Optimal Bayesian experimental design for models with intractable likelihoods using indirect inference applied to biological process models

This paper addresses the problem of determining optimal designs for biological process models with intractable likelihoods, with the goal of parameter inference. The Bayesian approach is to choose a design that maximises the mean of a utility, and the utility is a function of the posterior distribution. Therefore, its estimation requires likelihood evaluations. However, many problems in experimental design involve models with intractable likelihoods, that is, likelihoods that are neither analytic nor can be computed in a reasonable amount of time. We propose a novel solution using indirect inference (II), a well established method in the literature, and the Markov chain Monte Carlo (MCMC) algorithm of Müller et al. (2004). Indirect inference employs an auxiliary model with a tractable likelihood in conjunction with the generative model, the assumed true model of interest, which has an intractable likelihood. Our approach is to estimate a map between the parameters of the generative and auxiliary models, using simulations from the generative model. An II posterior distribution is formed to expedite utility estimation. We also present a modification to the utility that allows the Müller algorithm to sample from a substantially sharpened utility surface, with little computational effort. Unlike competing methods, the II approach can handle complex design problems for models with intractable likelihoods on a continuous design space, with possible extension to many observations. The methodology is demonstrated using two stochastic models; a simple tractable death process used to validate the approach, and a motivating stochastic model for the population evolution of macroparasites.

Creating flexible mappings between building information models and cost information

During the early design stages of construction projects, accurate and timely cost feedback is critical to design decision making. This is particularly challenging for cost estimators, as they must quickly and accurately estimate the cost of the building when the design is still incomplete and evolving. State-of-the-art software tools typically use a rule-based approach to generate detailed quantities from the design details present in a building model and relate them to the cost items in a cost estimating database. In this paper, we propose a generic approach for creating and maintaining a cost estimate using flexible mappings between a building model and a cost estimate. The approach uses queries on the building design that are used to populate views, and each view is then associated with one or more cost items. The benefit of this approach is that the flexibility of modern query languages allows the estimator to encode a broad variety of relationships between the design and estimate. It also avoids the use of a common standard to which both designers and estimators must conform, allowing the estimator added flexibility and functionality to their work.

Compressed sensing using hidden Markov models with application to vision based aircraft tracking

This paper investigates compressed sensing using hidden Markov models (HMMs) and hence provides an extension of recent single frame, bounded error sparse decoding problems into a class of sparse estimation problems containing both temporal evolution and stochastic aspects. This paper presents two optimal estimators for compressed HMMs. The impact of measurement compression on HMM filtering performance is experimentally examined in the context of an important image based aircraft target tracking application. Surprisingly, tracking of dim small-sized targets (as small as 5-10 pixels, with local detectability/SNR as low as − 1.05 dB) was only mildly impacted by compressed sensing down to 15% of original image size.

Models of social media adoption in emergency management organisations

Recent natural disasters such as the Haitian earthquake 2011, the South East Queensland floods 2011, the Japanese earthquake and tsunami 2011 and Hurricane Sandy in the United States of America in 2012, have seen social media platforms changing the face of emergency management communications, not only in times of crisis and also during business-as-usual operations. With social media being such an important and powerful communication tool, especially for emergency management organisations, the question arises as to whether the use of social media in these organisations emerged by considered strategic design or more as a reactive response to a new and popular communication channel. This paper provides insight into how the social media function has been positioned, staffed and managed in organisations throughout the world, with a particular focus on how these factors influence the style of communication used on social media platforms. This study has identified that the social media function falls on a continuum between two polarised models, namely the authoritative one-way communication approach and the more interactive approach that seeks to network and engage with the community through multi-way communication. Factors such the size of the organisation; dedicated resourcing of the social media function; organisational culture and mission statement; the presence of a social media champion within the organisation; management style and knowledge about social media play a key role in determining where on the continuum organisations sit in relation to their social media capability. This review, together with a forthcoming survey of Australian emergency management organisations and local governments, will fill a gap in the current body of knowledge about the evolution, positioning and usage of social media in organisations working in the emergency management field in Australia. These findings will be fed back to Industry for potential inclusion in future strategies and practices.

Degradation modeling and monitoring of machines using operation-specific hidden Markov models

In this paper, a novel data-driven approach to monitoring of systems operating under variable operating conditions is described. The method is based on characterizing the degradation process via a set of operation-specific hidden Markov models (HMMs), whose hidden states represent the unobservable degradation states of the monitored system while its observable symbols represent the sensor readings. Using the HMM framework, modeling, identification and monitoring methods are detailed that allow one to identify a HMM of degradation for each operation from mixed-operation data and perform operation-specific monitoring of the system. Using a large data set provided by a major manufacturer, the new methods are applied to a semiconductor manufacturing process running multiple operations in a production environment.

