation of atraumatic bilateral pelvic limb lameness. Radiographic and subsequent histopathological assessment of the femoral heads following bilateral femoral head ostectomy was consistent with capital physeal dysplasia. At six-months postoperatively, pelvic limb function was deemed normal with no evidence of ongoing discomfort. This is the first report of capital physeal dysplasia in the ferret and femoral head ostectomy appears to be an appropriate intervention in the management of these patients

The water cycle and regolith-atmosphere interaction at Gale crater, Mars

We perform mesoscale simulations of the water cycle in a region around Gale crater, including the diffusion of water vapour in and out of the regolith, and compare our results with measurements from the REMS instrument on board the Curiosity rover. Simulations are performed at three times of year, and show that diffusion in and out of the regolith and adsorption/desorption needs to be taken into account in order to match the diurnal variation of relative humidity measured by REMS. During the evening and night, local downslope flows transport water vapour down the walls of Gale crater. When including regolith-atmosphere interaction, the amount of vapour reaching the crater floor is reduced (by factors of 2–3 depending on season) due to vapour diffusing into the regolith along the crater walls. The transport of vapour into Gale crater is also affected by the regional katabatic flow over the dichotomy boundary, with the largest flux of vapour into the regolith initially occurring on the northern crater wall, and moving to the southern wall by early morning. Upslope winds during the day transport vapour desorbing and mixing out of the regolith up crater walls, where it can then be transported a few hundred metres into the atmosphere at convergence boundaries. Regolith-atmosphere interaction limits the formation of surface ice by reducing water vapour abundances in the lower atmosphere, though in some seasons ice can still form in the early morning on eastern crater walls. Subsurface ice amounts are small in all seasons, with ice only existing in the upper few millimetres of regolith during the night. The results at Gale crater are representative of the behaviour at other craters in the mesoscale domain