Semantic context and visual feature effects in object naming : an fMRI study using arterial spin labeling

Previous behavioral studies reported a robust effect of increased naming latencies when objects to be named were blocked within semantic category, compared to items blocked between category. This semantic context effect has been attributed to various mechanisms including inhibition or excitation of lexico-semantic representations and incremental learning of associations between semantic features and names, and is hypothesized to increase demands on verbal self-monitoring during speech production. Objects within categories also share many visual structural features, introducing a potential confound when interpreting the level at which the context effect might occur. Consistent with previous findings, we report a significant increase in response latencies when naming categorically related objects within blocks, an effect associated with increased perfusion fMRI signal bilaterally in the hippocampus and in the left middle to posterior superior temporal cortex. No perfusion changes were observed in the middle section of the left middle temporal cortex, a region associated with retrieval of lexical-semantic information in previous object naming studies. Although a manipulation of visual feature similarity did not influence naming latencies, we observed perfusion increases in the perirhinal cortex for naming objects with similar visual features that interacted with the semantic context in which objects were named. These results provide support for the view that the semantic context effect in object naming occurs due to an incremental learning mechanism, and involves increased demands on verbal self-monitoring.

Using patient specific finite element models to understand the biomechanics of paediatric spinal deformity surgery

Adolescent idiopathic scoliosis (AIS) is a spinal deformity, which may require surgical correction by attaching rods to the patient’s spine using screws inserted into the vertebrae. Complication rates for deformity correction surgery are unacceptably high. Determining an achievable correction without overloading the adjacent spinal tissues or implants requires an understanding of the mechanical interaction between these components. We have developed novel patient specific modelling software to create individualized finite element models (FEM) representing the thoracolumbar spine and ribcage of scoliosis patients. We are using these models to better understand the biomechanics of spinal deformity correction.

What are pregnant women told about models of maternity care in Australia? A retrospective study of women's reports

Objective To describe women’s reports of the model of care options General Practitioners (GPs) discussed with them at the first pregnancy consultation and women’s self-reported role in decisionmaking about model of care. Methods Women who had recently given birth responded to survey items about the models of care GPs discussed, their role in final decision-making, and socio-demographic, obstetric history, and early pregnancy characteristics. Results The proportion of women with whom each model of care was discussed varied between 8.2% (for private midwifery care with home birth) and 64.4% (GP shared care). Only 7.7% of women reported that all seven models were discussed. Exclusive discussion about private obstetric care and about all public models was common, and women’s health insurance status was the strongest predictor of the presence of discussions about each model. Most women (82.6%) reported active involvement in final decision-making about model of care. Conclusion Although most women report involvement in maternity model of care decisions, they remain largely uninformed about the breadth of available model of care options. Practical implications Strategies that facilitate women’s access to information on the differentiating features and outcomes for all models of care should be prioritized to better ensure equitable and quality decisions.

Specialist versus generic models of psychiatry training and service provision for people with intellectual disabilities

Background  Models of service provision and professional training differ between countries. This study aims to investigate a specialist intellectual disabilities model and a generic mental health model, specifically comparing psychiatrists’ knowledge and competencies, and service quality and accessibility in meeting the mental health needs of people with intellectual disabilities. Method  Data were collected from consultant and trainee psychiatrists within a specialist intellectual disabilities model (UK) and a generic mental health model (Australia). Results  The sample sizes were 294 (UK) and 205 (Australia). Statistically significant differences were found, with UK participants having positive views about the specialist intellectual disabilities service model they worked within, demonstrating flexible and accessible working practices and service provision, responsive to the range of mental health needs of the population with intellectual disabilities, and providing a wide range of treatments and supports. The UK participants were knowledgeable, well trained and confident in their work. They wanted to work with people with intellectual disabilities. In all of these areas, the converse was found from the Australian generic mental health service model. Conclusions  The specialist intellectual disabilities model of service provision and training has advantages over the generic mental health model.

Designing channels for brand value : four meta-models

Channels are becoming an increasingly important area for companies to innovate, specifically as they provide direct points of contact with their customers. However, little is known in regards to multi-channel strategies that embody strategic brand values and how customers experience these channels collectively. The purpose of this paper is to investigate how organisations configure multi- channel strategies to communicate their brand value and experience to their customers. Data was collated from sixty companies through a content analysis methodology within the retail sector. Results uncovered commonalities through the identification of four meta-models surrounding common brand values, intended emotive experience, individual channels and the customer segment. These meta-models are titled: High Quality, Trust, Convenience and Community. This research also presents implications of a multi-channel design tool based on findings from this study to help reinforce company brand values and design an overall connected customer experience.

Mathematical Models of Tumor-Immune System Dynamics

"This collection of papers offers a broad synopsis of state-of-the-art mathematical methods used in modeling the interaction between tumors and the immune system. These papers were presented at the four-day workshop on Mathematical Models of Tumor-Immune System Dynamics held in Sydney, Australia from January 7th to January 10th, 2013. The workshop brought together applied mathematicians, biologists, and clinicians actively working in the field of cancer immunology to share their current research and to increase awareness of the innovative mathematical tools that are applicable to the growing field of cancer immunology. Recent progress in cancer immunology and advances in immunotherapy suggest that the immune system plays a fundamental role in host defense against tumors and could be utilized to prevent or cure cancer. Although theoretical and experimental studies of tumor-immune system dynamics have a long history, there are still many unanswered questions about the mechanisms that govern the interaction between the immune system and a growing tumor. The multidimensional nature of these complex interactions requires a cross-disciplinary approach to capture more realistic dynamics of the essential biology. The papers presented in this volume explore these issues and the results will be of interest to graduate students and researchers in a variety of fields within mathematical and biological sciences."--Publisher website

One-step macroscopic alignment of conjugated polymer systems by epitaxial crystallization during spin-coating

The one-step preparation of highly anisotropic polymer semiconductor thin films directly from solution is demonstrated. The conjugated polymer poly(3-hexylthiophene) (P3HT) as well as P3HT:fullerene bulk-heterojunction blends can be spin-coated from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene (TCB) and a second carrier solvent such as chlorobenzene. Solidification is initiated by growth of macroscopic TCB spherulites followed by epitaxial crystallization of P3HT on TCB crystals. Subsequent sublimation of TCB leaves behind a replica of the original TCB spherulites. Thus, highly ordered thin films are obtained, which feature square-centimeter-sized domains that are composed of one spherulite-like structure each. A combination of optical microscopy and polarized photoluminescence spectroscopy reveals radial alignment of the polymer backbone in case of P3HT, whereas P3HT:fullerene blends display a tangential orientation with respect to the center of spherulite-like structures. Moreover, grazing-incidence wide-angle X-ray scattering reveals an increased relative degree of crystallinity and predominantly flat-on conformation of P3HT crystallites in the blend. The use of other processing methods such as dip-coating is also feasible and offers uniaxial orientation of the macromolecule. Finally, the applicability of this method to a variety of other semi-crystalline conjugated polymer systems is established. Those include other poly(3-alkylthiophene)s, two polyfluorenes, the low band-gap polymer PCPDTBT, a diketopyrrolopyrrole (DPP) small molecule as well as a number of polymer:fullerene and polymer:polymer blends. Macroscopic spherulite-like structures of the conjugated polymer poly(3-hexylthiophene) (P3HT) grow directly during spin-coating. This is achieved by processing P3HT or P3HT:fullerene bulk heterojunction blends from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene and a second carrier solvent such as chlorobenzene. Epitaxial growth of the polymer on solidified solvent crystals gives rise to circular-symmetric, spherulite-like structures that feature a high degree of anisotropy.

Iron(II) spin transition complexes with dendritic ligands, Part I

The ligands G1- and G2-oligo (benzyl ether) (PBE) dendrons and their iron(II) complexes [Fe(Gn-PBE)3]A2·xH2O (with n = 1, 2 and A = triflate, tosylate) were prepared. The magnetic properties of the complexes were investigated by a SQUID magnetometer. All complexes exhibit gradual spin transition below room temperature. At very low temperatures the magnetic behaviour reflects zero-field splitting (ZFS) effects. 57Fe-Mössbauer spectroscopy was performed to distinguish between ZFS of high spin species and spin state conversion into the low spin state. Further characterisation was carried out by thermogravimetric analysis (TGA) and FT-IR spectroscopy. Structural features have been determined by powder XRD measurements.

Iron(II) spin-transition complexes with dendritic ligands, part II

The dendritic triazole-based complexes \[Fe(G1-BOC)3](triflate) 2·xH2O (1; G1-BOC = tert-butyl {3-\[3-(3-tert- butoxycarbonylaminopropyl)-5-(\[1,2,4]triazol-4-ylcarbamoyl)-phenyl]propyl} carbamate, triflate = CF3SO3-), \[Fe(G1-BOC) 3]-(tosylate)2·xH2O(2;tosylate = p-CH3PhSO3-),\[Fe(G1-DPBE)3]-(triflate) 2·xH2O {3; G1-DPBE = 3,5-bis(3,5- didodecaoxybenzyloxy)-N-\[1,2,4]triazol-4-ylbenzamide}, \[Fe(G1-DPBE) 3]-(tosylate)2·xH2O (4) and \[Fe(G1-DPBE)3](BF4)2·xH2O (5) were designed and synthesized. Magnetic and thermal properties of these novel complexes were characterized by magnetic susceptibility measurements, 57Fe Mössbauer spectroscopy and thermogravimetric analysis or differential scanning calorimetry, respectively. All dendritic complexes under study show different spin-transition behaviour with respect to the nature of different dendritic ligands and counteranions. Complexes 1 and 2 have pronounced effects of a spin-state change during the first heating process and gradual spintransition properties for further temperature treatments, whereas 3 and 4 exhibited a very sharp spin-state change in the first heating procedures. Complex 5 showed a gradual spin-transition curve. In this paper, we report how the magnetic properties of these complexes are correlated with noncoordinated water molecules and their effects on spin states.